Starting phenix.real_space_refine on Sat Dec 9 09:33:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uph_20839/12_2023/6uph_20839.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uph_20839/12_2023/6uph_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uph_20839/12_2023/6uph_20839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uph_20839/12_2023/6uph_20839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uph_20839/12_2023/6uph_20839.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uph_20839/12_2023/6uph_20839.pdb" } 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 Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E ASP 217": "OD1" <-> "OD2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.84, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 5.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 5.84 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: 4.06 Time building geometry restraints manager: 5.15 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: 97.98 - 105.20: 1050 105.20 - 112.41: 6315 112.41 - 119.63: 3586 119.63 - 126.84: 4731 126.84 - 134.06: 660 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 2.520 nonbonded pdb=" O6 DG I 11 " pdb=" N4 DC J -11 " model vdw 2.255 2.520 nonbonded pdb=" OH TYR B 99 " pdb=" OD2 ASP H 73 " model vdw 2.274 2.440 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 2.520 ... (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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.310 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.670 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.054 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 2.1154 time to fit residues: 314.2420 Evaluate side-chains 130 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.0097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 37 optimal weight: 0.0060 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS H 89 ASN H 100 GLN H 114 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2177 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= 0.182 Angle : 0.571 7.423 16342 Z= 0.342 Chirality : 0.034 0.124 1875 Planarity : 0.005 0.048 1234 Dihedral : 29.217 176.751 3391 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.94 % Allowed : 10.50 % Favored : 87.56 % 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: -2.03 (0.27), residues: 716 helix: -0.84 (0.21), residues: 514 sheet: None (None), residues: 0 loop : -2.36 (0.31), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 178 HIS 0.002 0.001 HIS B 76 PHE 0.009 0.001 PHE F 62 TYR 0.017 0.001 TYR E 140 ARG 0.003 0.000 ARG C 72 *********************** 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 160 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.935 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 150 average time/residue: 1.9686 time to fit residues: 309.6036 Evaluate side-chains 133 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1683 time to fit residues: 1.6019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 68 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN H 89 ASN H 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11345 Z= 0.341 Angle : 0.643 7.513 16342 Z= 0.379 Chirality : 0.040 0.149 1875 Planarity : 0.005 0.046 1234 Dihedral : 29.475 176.859 3391 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.91 % Allowed : 12.44 % Favored : 84.65 % 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: -0.42 (0.30), residues: 716 helix: 0.52 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -2.30 (0.32), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 178 HIS 0.002 0.001 HIS H 114 PHE 0.014 0.002 PHE F 62 TYR 0.012 0.002 TYR A 145 ARG 0.002 0.000 ARG F 41 *********************** 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 150 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.318 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 138 average time/residue: 1.8555 time to fit residues: 269.1055 Evaluate side-chains 134 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 1.0936 time to fit residues: 6.9775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11345 Z= 0.240 Angle : 0.592 7.243 16342 Z= 0.356 Chirality : 0.037 0.136 1875 Planarity : 0.004 0.042 1234 Dihedral : 29.438 177.399 3391 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.30 (0.31), residues: 716 helix: 1.11 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.23 (0.32), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 178 HIS 0.002 0.001 HIS D 54 PHE 0.013 0.002 PHE F 62 TYR 0.012 0.001 TYR E 140 ARG 0.001 0.000 ARG B 37 *********************** 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 138 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.903 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 130 average time/residue: 1.8987 time to fit residues: 259.0286 Evaluate side-chains 132 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1865 time to fit residues: 1.8977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2097 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= 0.214 Angle : 0.576 7.061 16342 Z= 0.346 Chirality : 0.036 0.126 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.402 177.632 3391 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.75 % Allowed : 14.22 % 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: 0.63 (0.31), residues: 716 helix: 1.39 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.20 (0.32), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 178 HIS 0.002 0.000 HIS D 54 PHE 0.012 0.001 PHE F 62 TYR 0.013 0.001 TYR E 140 ARG 0.002 0.000 ARG F 40 *********************** 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 146 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.098 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 135 average time/residue: 2.0001 time to fit residues: 284.2583 Evaluate side-chains 134 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.6380 time to fit residues: 3.2039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2169 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= 0.240 Angle : 0.575 6.844 16342 Z= 0.345 Chirality : 0.036 0.133 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.346 178.003 3391 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.95 (0.31), residues: 716 helix: 1.63 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.09 (0.33), residues: 202 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 0.013 0.002 PHE F 62 TYR 0.013 0.001 TYR E 140 ARG 0.002 0.000 ARG E 225 *********************** 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 145 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.881 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 139 average time/residue: 1.8363 time to fit residues: 268.5812 Evaluate side-chains 135 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2488 time to fit residues: 1.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11345 Z= 0.204 Angle : 0.563 6.869 16342 Z= 0.338 Chirality : 0.035 0.132 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.342 177.993 3391 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.78 % Allowed : 14.86 % 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: 1.09 (0.31), residues: 716 helix: 1.74 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 202 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 0.012 0.002 PHE F 62 TYR 0.013 0.001 TYR E 140 ARG 0.003 0.000 ARG C 89 *********************** 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 140 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.810 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 135 average time/residue: 1.9373 time to fit residues: 275.3107 Evaluate side-chains 135 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.8516 time to fit residues: 2.9223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 8 optimal weight: 0.0970 chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2203 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= 0.224 Angle : 0.563 6.882 16342 Z= 0.339 Chirality : 0.036 0.131 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.332 178.218 3391 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.78 % Allowed : 14.86 % 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: 1.13 (0.31), residues: 716 helix: 1.78 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 202 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 0.012 0.002 PHE F 62 TYR 0.012 0.001 TYR E 140 ARG 0.001 0.000 ARG C 72 *********************** 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 139 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.883 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 133 average time/residue: 1.8316 time to fit residues: 256.0626 Evaluate side-chains 134 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2213 time to fit residues: 1.6854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 overall best weight: 3.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2198 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= 0.254 Angle : 0.580 7.060 16342 Z= 0.346 Chirality : 0.037 0.139 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.348 178.162 3391 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.62 % Allowed : 15.02 % 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: 1.15 (0.31), residues: 716 helix: 1.79 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 202 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 B 62 TYR 0.013 0.002 TYR E 140 ARG 0.002 0.000 ARG F 40 *********************** 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 140 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.854 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 136 average time/residue: 1.9022 time to fit residues: 271.7904 Evaluate side-chains 137 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2656 time to fit residues: 1.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2215 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= 0.208 Angle : 0.570 6.825 16342 Z= 0.342 Chirality : 0.035 0.131 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.345 178.199 3391 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.45 % Allowed : 15.51 % 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: 1.19 (0.31), residues: 716 helix: 1.82 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.04 (0.33), residues: 202 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 0.013 0.001 TYR E 140 ARG 0.002 0.000 ARG E 225 ********************** 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 137 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.013 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 133 average time/residue: 1.8444 time to fit residues: 257.8130 Evaluate side-chains 134 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.2623 time to fit residues: 1.3986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130451 restraints weight = 12033.073| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.07 r_work: 0.3470 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2282 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= 0.162 Angle : 0.550 6.825 16342 Z= 0.333 Chirality : 0.034 0.124 1875 Planarity : 0.004 0.041 1234 Dihedral : 29.338 178.173 3391 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.45 % Allowed : 15.67 % Favored : 82.88 % 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: 1.34 (0.31), residues: 716 helix: 1.94 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 178 HIS 0.002 0.000 HIS C 83 PHE 0.011 0.001 PHE F 62 TYR 0.017 0.001 TYR E 140 ARG 0.002 0.000 ARG F 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4328.36 seconds wall clock time: 77 minutes 18.60 seconds (4638.60 seconds total)