Starting phenix.real_space_refine on Fri Feb 14 10:51:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uph_20839/02_2025/6uph_20839.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uph_20839/02_2025/6uph_20839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uph_20839/02_2025/6uph_20839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uph_20839/02_2025/6uph_20839.map" model { file = "/net/cci-nas-00/data/ceres_data/6uph_20839/02_2025/6uph_20839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uph_20839/02_2025/6uph_20839.cif" } resolution = 2.7 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= 0.033 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 238 5.49 5 S 10 5.16 5 C 5969 2.51 5 N 1975 2.21 5 O 2485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10677 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 766 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "B" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 630 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 744 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 752 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 794 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 630 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 762 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2424 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "J" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2455 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Time building chain proxies: 6.47, per 1000 atoms: 0.61 Number of scatterers: 10677 At special positions: 0 Unit cell: (119.709, 105.276, 118.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 238 15.00 O 2485 8.00 N 1975 7.00 C 5969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 777.1 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 71.6% alpha, 3.3% beta 83 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.538A pdb=" N ILE A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.715A pdb=" N ASP A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 207 removed outlier: 3.576A pdb=" N ILE A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.546A pdb=" N MET A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 222 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.611A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.751A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.665A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.797A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.576A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 removed outlier: 3.604A pdb=" N ALA C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.615A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.780A pdb=" N LYS D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR D 53 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 88 removed outlier: 3.518A pdb=" N LYS D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 109 through 127 removed outlier: 3.590A pdb=" N LYS D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 146 removed outlier: 3.886A pdb=" N ALA E 138 " --> pdb=" O PRO E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 167 removed outlier: 3.512A pdb=" N PHE E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 208 removed outlier: 3.681A pdb=" N MET E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS E 200 " --> pdb=" O GLY E 196 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 208 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 225 removed outlier: 3.699A pdb=" N MET E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.535A pdb=" N ARG F 37 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 4.043A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.759A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 removed outlier: 3.802A pdb=" N ALA G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.532A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.680A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 removed outlier: 3.556A pdb=" N LEU G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 54 removed outlier: 3.742A pdb=" N LYS H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 51 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 89 removed outlier: 3.506A pdb=" N ASN H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU H 76 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.684A pdb=" N HIS H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.839A pdb=" N ARG A 177 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.135A pdb=" N ARG C 43 " --> pdb=" O ILE D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.711A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 177 through 178 removed outlier: 6.708A pdb=" N ARG E 177 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.078A pdb=" N ARG G 43 " --> pdb=" O ILE H 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 335 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 203 hydrogen bonds 398 hydrogen bond angles 0 basepair planarities 83 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1727 1.33 - 1.45: 3818 1.45 - 1.57: 5306 1.57 - 1.68: 474 1.68 - 1.80: 20 Bond restraints: 11345 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CB ASN H 72 " pdb=" CG ASN H 72 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.44e+00 bond pdb=" CG PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 1.503 1.463 0.040 3.40e-02 8.65e+02 1.38e+00 bond pdb=" CG1 ILE D 106 " pdb=" CD1 ILE D 106 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.30e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.26e+00 ... (remaining 11340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15652 1.55 - 3.09: 651 3.09 - 4.64: 33 4.64 - 6.18: 4 6.18 - 7.73: 2 Bond angle restraints: 16342 Sorted by residual: angle pdb=" N GLY H 109 " pdb=" CA GLY H 109 " pdb=" C GLY H 109 " ideal model delta sigma weight residual 113.18 120.91 -7.73 2.37e+00 1.78e-01 1.06e+01 angle pdb=" C3' DT J 5 " pdb=" C2' DT J 5 " pdb=" C1' DT J 5 " ideal model delta sigma weight residual 101.60 97.98 3.62 1.50e+00 4.44e-01 5.81e+00 angle pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sigma weight residual 120.20 123.64 -3.44 1.50e+00 4.44e-01 5.27e+00 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 123.64 -3.44 1.50e+00 4.44e-01 5.25e+00 angle pdb=" N GLY D 109 " pdb=" CA GLY D 109 " pdb=" C GLY D 109 " ideal model delta sigma weight residual 110.77 114.99 -4.22 1.93e+00 2.68e-01 4.79e+00 ... (remaining 16337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 5127 34.93 - 69.86: 1057 69.86 - 104.78: 13 104.78 - 139.71: 0 139.71 - 174.64: 2 Dihedral angle restraints: 6199 sinusoidal: 4069 harmonic: 2130 Sorted by residual: dihedral pdb=" CA PRO H 108 " pdb=" C PRO H 108 " pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA PRO D 108 " pdb=" C PRO D 108 " pdb=" N GLY D 109 " pdb=" CA GLY D 109 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 45.36 174.64 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 867 0.027 - 0.054: 679 0.054 - 0.081: 240 0.081 - 0.108: 62 0.108 - 0.135: 27 Chirality restraints: 1875 Sorted by residual: chirality pdb=" CA PRO E 157 " pdb=" N PRO E 157 " pdb=" C PRO E 157 " pdb=" CB PRO E 157 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA PRO C 81 " pdb=" N PRO C 81 " pdb=" C PRO C 81 " pdb=" CB PRO C 81 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ASN H 72 " pdb=" N ASN H 72 " pdb=" C ASN H 72 " pdb=" CB ASN H 72 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1872 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 156 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO E 157 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 157 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 157 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 32 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 33 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 33 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 33 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 109 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 110 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.025 5.00e-02 4.00e+02 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1468 2.75 - 3.29: 8276 3.29 - 3.83: 17618 3.83 - 4.36: 25111 4.36 - 4.90: 34893 Nonbonded interactions: 87366 Sorted by model distance: nonbonded pdb=" N4 DC I 51 " pdb=" O6 DG J -51 " model vdw 2.216 3.120 nonbonded pdb=" O6 DG I 11 " pdb=" N4 DC J -11 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR B 99 " pdb=" OD2 ASP H 73 " model vdw 2.274 3.040 nonbonded pdb=" O2 DC I -20 " pdb=" N2 DG J 20 " model vdw 2.274 2.496 nonbonded pdb=" NZ LYS E 215 " pdb=" OE1 GLN E 219 " model vdw 2.321 3.120 ... (remaining 87361 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 'E' and resid 136 through 228) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 17 through 113) } ncs_group { reference = (chain 'D' and resid 38 through 129) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.080 Find NCS groups from input model: 0.270 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:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.007 0.051 11345 Z= 0.423 Angle : 0.667 7.727 16342 Z= 0.400 Chirality : 0.041 0.135 1875 Planarity : 0.004 0.051 1234 Dihedral : 26.073 174.641 4823 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: -5.67 (0.19), residues: 716 helix: -3.90 (0.12), residues: 517 sheet: None (None), residues: 0 loop : -2.57 (0.33), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP E 178 HIS 0.003 0.001 HIS G 113 PHE 0.014 0.002 PHE F 62 TYR 0.013 0.002 TYR A 145 ARG 0.007 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.886 Fit side-chains REVERT: E 155 LYS cc_start: 0.8637 (mttp) cc_final: 0.8279 (mtpt) REVERT: E 174 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6885 (mm110) REVERT: H 73 ASP cc_start: 0.8800 (t0) cc_final: 0.8453 (t0) outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 2.1065 time to fit residues: 312.6458 Evaluate side-chains 130 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 37 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS H 100 GLN H 114 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136586 restraints weight = 12196.999| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.04 r_work: 0.3552 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11345 Z= 0.177 Angle : 0.560 7.046 16342 Z= 0.339 Chirality : 0.034 0.130 1875 Planarity : 0.005 0.044 1234 Dihedral : 29.185 176.692 3395 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.13 % Allowed : 10.99 % Favored : 87.88 % 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: -1.79 (0.27), residues: 716 helix: -0.65 (0.21), residues: 515 sheet: None (None), residues: 0 loop : -2.33 (0.31), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 178 HIS 0.002 0.001 HIS E 200 PHE 0.011 0.001 PHE F 62 TYR 0.016 0.001 TYR E 140 ARG 0.003 0.000 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.902 Fit side-chains REVERT: A 143 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7809 (mtm110) REVERT: C 109 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8555 (mp) REVERT: D 98 GLU cc_start: 0.8764 (mp0) cc_final: 0.8498 (mp0) REVERT: E 174 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6988 (mm-40) REVERT: H 73 ASP cc_start: 0.8908 (t0) cc_final: 0.8088 (t70) REVERT: H 76 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7841 (tm-30) outliers start: 7 outliers final: 1 residues processed: 146 average time/residue: 1.9358 time to fit residues: 296.1158 Evaluate side-chains 131 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 83 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN G 105 GLN H 89 ASN H 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131455 restraints weight = 12315.028| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.04 r_work: 0.3503 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11345 Z= 0.256 Angle : 0.587 6.947 16342 Z= 0.350 Chirality : 0.037 0.124 1875 Planarity : 0.004 0.042 1234 Dihedral : 29.290 176.938 3391 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.94 % Allowed : 12.44 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.30), residues: 716 helix: 0.78 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -2.25 (0.32), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 178 HIS 0.003 0.001 HIS D 54 PHE 0.013 0.002 PHE F 62 TYR 0.017 0.002 TYR A 140 ARG 0.002 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.785 Fit side-chains REVERT: A 143 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7807 (mtm110) REVERT: C 92 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: C 109 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8537 (mp) REVERT: D 76 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: E 174 GLN cc_start: 0.7508 (mm-40) cc_final: 0.6984 (mm-40) REVERT: F 60 LYS cc_start: 0.9043 (tppp) cc_final: 0.8755 (tttp) REVERT: F 64 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: H 73 ASP cc_start: 0.8945 (t0) cc_final: 0.8483 (t70) outliers start: 12 outliers final: 3 residues processed: 135 average time/residue: 1.9255 time to fit residues: 272.5364 Evaluate side-chains 132 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 63 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132601 restraints weight = 12217.730| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.04 r_work: 0.3505 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11345 Z= 0.188 Angle : 0.557 6.850 16342 Z= 0.337 Chirality : 0.035 0.124 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.290 176.859 3391 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.26 % Allowed : 13.25 % Favored : 84.49 % 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: 0.53 (0.31), residues: 716 helix: 1.27 (0.24), residues: 515 sheet: None (None), residues: 0 loop : -2.09 (0.33), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 178 HIS 0.002 0.000 HIS D 54 PHE 0.011 0.001 PHE F 62 TYR 0.016 0.001 TYR A 140 ARG 0.001 0.000 ARG E 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.878 Fit side-chains REVERT: A 143 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7797 (mtm110) REVERT: C 109 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8514 (mp) REVERT: D 76 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: E 174 GLN cc_start: 0.7501 (mm-40) cc_final: 0.6991 (mm110) REVERT: E 199 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: F 60 LYS cc_start: 0.9023 (tppp) cc_final: 0.8742 (tttp) REVERT: F 64 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: F 93 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.6809 (ttm-80) REVERT: H 73 ASP cc_start: 0.8931 (t0) cc_final: 0.8587 (t70) REVERT: H 76 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7857 (tm-30) outliers start: 14 outliers final: 5 residues processed: 130 average time/residue: 1.9971 time to fit residues: 272.3737 Evaluate side-chains 137 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.154230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127490 restraints weight = 12006.590| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.06 r_work: 0.3439 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11345 Z= 0.298 Angle : 0.606 7.331 16342 Z= 0.360 Chirality : 0.038 0.138 1875 Planarity : 0.004 0.042 1234 Dihedral : 29.383 177.452 3391 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.42 % Allowed : 13.73 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.31), residues: 716 helix: 1.40 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -2.05 (0.33), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 178 HIS 0.002 0.001 HIS H 54 PHE 0.013 0.002 PHE B 62 TYR 0.021 0.002 TYR A 140 ARG 0.002 0.000 ARG E 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.887 Fit side-chains REVERT: A 143 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7798 (mtm110) REVERT: C 74 ASN cc_start: 0.8343 (m-40) cc_final: 0.7997 (t0) REVERT: C 109 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8587 (mp) REVERT: D 76 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: E 174 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6953 (mm-40) REVERT: E 199 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: F 60 LYS cc_start: 0.9024 (tppp) cc_final: 0.8766 (tttp) REVERT: F 64 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: F 93 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.6736 (ttm-80) REVERT: H 73 ASP cc_start: 0.8943 (t0) cc_final: 0.8646 (t0) REVERT: H 76 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: H 81 GLU cc_start: 0.8654 (tp30) cc_final: 0.8093 (tp30) outliers start: 15 outliers final: 4 residues processed: 137 average time/residue: 1.9705 time to fit residues: 283.0182 Evaluate side-chains 138 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.155041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128374 restraints weight = 12040.869| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.06 r_work: 0.3450 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11345 Z= 0.206 Angle : 0.579 8.154 16342 Z= 0.347 Chirality : 0.036 0.131 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.387 177.344 3391 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.10 % Allowed : 14.54 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.31), residues: 716 helix: 1.56 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 178 HIS 0.002 0.001 HIS H 114 PHE 0.012 0.002 PHE F 62 TYR 0.019 0.001 TYR A 140 ARG 0.002 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.857 Fit side-chains REVERT: A 143 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7803 (mtm110) REVERT: C 74 ASN cc_start: 0.8316 (m-40) cc_final: 0.7981 (t0) REVERT: C 109 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8575 (mp) REVERT: D 76 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: E 174 GLN cc_start: 0.7480 (mm-40) cc_final: 0.6950 (mm-40) REVERT: E 199 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: F 60 LYS cc_start: 0.9007 (tppp) cc_final: 0.8750 (tttp) REVERT: F 64 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: F 93 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6730 (ttm-80) REVERT: H 73 ASP cc_start: 0.8943 (t0) cc_final: 0.8616 (t0) REVERT: H 76 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: H 81 GLU cc_start: 0.8637 (tp30) cc_final: 0.8024 (tp30) outliers start: 13 outliers final: 5 residues processed: 135 average time/residue: 2.0010 time to fit residues: 282.9500 Evaluate side-chains 141 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN G 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128137 restraints weight = 12175.536| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.08 r_work: 0.3447 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11345 Z= 0.262 Angle : 0.586 7.092 16342 Z= 0.350 Chirality : 0.037 0.141 1875 Planarity : 0.004 0.042 1234 Dihedral : 29.363 178.126 3391 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.26 % Allowed : 14.54 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.31), residues: 716 helix: 1.63 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 178 HIS 0.002 0.000 HIS H 54 PHE 0.012 0.002 PHE B 62 TYR 0.022 0.002 TYR A 140 ARG 0.002 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.824 Fit side-chains REVERT: A 143 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7797 (mtm110) REVERT: C 74 ASN cc_start: 0.8279 (m-40) cc_final: 0.7941 (t0) REVERT: C 109 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8586 (mp) REVERT: D 76 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: E 174 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6765 (mt0) REVERT: E 199 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: F 60 LYS cc_start: 0.9016 (tppp) cc_final: 0.8762 (tttp) REVERT: F 64 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8428 (mt-10) REVERT: F 93 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.6749 (ttm-80) REVERT: H 73 ASP cc_start: 0.8951 (t0) cc_final: 0.8624 (t0) REVERT: H 76 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: H 81 GLU cc_start: 0.8655 (tp30) cc_final: 0.8086 (tp30) outliers start: 14 outliers final: 5 residues processed: 136 average time/residue: 1.9073 time to fit residues: 272.1309 Evaluate side-chains 140 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131999 restraints weight = 12187.513| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.04 r_work: 0.3504 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11345 Z= 0.168 Angle : 0.553 6.516 16342 Z= 0.334 Chirality : 0.034 0.129 1875 Planarity : 0.003 0.040 1234 Dihedral : 29.349 177.701 3391 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.26 % Allowed : 14.38 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.31), residues: 716 helix: 1.84 (0.24), residues: 515 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 178 HIS 0.002 0.000 HIS D 54 PHE 0.010 0.001 PHE F 62 TYR 0.021 0.001 TYR A 140 ARG 0.002 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.895 Fit side-chains REVERT: A 143 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7835 (mtm110) REVERT: C 74 ASN cc_start: 0.8245 (m-40) cc_final: 0.7937 (t0) REVERT: C 109 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8552 (mp) REVERT: D 76 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: E 174 GLN cc_start: 0.7478 (mm-40) cc_final: 0.6781 (mt0) REVERT: E 199 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: E 225 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8179 (ptt180) REVERT: F 60 LYS cc_start: 0.9007 (tppp) cc_final: 0.8746 (tttp) REVERT: F 64 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8352 (mt-10) REVERT: F 93 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.6774 (ttm-80) REVERT: H 73 ASP cc_start: 0.8929 (t0) cc_final: 0.8479 (t0) REVERT: H 76 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7863 (tm-30) outliers start: 14 outliers final: 5 residues processed: 137 average time/residue: 1.9048 time to fit residues: 273.9426 Evaluate side-chains 142 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 81 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128141 restraints weight = 12176.146| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.07 r_work: 0.3447 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11345 Z= 0.266 Angle : 0.587 7.047 16342 Z= 0.350 Chirality : 0.037 0.145 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.342 178.212 3391 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.10 % Allowed : 14.70 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.31), residues: 716 helix: 1.82 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.92 (0.33), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 178 HIS 0.002 0.000 HIS H 54 PHE 0.012 0.002 PHE B 62 TYR 0.023 0.002 TYR A 140 ARG 0.001 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.816 Fit side-chains REVERT: A 143 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7793 (mtm110) REVERT: C 74 ASN cc_start: 0.8252 (m-40) cc_final: 0.7930 (t0) REVERT: C 109 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8598 (mp) REVERT: D 76 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: E 174 GLN cc_start: 0.7478 (mm-40) cc_final: 0.6765 (mt0) REVERT: E 199 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: E 225 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8146 (ptt180) REVERT: F 60 LYS cc_start: 0.9007 (tppp) cc_final: 0.8759 (tttp) REVERT: F 64 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: H 73 ASP cc_start: 0.8953 (t0) cc_final: 0.8630 (t0) REVERT: H 76 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7850 (tm-30) outliers start: 13 outliers final: 5 residues processed: 137 average time/residue: 2.0156 time to fit residues: 289.1523 Evaluate side-chains 142 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN G 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.155034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128342 restraints weight = 12071.225| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.06 r_work: 0.3449 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11345 Z= 0.244 Angle : 0.583 7.029 16342 Z= 0.348 Chirality : 0.036 0.143 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.343 178.236 3391 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.78 % Allowed : 15.19 % Favored : 83.04 % 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: 1.23 (0.31), residues: 716 helix: 1.81 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.92 (0.33), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 178 HIS 0.002 0.000 HIS H 54 PHE 0.012 0.002 PHE B 62 TYR 0.023 0.002 TYR A 140 ARG 0.002 0.000 ARG F 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.787 Fit side-chains REVERT: A 143 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7795 (mtm110) REVERT: C 74 ASN cc_start: 0.8255 (m-40) cc_final: 0.7936 (t0) REVERT: C 109 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8597 (mp) REVERT: D 76 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: E 174 GLN cc_start: 0.7476 (mm-40) cc_final: 0.6766 (mt0) REVERT: E 199 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: E 225 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8182 (ptt180) REVERT: F 60 LYS cc_start: 0.9004 (tppp) cc_final: 0.8755 (tttp) REVERT: F 64 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: H 73 ASP cc_start: 0.8951 (t0) cc_final: 0.8527 (t0) REVERT: H 76 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7847 (tm-30) outliers start: 11 outliers final: 5 residues processed: 135 average time/residue: 1.9662 time to fit residues: 278.0169 Evaluate side-chains 140 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128223 restraints weight = 12007.231| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.07 r_work: 0.3449 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11345 Z= 0.268 Angle : 0.587 7.056 16342 Z= 0.350 Chirality : 0.037 0.144 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.344 178.354 3391 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.94 % Allowed : 15.02 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.31), residues: 716 helix: 1.81 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.92 (0.33), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 178 HIS 0.002 0.001 HIS H 54 PHE 0.012 0.002 PHE B 62 TYR 0.023 0.002 TYR A 140 ARG 0.003 0.000 ARG F 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8233.30 seconds wall clock time: 145 minutes 28.02 seconds (8728.02 seconds total)