Starting phenix.real_space_refine on Mon Mar 11 18:54:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/03_2024/7vfp_31957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/03_2024/7vfp_31957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/03_2024/7vfp_31957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/03_2024/7vfp_31957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/03_2024/7vfp_31957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/03_2024/7vfp_31957_updated.pdb" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 5789 2.51 5 N 1513 2.21 5 O 1504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "F PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8857 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 5.40, per 1000 atoms: 0.61 Number of scatterers: 8857 At special positions: 0 Unit cell: (104.832, 98.176, 113.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 46 16.00 P 3 15.00 Mg 1 11.99 O 1504 8.00 N 1513 7.00 C 5789 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: 3.81 Conformation dependent library (CDL) restraints added in 2.2 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 61.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.977A pdb=" N LEU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 65 through 68 No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.688A pdb=" N PHE A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.877A pdb=" N ARG A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TRP A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.503A pdb=" N GLN A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.611A pdb=" N ALA B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 removed outlier: 3.546A pdb=" N ASN B 23 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Proline residue: B 24 - end of helix Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.629A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 118 removed outlier: 4.062A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix removed outlier: 3.580A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 153 Proline residue: B 138 - end of helix removed outlier: 3.868A pdb=" N GLY B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 142 " --> pdb=" O PRO B 138 " (cutoff:3.500A) Proline residue: B 146 - end of helix removed outlier: 3.517A pdb=" N LEU B 150 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 167 through 184 Proline residue: B 171 - end of helix removed outlier: 3.583A pdb=" N ALA B 183 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 219 removed outlier: 4.021A pdb=" N THR B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'C' and resid 12 through 19 Processing helix chain 'C' and resid 22 through 39 Processing helix chain 'C' and resid 51 through 83 removed outlier: 3.574A pdb=" N TYR C 58 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL C 61 " --> pdb=" O TYR C 58 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 3.634A pdb=" N LEU C 82 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 83 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 114 removed outlier: 4.311A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 116 through 119 No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 127 through 148 Processing helix chain 'C' and resid 158 through 184 Proline residue: C 171 - end of helix removed outlier: 3.591A pdb=" N HIS C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 200 through 230 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'D' and resid 18 through 53 Proline residue: D 31 - end of helix removed outlier: 4.080A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN D 52 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 47 Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.840A pdb=" N HIS E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 69 through 74' Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.744A pdb=" N PHE E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 114 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.919A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing helix chain 'F' and resid 3 through 16 Processing helix chain 'F' and resid 21 through 38 removed outlier: 3.914A pdb=" N LEU F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 43 through 68 Proline residue: F 51 - end of helix removed outlier: 4.435A pdb=" N ARG F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 74 No H-bonds generated for 'chain 'F' and resid 71 through 74' Processing helix chain 'F' and resid 89 through 119 removed outlier: 4.148A pdb=" N LEU F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Proline residue: F 107 - end of helix Proline residue: F 113 - end of helix Processing helix chain 'F' and resid 123 through 151 Proline residue: F 138 - end of helix Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.547A pdb=" N LEU F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 184 removed outlier: 3.780A pdb=" N ILE F 170 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Proline residue: F 171 - end of helix Processing helix chain 'F' and resid 190 through 219 removed outlier: 3.772A pdb=" N THR F 205 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) Proline residue: F 208 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.587A pdb=" N GLU A 57 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.566A pdb=" N LEU A 150 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 2 through 5 Processing sheet with id= D, first strand: chain 'E' and resid 195 through 197 removed outlier: 3.853A pdb=" N GLN E 31 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL E 179 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE E 32 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU E 181 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU E 77 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP E 151 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 79 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.785A pdb=" N CYS E 9 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE E 17 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG E 11 " --> pdb=" O THR E 15 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 433 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 3509 1.39 - 1.56: 5472 1.56 - 1.73: 5 1.73 - 1.90: 87 1.90 - 2.07: 4 Bond restraints: 9077 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C8 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.15e+01 bond pdb=" C5 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.92e+01 bond pdb=" C4 ATP E 301 " pdb=" N9 ATP E 301 " ideal model delta sigma weight residual 1.374 1.338 0.036 1.00e-02 1.00e+04 1.27e+01 ... (remaining 9072 not shown) Histogram of bond angle deviations from ideal: 88.24 - 105.94: 238 105.94 - 123.64: 11786 123.64 - 141.34: 381 141.34 - 159.03: 0 159.03 - 176.73: 2 Bond angle restraints: 12407 Sorted by residual: angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 119.55 20.32 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 118.86 17.97 1.00e+00 1.00e+00 3.23e+02 angle pdb=" C5 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 126.80 118.32 8.48 1.00e+00 1.00e+00 7.19e+01 angle pdb=" N3 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N9 ATP E 301 " ideal model delta sigma weight residual 127.04 135.44 -8.40 1.15e+00 7.59e-01 5.36e+01 angle pdb=" N1 ATP E 301 " pdb=" C2 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 128.69 123.66 5.03 1.00e+00 1.00e+00 2.53e+01 ... (remaining 12402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4769 17.41 - 34.81: 447 34.81 - 52.22: 80 52.22 - 69.63: 8 69.63 - 87.03: 8 Dihedral angle restraints: 5312 sinusoidal: 2088 harmonic: 3224 Sorted by residual: dihedral pdb=" CA TRP C 39 " pdb=" C TRP C 39 " pdb=" N GLY C 40 " pdb=" CA GLY C 40 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU A 127 " pdb=" C LEU A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual 180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASP F 76 " pdb=" C ASP F 76 " pdb=" N GLY F 77 " pdb=" CA GLY F 77 " ideal model delta harmonic sigma weight residual 180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 5309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1195 0.058 - 0.116: 234 0.116 - 0.174: 25 0.174 - 0.232: 3 0.232 - 0.290: 1 Chirality restraints: 1458 Sorted by residual: chirality pdb=" CB ILE A 149 " pdb=" CA ILE A 149 " pdb=" CG1 ILE A 149 " pdb=" CG2 ILE A 149 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE A 180 " pdb=" CA ILE A 180 " pdb=" CG1 ILE A 180 " pdb=" CG2 ILE A 180 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 10 " pdb=" CA ILE C 10 " pdb=" CG1 ILE C 10 " pdb=" CG2 ILE C 10 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1455 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 6 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C ILE B 6 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE B 6 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE B 7 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 97 " -0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO C 98 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 98 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 98 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 106 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO F 107 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 107 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 107 " 0.022 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 69 2.53 - 3.12: 7218 3.12 - 3.71: 14827 3.71 - 4.31: 19114 4.31 - 4.90: 31015 Nonbonded interactions: 72243 Sorted by model distance: nonbonded pdb="MG MG E 300 " pdb=" O2B ATP E 301 " model vdw 1.933 2.170 nonbonded pdb=" OG1 THR E 41 " pdb="MG MG E 300 " model vdw 2.036 2.170 nonbonded pdb="MG MG E 300 " pdb=" O HOH E 402 " model vdw 2.050 2.170 nonbonded pdb="MG MG E 300 " pdb=" O HOH E 401 " model vdw 2.052 2.170 nonbonded pdb="MG MG E 300 " pdb=" O3G ATP E 301 " model vdw 2.082 2.170 ... (remaining 72238 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 -1 through 200) } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 7.460 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.830 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.004 0.082 9077 Z= 0.254 Angle : 0.841 20.325 12407 Z= 0.481 Chirality : 0.045 0.290 1458 Planarity : 0.005 0.052 1526 Dihedral : 13.882 87.031 3228 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.05 (0.25), residues: 1118 helix: 0.89 (0.21), residues: 642 sheet: -2.00 (0.64), residues: 49 loop : -0.97 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 146 HIS 0.004 0.001 HIS F 17 PHE 0.026 0.002 PHE B 175 TYR 0.011 0.002 TYR C 15 ARG 0.008 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8003 (ppp) cc_final: 0.7467 (ppp) REVERT: A 99 HIS cc_start: 0.8130 (t-90) cc_final: 0.7803 (t-90) REVERT: A 181 LEU cc_start: 0.8560 (mt) cc_final: 0.8264 (mt) REVERT: B 5 ARG cc_start: 0.8925 (mtm180) cc_final: 0.8494 (mtp180) REVERT: B 44 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8741 (tm-30) REVERT: B 73 ASP cc_start: 0.8203 (m-30) cc_final: 0.7826 (m-30) REVERT: B 83 MET cc_start: 0.7590 (tmm) cc_final: 0.6997 (tmm) REVERT: B 133 LEU cc_start: 0.9593 (tp) cc_final: 0.9374 (tp) REVERT: B 175 PHE cc_start: 0.8992 (m-80) cc_final: 0.8719 (m-80) REVERT: C 88 MET cc_start: 0.8655 (mmp) cc_final: 0.8386 (mmt) REVERT: C 90 ASN cc_start: 0.8851 (m-40) cc_final: 0.8540 (m-40) REVERT: C 165 ILE cc_start: 0.9607 (mm) cc_final: 0.9353 (mm) REVERT: C 169 ASN cc_start: 0.9103 (m110) cc_final: 0.8759 (m-40) REVERT: C 215 THR cc_start: 0.9396 (p) cc_final: 0.8760 (p) REVERT: C 219 MET cc_start: 0.8718 (mpp) cc_final: 0.8486 (mpp) REVERT: C 228 MET cc_start: 0.8729 (ttm) cc_final: 0.8239 (tmm) REVERT: E 113 GLN cc_start: 0.8486 (tp40) cc_final: 0.8197 (tp40) REVERT: F 15 PHE cc_start: 0.7944 (m-80) cc_final: 0.7684 (m-80) REVERT: F 68 ARG cc_start: 0.8488 (ppt170) cc_final: 0.8172 (ttp80) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1803 time to fit residues: 74.4656 Evaluate side-chains 243 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 0.0060 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 101 optimal weight: 0.7980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9077 Z= 0.194 Angle : 0.697 6.603 12407 Z= 0.343 Chirality : 0.043 0.206 1458 Planarity : 0.006 0.043 1526 Dihedral : 6.593 71.882 1248 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.36 % Rotamer: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1118 helix: 0.64 (0.21), residues: 663 sheet: -1.84 (0.61), residues: 60 loop : -0.71 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 119 HIS 0.006 0.001 HIS B 100 PHE 0.025 0.002 PHE F 15 TYR 0.012 0.001 TYR C 15 ARG 0.005 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7958 (ppp) cc_final: 0.7489 (ppp) REVERT: A 99 HIS cc_start: 0.8142 (t-90) cc_final: 0.7842 (t-90) REVERT: B 5 ARG cc_start: 0.8848 (mtm180) cc_final: 0.8466 (mtp180) REVERT: B 73 ASP cc_start: 0.8061 (m-30) cc_final: 0.7806 (m-30) REVERT: B 133 LEU cc_start: 0.9635 (tp) cc_final: 0.9395 (tp) REVERT: B 175 PHE cc_start: 0.9097 (m-80) cc_final: 0.8819 (m-80) REVERT: C 87 LYS cc_start: 0.8951 (tttp) cc_final: 0.7577 (tppt) REVERT: C 118 MET cc_start: 0.8215 (ptp) cc_final: 0.7793 (ptp) REVERT: C 228 MET cc_start: 0.8721 (ttm) cc_final: 0.8244 (tmm) REVERT: C 230 LYS cc_start: 0.8247 (pptt) cc_final: 0.7811 (pptt) REVERT: D 20 PHE cc_start: 0.8880 (m-80) cc_final: 0.8490 (m-10) REVERT: D 27 MET cc_start: 0.9032 (tpp) cc_final: 0.8654 (tpp) REVERT: D 42 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8394 (tm-30) REVERT: F 15 PHE cc_start: 0.7992 (m-80) cc_final: 0.7695 (m-80) REVERT: F 68 ARG cc_start: 0.8523 (ppt170) cc_final: 0.8244 (ttp80) REVERT: F 71 ARG cc_start: 0.7549 (ttt180) cc_final: 0.6925 (ttm-80) REVERT: F 73 ASP cc_start: 0.8785 (m-30) cc_final: 0.8470 (m-30) REVERT: F 164 LEU cc_start: 0.9211 (mt) cc_final: 0.8958 (mt) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.1813 time to fit residues: 74.2603 Evaluate side-chains 239 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 169 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9077 Z= 0.324 Angle : 0.755 8.010 12407 Z= 0.371 Chirality : 0.045 0.200 1458 Planarity : 0.006 0.045 1526 Dihedral : 6.543 67.500 1248 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1118 helix: 0.47 (0.20), residues: 676 sheet: -1.52 (0.66), residues: 48 loop : -0.92 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 55 HIS 0.006 0.001 HIS B 100 PHE 0.021 0.002 PHE F 15 TYR 0.009 0.002 TYR B 192 ARG 0.007 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 275 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8083 (ppp) cc_final: 0.7686 (ppp) REVERT: A 76 LEU cc_start: 0.9170 (tt) cc_final: 0.8521 (tt) REVERT: A 85 ILE cc_start: 0.6404 (pt) cc_final: 0.6102 (pt) REVERT: A 99 HIS cc_start: 0.8183 (t-90) cc_final: 0.7865 (t-170) REVERT: A 109 GLU cc_start: 0.9550 (tt0) cc_final: 0.9239 (tm-30) REVERT: A 141 TRP cc_start: 0.7691 (m100) cc_final: 0.7305 (m100) REVERT: B 2 MET cc_start: 0.5798 (tpt) cc_final: 0.5030 (mmt) REVERT: B 44 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8656 (tm-30) REVERT: B 73 ASP cc_start: 0.8182 (m-30) cc_final: 0.7856 (m-30) REVERT: B 133 LEU cc_start: 0.9648 (tp) cc_final: 0.9429 (tp) REVERT: B 175 PHE cc_start: 0.9118 (m-80) cc_final: 0.8845 (m-80) REVERT: C 87 LYS cc_start: 0.8553 (tttp) cc_final: 0.7986 (tptm) REVERT: C 90 ASN cc_start: 0.8869 (m-40) cc_final: 0.8506 (m-40) REVERT: C 91 LEU cc_start: 0.9349 (tp) cc_final: 0.9037 (tp) REVERT: C 228 MET cc_start: 0.8709 (ttm) cc_final: 0.8216 (tmm) REVERT: D 27 MET cc_start: 0.9106 (tpp) cc_final: 0.8760 (tpp) REVERT: E 6 GLU cc_start: 0.8305 (pp20) cc_final: 0.7938 (pp20) REVERT: E 50 LEU cc_start: 0.9345 (mp) cc_final: 0.9084 (mp) REVERT: F 15 PHE cc_start: 0.8107 (m-80) cc_final: 0.7882 (m-80) REVERT: F 68 ARG cc_start: 0.8705 (ppt170) cc_final: 0.8484 (ttp80) REVERT: F 73 ASP cc_start: 0.8673 (m-30) cc_final: 0.8357 (m-30) REVERT: F 164 LEU cc_start: 0.9347 (mt) cc_final: 0.9072 (mt) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.1857 time to fit residues: 71.9445 Evaluate side-chains 223 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9077 Z= 0.208 Angle : 0.706 7.168 12407 Z= 0.340 Chirality : 0.044 0.198 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.394 65.907 1248 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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 (0.26), residues: 1118 helix: 0.57 (0.21), residues: 676 sheet: -1.38 (0.67), residues: 48 loop : -0.88 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 55 HIS 0.006 0.001 HIS B 100 PHE 0.020 0.002 PHE B 142 TYR 0.007 0.001 TYR C 15 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7987 (ppp) cc_final: 0.7648 (ppp) REVERT: A 47 LEU cc_start: 0.8667 (mt) cc_final: 0.8450 (mt) REVERT: A 78 TRP cc_start: 0.7491 (t60) cc_final: 0.7136 (t60) REVERT: A 85 ILE cc_start: 0.6108 (pt) cc_final: 0.5815 (pt) REVERT: A 99 HIS cc_start: 0.8022 (t-90) cc_final: 0.7779 (t-170) REVERT: A 109 GLU cc_start: 0.9540 (tt0) cc_final: 0.9285 (tm-30) REVERT: A 141 TRP cc_start: 0.7570 (m100) cc_final: 0.7268 (m100) REVERT: A 178 ILE cc_start: 0.7399 (pt) cc_final: 0.6655 (mm) REVERT: B 2 MET cc_start: 0.5687 (tpt) cc_final: 0.4153 (ttm) REVERT: B 44 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8552 (tm-30) REVERT: B 73 ASP cc_start: 0.8221 (m-30) cc_final: 0.7938 (m-30) REVERT: B 133 LEU cc_start: 0.9613 (tp) cc_final: 0.9351 (tp) REVERT: B 175 PHE cc_start: 0.9139 (m-80) cc_final: 0.8881 (m-80) REVERT: C 86 MET cc_start: 0.8050 (mmm) cc_final: 0.7813 (mmm) REVERT: C 90 ASN cc_start: 0.8778 (m-40) cc_final: 0.8506 (m-40) REVERT: C 91 LEU cc_start: 0.9229 (tp) cc_final: 0.8930 (tp) REVERT: C 118 MET cc_start: 0.8268 (ptp) cc_final: 0.7670 (ptp) REVERT: C 228 MET cc_start: 0.8686 (ttm) cc_final: 0.8261 (tmm) REVERT: D 20 PHE cc_start: 0.8932 (m-80) cc_final: 0.8594 (m-10) REVERT: D 27 MET cc_start: 0.9127 (tpp) cc_final: 0.8739 (tpp) REVERT: E 6 GLU cc_start: 0.8271 (pp20) cc_final: 0.7964 (pp20) REVERT: F 68 ARG cc_start: 0.8621 (ppt170) cc_final: 0.8315 (ttp80) REVERT: F 73 ASP cc_start: 0.8606 (m-30) cc_final: 0.8284 (m-30) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1730 time to fit residues: 72.8011 Evaluate side-chains 235 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9077 Z= 0.245 Angle : 0.710 6.524 12407 Z= 0.345 Chirality : 0.044 0.198 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.301 63.750 1248 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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: -0.09 (0.26), residues: 1118 helix: 0.65 (0.21), residues: 680 sheet: -1.26 (0.69), residues: 48 loop : -1.06 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 29 HIS 0.006 0.001 HIS F 17 PHE 0.034 0.002 PHE C 103 TYR 0.019 0.002 TYR C 71 ARG 0.009 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7994 (ppp) cc_final: 0.7653 (ppp) REVERT: A 47 LEU cc_start: 0.8670 (mt) cc_final: 0.8454 (mt) REVERT: A 85 ILE cc_start: 0.6162 (pt) cc_final: 0.5883 (pt) REVERT: A 99 HIS cc_start: 0.8063 (t-90) cc_final: 0.7742 (t-170) REVERT: A 109 GLU cc_start: 0.9552 (tt0) cc_final: 0.9295 (tm-30) REVERT: B 5 ARG cc_start: 0.8346 (ptp90) cc_final: 0.7980 (ptm160) REVERT: B 44 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 71 ARG cc_start: 0.8604 (tpt-90) cc_final: 0.8269 (tpt-90) REVERT: B 73 ASP cc_start: 0.8317 (m-30) cc_final: 0.8035 (m-30) REVERT: B 133 LEU cc_start: 0.9613 (tp) cc_final: 0.9372 (tp) REVERT: B 175 PHE cc_start: 0.9128 (m-80) cc_final: 0.8891 (m-80) REVERT: C 86 MET cc_start: 0.8102 (mmm) cc_final: 0.7858 (mmm) REVERT: C 90 ASN cc_start: 0.8753 (m-40) cc_final: 0.8448 (m-40) REVERT: C 91 LEU cc_start: 0.9226 (tp) cc_final: 0.8927 (tp) REVERT: C 228 MET cc_start: 0.8684 (ttm) cc_final: 0.8252 (tmm) REVERT: D 27 MET cc_start: 0.9116 (tpp) cc_final: 0.8703 (tpp) REVERT: E 6 GLU cc_start: 0.8257 (pp20) cc_final: 0.8023 (pp20) REVERT: F 15 PHE cc_start: 0.8174 (m-80) cc_final: 0.7704 (m-80) REVERT: F 68 ARG cc_start: 0.8689 (ppt170) cc_final: 0.8358 (ttp80) REVERT: F 73 ASP cc_start: 0.8680 (m-30) cc_final: 0.8379 (m-30) REVERT: F 143 LEU cc_start: 0.9374 (tp) cc_final: 0.9148 (tp) REVERT: F 168 LEU cc_start: 0.9557 (mt) cc_final: 0.9329 (mt) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1903 time to fit residues: 78.5743 Evaluate side-chains 237 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.0000 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 0.0070 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9077 Z= 0.203 Angle : 0.715 7.717 12407 Z= 0.339 Chirality : 0.043 0.231 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.209 64.920 1248 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 0.03 (0.26), residues: 1118 helix: 0.74 (0.21), residues: 674 sheet: -1.27 (0.69), residues: 48 loop : -0.96 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 119 HIS 0.006 0.001 HIS F 17 PHE 0.024 0.002 PHE F 15 TYR 0.014 0.001 TYR C 71 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7973 (ppp) cc_final: 0.7639 (ppp) REVERT: A 85 ILE cc_start: 0.6082 (pt) cc_final: 0.5783 (pt) REVERT: A 99 HIS cc_start: 0.8089 (t-90) cc_final: 0.7839 (t-170) REVERT: A 109 GLU cc_start: 0.9543 (tt0) cc_final: 0.9300 (tm-30) REVERT: B 2 MET cc_start: 0.5504 (tpt) cc_final: 0.5266 (tpt) REVERT: B 44 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8578 (tm-30) REVERT: B 72 ASP cc_start: 0.9168 (p0) cc_final: 0.8954 (p0) REVERT: B 73 ASP cc_start: 0.8322 (m-30) cc_final: 0.8071 (m-30) REVERT: B 133 LEU cc_start: 0.9600 (tp) cc_final: 0.9356 (tp) REVERT: B 175 PHE cc_start: 0.9107 (m-80) cc_final: 0.8876 (m-80) REVERT: C 86 MET cc_start: 0.8120 (mmm) cc_final: 0.7832 (mmm) REVERT: C 90 ASN cc_start: 0.8695 (m-40) cc_final: 0.8390 (m-40) REVERT: C 91 LEU cc_start: 0.9188 (tp) cc_final: 0.8895 (tp) REVERT: C 228 MET cc_start: 0.8657 (ttm) cc_final: 0.8217 (tmm) REVERT: D 20 PHE cc_start: 0.8923 (m-10) cc_final: 0.8647 (m-10) REVERT: D 27 MET cc_start: 0.9122 (tpp) cc_final: 0.8708 (tpp) REVERT: E 6 GLU cc_start: 0.8222 (pp20) cc_final: 0.7951 (pp20) REVERT: E 93 GLU cc_start: 0.8816 (pt0) cc_final: 0.8548 (mp0) REVERT: F 15 PHE cc_start: 0.8115 (m-80) cc_final: 0.7854 (m-80) REVERT: F 73 ASP cc_start: 0.8662 (m-30) cc_final: 0.8344 (m-30) REVERT: F 111 LEU cc_start: 0.9217 (tp) cc_final: 0.8925 (tt) REVERT: F 143 LEU cc_start: 0.9361 (tp) cc_final: 0.9110 (tp) REVERT: F 168 LEU cc_start: 0.9521 (mt) cc_final: 0.9291 (mt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1705 time to fit residues: 72.3411 Evaluate side-chains 252 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9077 Z= 0.242 Angle : 0.721 8.380 12407 Z= 0.345 Chirality : 0.044 0.235 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.148 63.769 1248 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -0.02 (0.26), residues: 1118 helix: 0.69 (0.21), residues: 674 sheet: -1.25 (0.69), residues: 48 loop : -0.96 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 29 HIS 0.004 0.001 HIS F 17 PHE 0.029 0.002 PHE C 103 TYR 0.014 0.001 TYR C 71 ARG 0.008 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7999 (ppp) cc_final: 0.7650 (ppp) REVERT: A 85 ILE cc_start: 0.6172 (pt) cc_final: 0.5901 (pt) REVERT: A 99 HIS cc_start: 0.8125 (t-90) cc_final: 0.7861 (t-170) REVERT: A 109 GLU cc_start: 0.9557 (tt0) cc_final: 0.9305 (tm-30) REVERT: B 2 MET cc_start: 0.5830 (tpt) cc_final: 0.5241 (tpt) REVERT: B 10 GLU cc_start: 0.8990 (mp0) cc_final: 0.8725 (mp0) REVERT: B 44 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8629 (tm-30) REVERT: B 68 ARG cc_start: 0.8435 (ttp80) cc_final: 0.7553 (mmm160) REVERT: B 73 ASP cc_start: 0.8362 (m-30) cc_final: 0.8084 (m-30) REVERT: B 133 LEU cc_start: 0.9609 (tp) cc_final: 0.9369 (tp) REVERT: B 175 PHE cc_start: 0.9098 (m-80) cc_final: 0.8891 (m-80) REVERT: C 86 MET cc_start: 0.8174 (mmm) cc_final: 0.7870 (mmm) REVERT: C 90 ASN cc_start: 0.8712 (m-40) cc_final: 0.8348 (m-40) REVERT: C 91 LEU cc_start: 0.9211 (tp) cc_final: 0.8919 (tp) REVERT: C 228 MET cc_start: 0.8664 (ttm) cc_final: 0.8230 (tmm) REVERT: D 20 PHE cc_start: 0.8955 (m-10) cc_final: 0.8686 (m-10) REVERT: D 27 MET cc_start: 0.9132 (tpp) cc_final: 0.8571 (tpp) REVERT: E 6 GLU cc_start: 0.8234 (pp20) cc_final: 0.7943 (pp20) REVERT: E 93 GLU cc_start: 0.8856 (pt0) cc_final: 0.8584 (mp0) REVERT: F 15 PHE cc_start: 0.8115 (m-80) cc_final: 0.7853 (m-80) REVERT: F 73 ASP cc_start: 0.8659 (m-30) cc_final: 0.8315 (m-30) REVERT: F 101 TRP cc_start: 0.8572 (t60) cc_final: 0.8360 (t60) REVERT: F 111 LEU cc_start: 0.9199 (tp) cc_final: 0.8903 (tt) REVERT: F 143 LEU cc_start: 0.9364 (tp) cc_final: 0.9122 (tp) REVERT: F 168 LEU cc_start: 0.9543 (mt) cc_final: 0.9292 (mt) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1785 time to fit residues: 71.4256 Evaluate side-chains 245 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9077 Z= 0.211 Angle : 0.735 8.745 12407 Z= 0.346 Chirality : 0.045 0.239 1458 Planarity : 0.005 0.046 1526 Dihedral : 6.105 64.377 1248 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1118 helix: 0.75 (0.21), residues: 672 sheet: -1.28 (0.70), residues: 48 loop : -0.99 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 146 HIS 0.003 0.001 HIS A 73 PHE 0.020 0.002 PHE F 15 TYR 0.013 0.001 TYR C 71 ARG 0.023 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 0.953 Fit side-chains REVERT: A 1 MET cc_start: 0.7967 (ppp) cc_final: 0.7622 (ppp) REVERT: A 85 ILE cc_start: 0.6101 (pt) cc_final: 0.5812 (pt) REVERT: A 99 HIS cc_start: 0.8090 (t-90) cc_final: 0.7842 (t-170) REVERT: A 109 GLU cc_start: 0.9549 (tt0) cc_final: 0.9280 (tm-30) REVERT: B 2 MET cc_start: 0.5530 (tpt) cc_final: 0.5310 (tpt) REVERT: B 10 GLU cc_start: 0.8954 (mp0) cc_final: 0.8707 (mp0) REVERT: B 44 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8607 (tm-30) REVERT: B 72 ASP cc_start: 0.9141 (p0) cc_final: 0.8910 (p0) REVERT: B 73 ASP cc_start: 0.8304 (m-30) cc_final: 0.8067 (m-30) REVERT: B 133 LEU cc_start: 0.9595 (tp) cc_final: 0.9365 (tp) REVERT: B 175 PHE cc_start: 0.9098 (m-80) cc_final: 0.8887 (m-80) REVERT: C 86 MET cc_start: 0.8167 (mmm) cc_final: 0.7882 (mmm) REVERT: C 90 ASN cc_start: 0.8668 (m-40) cc_final: 0.8351 (m-40) REVERT: C 91 LEU cc_start: 0.9188 (tp) cc_final: 0.8897 (tp) REVERT: C 228 MET cc_start: 0.8645 (ttm) cc_final: 0.8233 (tmm) REVERT: D 20 PHE cc_start: 0.8936 (m-10) cc_final: 0.8652 (m-10) REVERT: D 27 MET cc_start: 0.9118 (tpp) cc_final: 0.8604 (tpp) REVERT: E 6 GLU cc_start: 0.8204 (pp20) cc_final: 0.7906 (pp20) REVERT: E 93 GLU cc_start: 0.8860 (pt0) cc_final: 0.8576 (mp0) REVERT: F 15 PHE cc_start: 0.8044 (m-80) cc_final: 0.7821 (m-80) REVERT: F 73 ASP cc_start: 0.8649 (m-30) cc_final: 0.8332 (m-30) REVERT: F 111 LEU cc_start: 0.9185 (tp) cc_final: 0.8885 (tt) REVERT: F 143 LEU cc_start: 0.9355 (tp) cc_final: 0.9094 (tp) REVERT: F 168 LEU cc_start: 0.9515 (mt) cc_final: 0.9287 (mt) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1765 time to fit residues: 70.9024 Evaluate side-chains 243 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9077 Z= 0.204 Angle : 0.742 9.077 12407 Z= 0.350 Chirality : 0.045 0.242 1458 Planarity : 0.005 0.049 1526 Dihedral : 6.049 63.598 1248 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -0.01 (0.26), residues: 1118 helix: 0.71 (0.21), residues: 679 sheet: -1.27 (0.70), residues: 48 loop : -0.99 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 146 HIS 0.003 0.001 HIS B 100 PHE 0.031 0.002 PHE C 103 TYR 0.013 0.001 TYR C 71 ARG 0.012 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.043 Fit side-chains REVERT: A 1 MET cc_start: 0.7974 (ppp) cc_final: 0.7628 (ppp) REVERT: A 85 ILE cc_start: 0.6119 (pt) cc_final: 0.5793 (pt) REVERT: A 99 HIS cc_start: 0.8101 (t-90) cc_final: 0.7826 (t-170) REVERT: A 109 GLU cc_start: 0.9538 (tt0) cc_final: 0.9274 (tm-30) REVERT: B 2 MET cc_start: 0.5745 (tpt) cc_final: 0.5434 (tpt) REVERT: B 10 GLU cc_start: 0.8930 (mp0) cc_final: 0.8641 (mp0) REVERT: B 44 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 68 ARG cc_start: 0.8420 (ttp80) cc_final: 0.7586 (mmm160) REVERT: B 73 ASP cc_start: 0.8337 (m-30) cc_final: 0.8102 (m-30) REVERT: B 133 LEU cc_start: 0.9570 (tp) cc_final: 0.9336 (tp) REVERT: B 175 PHE cc_start: 0.9094 (m-80) cc_final: 0.8889 (m-80) REVERT: C 86 MET cc_start: 0.8154 (mmm) cc_final: 0.7883 (mmm) REVERT: C 90 ASN cc_start: 0.8614 (m-40) cc_final: 0.8301 (m-40) REVERT: C 91 LEU cc_start: 0.9164 (tp) cc_final: 0.8914 (tp) REVERT: C 228 MET cc_start: 0.8628 (ttm) cc_final: 0.8231 (tmm) REVERT: D 20 PHE cc_start: 0.8908 (m-10) cc_final: 0.8600 (m-10) REVERT: D 27 MET cc_start: 0.9109 (tpp) cc_final: 0.8596 (tpp) REVERT: E 6 GLU cc_start: 0.8193 (pp20) cc_final: 0.7912 (pp20) REVERT: E 24 LEU cc_start: 0.8893 (mt) cc_final: 0.8046 (mt) REVERT: F 15 PHE cc_start: 0.8019 (m-80) cc_final: 0.7668 (m-80) REVERT: F 73 ASP cc_start: 0.8661 (m-30) cc_final: 0.8363 (m-30) REVERT: F 111 LEU cc_start: 0.9169 (tp) cc_final: 0.8886 (tt) REVERT: F 143 LEU cc_start: 0.9334 (tp) cc_final: 0.9053 (tp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1956 time to fit residues: 80.3331 Evaluate side-chains 239 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9077 Z= 0.227 Angle : 0.746 9.189 12407 Z= 0.353 Chirality : 0.045 0.242 1458 Planarity : 0.005 0.049 1526 Dihedral : 6.065 64.476 1248 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.01 (0.26), residues: 1118 helix: 0.76 (0.21), residues: 674 sheet: -1.23 (0.70), residues: 48 loop : -1.04 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 123 HIS 0.005 0.001 HIS F 17 PHE 0.020 0.001 PHE F 15 TYR 0.013 0.001 TYR C 71 ARG 0.011 0.001 ARG D 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.017 Fit side-chains REVERT: A 1 MET cc_start: 0.8007 (ppp) cc_final: 0.7649 (ppp) REVERT: A 85 ILE cc_start: 0.6203 (pt) cc_final: 0.5869 (pt) REVERT: A 99 HIS cc_start: 0.8112 (t-90) cc_final: 0.7846 (t-170) REVERT: A 109 GLU cc_start: 0.9546 (tt0) cc_final: 0.9309 (tm-30) REVERT: B 2 MET cc_start: 0.5724 (tpt) cc_final: 0.5397 (tpt) REVERT: B 10 GLU cc_start: 0.8987 (mp0) cc_final: 0.8677 (mp0) REVERT: B 44 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8677 (tm-30) REVERT: B 68 ARG cc_start: 0.8473 (ttp80) cc_final: 0.7619 (mmm160) REVERT: B 73 ASP cc_start: 0.8325 (m-30) cc_final: 0.8118 (m-30) REVERT: B 84 LEU cc_start: 0.8724 (tp) cc_final: 0.8361 (tp) REVERT: B 133 LEU cc_start: 0.9601 (tp) cc_final: 0.9386 (tp) REVERT: C 86 MET cc_start: 0.8181 (mmm) cc_final: 0.7903 (mmm) REVERT: C 90 ASN cc_start: 0.8617 (m-40) cc_final: 0.8336 (m-40) REVERT: C 91 LEU cc_start: 0.9175 (tp) cc_final: 0.8900 (tp) REVERT: C 228 MET cc_start: 0.8646 (ttm) cc_final: 0.8236 (tmm) REVERT: D 20 PHE cc_start: 0.8934 (m-10) cc_final: 0.8615 (m-10) REVERT: D 27 MET cc_start: 0.9118 (tpp) cc_final: 0.8599 (tpp) REVERT: E 6 GLU cc_start: 0.8232 (pp20) cc_final: 0.7930 (pp20) REVERT: E 24 LEU cc_start: 0.8965 (mt) cc_final: 0.8724 (mt) REVERT: F 73 ASP cc_start: 0.8715 (m-30) cc_final: 0.8409 (m-30) REVERT: F 111 LEU cc_start: 0.9175 (tp) cc_final: 0.8877 (tt) REVERT: F 143 LEU cc_start: 0.9338 (tp) cc_final: 0.9092 (tp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1699 time to fit residues: 69.1008 Evaluate side-chains 237 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.100251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081450 restraints weight = 31196.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.083765 restraints weight = 17851.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.085412 restraints weight = 12083.957| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9077 Z= 0.213 Angle : 0.727 9.101 12407 Z= 0.343 Chirality : 0.045 0.240 1458 Planarity : 0.005 0.046 1526 Dihedral : 5.993 64.370 1248 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.09 (0.26), residues: 1118 helix: 0.82 (0.21), residues: 674 sheet: -1.17 (0.69), residues: 48 loop : -1.02 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 123 HIS 0.009 0.001 HIS F 17 PHE 0.034 0.001 PHE F 15 TYR 0.013 0.001 TYR C 71 ARG 0.010 0.000 ARG D 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.73 seconds wall clock time: 39 minutes 41.46 seconds (2381.46 seconds total)