Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 09:27:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/10_2023/7vfp_31957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/10_2023/7vfp_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_31957/10_2023/7vfp_31957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/10_2023/7vfp_31957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/10_2023/7vfp_31957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/10_2023/7vfp_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-1.21rc1-5097/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: 4.97, per 1000 atoms: 0.56 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: 3.28 Conformation dependent library (CDL) restraints added in 1.3 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: 1.53 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: 2.32 Time building geometry restraints manager: 3.59 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: 4755 17.41 - 34.81: 436 34.81 - 52.22: 74 52.22 - 69.63: 8 69.63 - 87.03: 8 Dihedral angle restraints: 5281 sinusoidal: 2057 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 5278 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.250 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.490 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.120 ------------------------------------------------------------------------------- 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 : 13.738 87.031 3197 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 *********************** 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 : 0.977 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1820 time to fit residues: 75.5119 Evaluate side-chains 236 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2713 ------------------------------------------------------------------------------- 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: 9.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 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: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN 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 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9077 Z= 0.234 Angle : 0.707 6.263 12407 Z= 0.352 Chirality : 0.044 0.207 1458 Planarity : 0.006 0.044 1526 Dihedral : 5.717 71.834 1217 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.36 % Rotamer: Outliers : 0.11 % Allowed : 5.78 % Favored : 94.11 % 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 (0.26), residues: 1118 helix: 0.64 (0.21), residues: 663 sheet: -1.56 (0.67), residues: 50 loop : -0.84 (0.32), residues: 405 *********************** 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 285 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.1823 time to fit residues: 73.4081 Evaluate side-chains 230 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3087 ------------------------------------------------------------------------------- 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: 8.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.0040 chunk 110 optimal weight: 0.0770 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.3554 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9077 Z= 0.227 Angle : 0.701 6.364 12407 Z= 0.341 Chirality : 0.044 0.196 1458 Planarity : 0.005 0.044 1526 Dihedral : 5.592 68.487 1217 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1118 helix: 0.59 (0.21), residues: 668 sheet: -1.22 (0.70), residues: 48 loop : -0.95 (0.31), residues: 402 *********************** 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 287 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 287 average time/residue: 0.1860 time to fit residues: 75.5513 Evaluate side-chains 220 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3382 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- 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 50 GLN C 90 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 17 HIS F 100 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9077 Z= 0.234 Angle : 0.706 6.679 12407 Z= 0.345 Chirality : 0.044 0.204 1458 Planarity : 0.005 0.044 1526 Dihedral : 5.574 66.065 1217 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 0.33 % Allowed : 4.25 % Favored : 95.42 % 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: -0.14 (0.26), residues: 1118 helix: 0.54 (0.21), residues: 676 sheet: -1.38 (0.68), residues: 48 loop : -0.91 (0.31), residues: 394 *********************** 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 286 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 283 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 285 average time/residue: 0.1789 time to fit residues: 73.8962 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2895 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 0.0970 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- 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: 0.7970 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9077 Z= 0.273 Angle : 0.735 7.231 12407 Z= 0.358 Chirality : 0.044 0.209 1458 Planarity : 0.005 0.046 1526 Dihedral : 5.545 64.373 1217 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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 (0.26), residues: 1118 helix: 0.49 (0.21), residues: 684 sheet: -1.29 (0.69), residues: 48 loop : -1.03 (0.32), residues: 386 *********************** 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 281 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1807 time to fit residues: 72.1753 Evaluate side-chains 223 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2421 ------------------------------------------------------------------------------- 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: 8.9990 chunk 21 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 0.0040 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- 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** A 99 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2450 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= 0.218 Angle : 0.734 7.373 12407 Z= 0.349 Chirality : 0.044 0.214 1458 Planarity : 0.005 0.047 1526 Dihedral : 5.477 64.305 1217 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1118 helix: 0.64 (0.21), residues: 673 sheet: -1.30 (0.69), residues: 48 loop : -0.99 (0.32), residues: 397 *********************** 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 287 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1802 time to fit residues: 73.6741 Evaluate side-chains 230 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3273 ------------------------------------------------------------------------------- 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: 8.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.0470 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.0000 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 99 HIS ** 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 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9077 Z= 0.195 Angle : 0.732 8.787 12407 Z= 0.347 Chirality : 0.044 0.209 1458 Planarity : 0.005 0.046 1526 Dihedral : 5.404 65.089 1217 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -0.08 (0.26), residues: 1118 helix: 0.60 (0.21), residues: 674 sheet: -1.22 (0.69), residues: 48 loop : -0.92 (0.32), residues: 396 *********************** 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 293 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1775 time to fit residues: 74.3004 Evaluate side-chains 244 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2765 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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: 0.7887 moved from start: 0.2841 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= 0.219 Angle : 0.766 10.719 12407 Z= 0.361 Chirality : 0.045 0.245 1458 Planarity : 0.005 0.058 1526 Dihedral : 5.415 63.675 1217 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 0.11 % Allowed : 1.20 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1118 helix: 0.59 (0.21), residues: 675 sheet: -1.05 (0.72), residues: 48 loop : -0.96 (0.32), residues: 395 *********************** 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 285 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.1725 time to fit residues: 70.9543 Evaluate side-chains 235 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2956 ------------------------------------------------------------------------------- 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: 0.3980 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2984 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= 0.203 Angle : 0.759 9.589 12407 Z= 0.355 Chirality : 0.045 0.230 1458 Planarity : 0.005 0.049 1526 Dihedral : 5.348 63.479 1217 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.35 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.12 (0.26), residues: 1118 helix: 0.57 (0.21), residues: 678 sheet: -0.95 (0.73), residues: 48 loop : -1.00 (0.32), residues: 392 *********************** 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 279 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1738 time to fit residues: 70.1440 Evaluate side-chains 240 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3674 ------------------------------------------------------------------------------- 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: 0.8980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7891 moved from start: 0.3060 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= 0.220 Angle : 0.768 10.562 12407 Z= 0.358 Chirality : 0.045 0.244 1458 Planarity : 0.005 0.049 1526 Dihedral : 5.332 62.517 1217 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.20 % 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 (0.26), residues: 1118 helix: 0.64 (0.21), residues: 679 sheet: -0.93 (0.72), residues: 48 loop : -0.99 (0.32), residues: 391 ********************** 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 277 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.085 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1718 time to fit residues: 69.0177 Evaluate side-chains 234 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3636 ------------------------------------------------------------------------------- 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: 7.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.0570 chunk 5 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 82 GLN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.102227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.083439 restraints weight = 31197.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.085810 restraints weight = 17658.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087468 restraints weight = 11792.216| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9077 Z= 0.203 Angle : 0.762 9.533 12407 Z= 0.356 Chirality : 0.046 0.236 1458 Planarity : 0.005 0.046 1526 Dihedral : 5.309 62.901 1217 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % 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: -0.03 (0.26), residues: 1118 helix: 0.63 (0.21), residues: 679 sheet: -0.84 (0.72), residues: 48 loop : -0.94 (0.32), residues: 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.32 seconds wall clock time: 38 minutes 3.05 seconds (2283.05 seconds total)