Starting phenix.real_space_refine on Wed Sep 25 00:57:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/09_2024/7vfp_31957.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/09_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_31957/09_2024/7vfp_31957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/09_2024/7vfp_31957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/09_2024/7vfp_31957.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfp_31957/09_2024/7vfp_31957.cif" } 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. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.91, per 1000 atoms: 0.67 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.0 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... Secondary structure from input PDB file: 52 helices and 6 sheets defined 68.1% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.914A pdb=" N THR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 90 through 99 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 106 through 114 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 158 through 176 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 190 through 194 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.611A pdb=" N ALA B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 21 No H-bonds generated for 'chain 'B' and resid 19 through 21' Processing helix chain 'B' and resid 22 through 39 removed outlier: 4.170A pdb=" N PHE B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 49 through 76 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) removed outlier: 3.665A pdb=" N ASP B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 119 removed outlier: 3.534A pdb=" N VAL B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) 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 122 through 154 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 158 through 165 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 189 through 220 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 removed outlier: 3.841A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 21 through 40 Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.821A pdb=" N SER C 53 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 84 Proline residue: C 62 - end of helix removed outlier: 3.588A pdb=" N VAL C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 115 removed outlier: 3.504A pdb=" N ASN C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) 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 115 through 120 Processing helix chain 'C' and resid 126 through 149 removed outlier: 3.712A pdb=" N PHE C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 185 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 195 through 198 Processing helix chain 'C' and resid 199 through 229 Processing helix chain 'C' and resid 230 through 231 No H-bonds generated for 'chain 'C' and resid 230 through 231' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'D' and resid 17 through 54 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 39 through 48 Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.840A pdb=" N HIS E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 removed outlier: 3.744A pdb=" N PHE E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 removed outlier: 3.942A pdb=" N ALA E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 128 through 138 removed outlier: 3.919A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'E' and resid 172 through 176 removed outlier: 3.564A pdb=" N GLN E 175 " --> pdb=" O HIS E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 removed outlier: 3.582A pdb=" N ILE E 194 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 21 through 39 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 42 through 67 removed outlier: 3.758A pdb=" N LEU F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Proline residue: F 51 - end of helix Processing helix chain 'F' and resid 88 through 120 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 122 through 152 Proline residue: F 138 - end of helix Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 158 through 165 removed outlier: 3.610A pdb=" N SER F 162 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 185 removed outlier: 3.665A pdb=" N MET F 185 " --> pdb=" O ASP F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 220 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 removed outlier: 3.774A pdb=" N GLN F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 6.026A pdb=" N ALA A 4 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 59 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU A 6 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU A 57 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 removed outlier: 5.915A pdb=" N ILE A 79 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 150 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.246A pdb=" N LEU E 16 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ARG E 11 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER E 18 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N CYS E 9 " --> pdb=" O SER E 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.246A pdb=" N LEU E 16 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ARG E 11 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER E 18 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N CYS E 9 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU E 7 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA E 55 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 77 through 79 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) removed outlier: 6.461A pdb=" N VAL E 30 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TRP E 29 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE E 197 " --> pdb=" O TRP E 29 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN E 31 " --> pdb=" O ILE E 197 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1428 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: 2.56 Time building geometry restraints manager: 2.79 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: 0.00 - 4.06: 12307 4.06 - 8.13: 95 8.13 - 12.19: 3 12.19 - 16.26: 0 16.26 - 20.32: 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: 64 2.53 - 3.12: 7128 3.12 - 3.71: 14804 3.71 - 4.31: 18987 4.31 - 4.90: 30992 Nonbonded interactions: 71975 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 71970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid -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: 1.880 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.190 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.070 ------------------------------------------------------------------------------- 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= 0.257 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 : 1.435 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: 0.1811 time to fit residues: 75.5897 Evaluate side-chains 243 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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: 5.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN E 96 HIS E 160 ASN E 171 GLN F 100 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9077 Z= 0.212 Angle : 0.717 8.024 12407 Z= 0.354 Chirality : 0.044 0.197 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.589 71.957 1248 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 0.11 % Allowed : 5.45 % Favored : 94.44 % 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: 0.11 (0.25), residues: 1118 helix: 0.77 (0.20), residues: 694 sheet: -1.47 (0.69), residues: 49 loop : -0.92 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 119 HIS 0.006 0.001 HIS B 100 PHE 0.024 0.002 PHE F 15 TYR 0.016 0.001 TYR D 17 ARG 0.006 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 295 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8008 (ppp) cc_final: 0.7713 (ppp) REVERT: A 47 LEU cc_start: 0.8668 (mt) cc_final: 0.8458 (mt) REVERT: A 99 HIS cc_start: 0.8177 (t-90) cc_final: 0.7903 (t-90) REVERT: B 1 MET cc_start: 0.8341 (tmm) cc_final: 0.8091 (tmm) REVERT: B 5 ARG cc_start: 0.8918 (mtm180) cc_final: 0.8453 (mtp180) REVERT: B 44 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8674 (tm-30) REVERT: B 73 ASP cc_start: 0.7962 (m-30) cc_final: 0.7682 (m-30) REVERT: B 133 LEU cc_start: 0.9624 (tp) cc_final: 0.9390 (tp) REVERT: B 175 PHE cc_start: 0.8946 (m-10) cc_final: 0.8618 (m-80) REVERT: C 86 MET cc_start: 0.8259 (mmm) cc_final: 0.7982 (mmm) REVERT: C 90 ASN cc_start: 0.8992 (m-40) cc_final: 0.8613 (m-40) REVERT: C 169 ASN cc_start: 0.9028 (m110) cc_final: 0.8824 (m-40) REVERT: C 228 MET cc_start: 0.8693 (ttm) cc_final: 0.8151 (tmm) REVERT: C 230 LYS cc_start: 0.8451 (pptt) cc_final: 0.7977 (pptt) REVERT: D 20 PHE cc_start: 0.8900 (m-80) cc_final: 0.8656 (m-10) REVERT: D 27 MET cc_start: 0.9033 (tpp) cc_final: 0.8676 (tpp) REVERT: E 1 MET cc_start: 0.8036 (pmm) cc_final: 0.7811 (pmm) REVERT: F 15 PHE cc_start: 0.8014 (m-80) cc_final: 0.7813 (m-80) REVERT: F 68 ARG cc_start: 0.8498 (ppt170) cc_final: 0.8283 (ttp80) REVERT: F 71 ARG cc_start: 0.7583 (ttt180) cc_final: 0.6943 (ttm-80) REVERT: F 73 ASP cc_start: 0.8705 (m-30) cc_final: 0.8354 (m-30) REVERT: F 164 LEU cc_start: 0.9269 (mt) cc_final: 0.9032 (mt) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.1763 time to fit residues: 73.6231 Evaluate side-chains 236 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 0.0370 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.4860 ------------------------------------------------------------------------------- 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** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN E 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9077 Z= 0.235 Angle : 0.708 6.724 12407 Z= 0.347 Chirality : 0.045 0.194 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.431 68.209 1248 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % 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: 0.07 (0.25), residues: 1118 helix: 0.81 (0.20), residues: 695 sheet: -1.58 (0.69), residues: 48 loop : -1.06 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 55 HIS 0.005 0.001 HIS B 100 PHE 0.019 0.002 PHE F 15 TYR 0.011 0.001 TYR D 17 ARG 0.007 0.000 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 286 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7984 (ppp) cc_final: 0.7668 (ppp) REVERT: A 47 LEU cc_start: 0.8667 (mt) cc_final: 0.8460 (mt) REVERT: A 76 LEU cc_start: 0.9083 (tt) cc_final: 0.8563 (tt) REVERT: A 85 ILE cc_start: 0.6115 (pt) cc_final: 0.5816 (pt) REVERT: A 99 HIS cc_start: 0.8213 (t-90) cc_final: 0.7961 (t-170) REVERT: A 109 GLU cc_start: 0.9554 (tt0) cc_final: 0.9304 (tm-30) REVERT: B 5 ARG cc_start: 0.8900 (mtm180) cc_final: 0.8364 (mtp180) REVERT: B 44 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8726 (tm-30) REVERT: B 133 LEU cc_start: 0.9599 (tp) cc_final: 0.9365 (tp) REVERT: B 175 PHE cc_start: 0.9019 (m-10) cc_final: 0.8725 (m-80) REVERT: C 90 ASN cc_start: 0.9011 (m-40) cc_final: 0.8623 (m-40) REVERT: C 118 MET cc_start: 0.8514 (ptp) cc_final: 0.6051 (ptp) REVERT: C 151 ASP cc_start: 0.8129 (t0) cc_final: 0.7871 (t0) REVERT: C 153 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.7270 (ptt-90) REVERT: C 169 ASN cc_start: 0.9032 (m110) cc_final: 0.8792 (m-40) REVERT: C 228 MET cc_start: 0.8696 (ttm) cc_final: 0.8146 (tmm) REVERT: D 27 MET cc_start: 0.9111 (tpp) cc_final: 0.8652 (tpp) REVERT: D 42 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8390 (tm-30) REVERT: E 1 MET cc_start: 0.8163 (pmm) cc_final: 0.7950 (pmm) REVERT: E 6 GLU cc_start: 0.7981 (pp20) cc_final: 0.7710 (pp20) REVERT: F 15 PHE cc_start: 0.8039 (m-80) cc_final: 0.7833 (m-80) REVERT: F 67 GLU cc_start: 0.8727 (tt0) cc_final: 0.8490 (tt0) REVERT: F 68 ARG cc_start: 0.8596 (ppt170) cc_final: 0.8355 (ttp80) REVERT: F 73 ASP cc_start: 0.8509 (m-30) cc_final: 0.8221 (m-30) REVERT: F 164 LEU cc_start: 0.9296 (mt) cc_final: 0.9066 (mt) outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.1791 time to fit residues: 72.9232 Evaluate side-chains 238 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 50 GLN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2047 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= 0.206 Angle : 0.697 6.384 12407 Z= 0.340 Chirality : 0.043 0.207 1458 Planarity : 0.005 0.051 1526 Dihedral : 6.303 66.675 1248 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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 (0.25), residues: 1118 helix: 0.82 (0.20), residues: 700 sheet: -1.60 (0.69), residues: 48 loop : -0.96 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 66 HIS 0.006 0.001 HIS B 100 PHE 0.019 0.002 PHE F 28 TYR 0.012 0.001 TYR D 17 ARG 0.007 0.000 ARG D 48 *********************** 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 287 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7943 (ppp) cc_final: 0.7622 (ppp) REVERT: A 47 LEU cc_start: 0.8677 (mt) cc_final: 0.8474 (mt) REVERT: A 85 ILE cc_start: 0.6117 (pt) cc_final: 0.5782 (pt) REVERT: A 99 HIS cc_start: 0.8191 (t-90) cc_final: 0.7937 (t-170) REVERT: A 109 GLU cc_start: 0.9546 (tt0) cc_final: 0.9303 (tm-30) REVERT: A 141 TRP cc_start: 0.7510 (m100) cc_final: 0.7120 (m100) REVERT: B 5 ARG cc_start: 0.8832 (mtm180) cc_final: 0.8331 (mtp180) REVERT: B 44 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8703 (tm-30) REVERT: B 73 ASP cc_start: 0.7954 (m-30) cc_final: 0.7713 (m-30) REVERT: B 133 LEU cc_start: 0.9617 (tp) cc_final: 0.9359 (tp) REVERT: B 175 PHE cc_start: 0.9034 (m-10) cc_final: 0.8727 (m-80) REVERT: C 90 ASN cc_start: 0.8948 (m-40) cc_final: 0.8579 (m-40) REVERT: C 118 MET cc_start: 0.8037 (ptp) cc_final: 0.6642 (ptp) REVERT: C 119 TRP cc_start: 0.7503 (m100) cc_final: 0.7115 (m100) REVERT: C 153 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.7297 (ptt-90) REVERT: C 169 ASN cc_start: 0.9023 (m110) cc_final: 0.8810 (m-40) REVERT: C 228 MET cc_start: 0.8651 (ttm) cc_final: 0.8177 (tmm) REVERT: D 27 MET cc_start: 0.9122 (tpp) cc_final: 0.8744 (tpp) REVERT: D 42 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8434 (tp-100) REVERT: E 6 GLU cc_start: 0.8023 (pp20) cc_final: 0.7763 (pp20) REVERT: E 7 LEU cc_start: 0.9141 (tp) cc_final: 0.8933 (tp) REVERT: F 68 ARG cc_start: 0.8586 (ppt170) cc_final: 0.8276 (ttp80) REVERT: F 73 ASP cc_start: 0.8515 (m-30) cc_final: 0.8228 (m-30) REVERT: F 164 LEU cc_start: 0.9266 (mt) cc_final: 0.9057 (mt) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1683 time to fit residues: 69.5620 Evaluate side-chains 239 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.0040 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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** E 171 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2286 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= 0.195 Angle : 0.716 10.009 12407 Z= 0.344 Chirality : 0.043 0.205 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.214 66.484 1248 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % 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: 0.18 (0.25), residues: 1118 helix: 0.93 (0.20), residues: 695 sheet: -1.62 (0.69), residues: 48 loop : -1.09 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.005 0.001 HIS F 17 PHE 0.039 0.002 PHE C 103 TYR 0.011 0.001 TYR D 17 ARG 0.011 0.000 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 297 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7920 (ppp) cc_final: 0.7590 (ppp) REVERT: A 35 SER cc_start: 0.7636 (m) cc_final: 0.7423 (t) REVERT: A 85 ILE cc_start: 0.5969 (pt) cc_final: 0.5644 (pt) REVERT: A 99 HIS cc_start: 0.8205 (t-90) cc_final: 0.7957 (t-170) REVERT: B 5 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8256 (mtp180) REVERT: B 133 LEU cc_start: 0.9572 (tp) cc_final: 0.9329 (tp) REVERT: B 175 PHE cc_start: 0.9023 (m-10) cc_final: 0.8731 (m-80) REVERT: C 90 ASN cc_start: 0.8883 (m-40) cc_final: 0.8490 (m-40) REVERT: C 91 LEU cc_start: 0.9198 (tp) cc_final: 0.8974 (tp) REVERT: C 118 MET cc_start: 0.8102 (ptp) cc_final: 0.6743 (ptp) REVERT: C 119 TRP cc_start: 0.7668 (m100) cc_final: 0.7193 (m100) REVERT: C 153 ARG cc_start: 0.7373 (ttp-170) cc_final: 0.7131 (ptt-90) REVERT: C 228 MET cc_start: 0.8638 (ttm) cc_final: 0.8206 (tmm) REVERT: D 20 PHE cc_start: 0.8912 (m-10) cc_final: 0.8697 (m-80) REVERT: D 27 MET cc_start: 0.9146 (tpp) cc_final: 0.8734 (tpp) REVERT: E 6 GLU cc_start: 0.7899 (pp20) cc_final: 0.7642 (pp20) REVERT: E 93 GLU cc_start: 0.8669 (mp0) cc_final: 0.8349 (tp30) REVERT: F 15 PHE cc_start: 0.8011 (m-80) cc_final: 0.7750 (m-80) REVERT: F 68 ARG cc_start: 0.8578 (ppt170) cc_final: 0.8274 (ttp80) REVERT: F 73 ASP cc_start: 0.8514 (m-30) cc_final: 0.8188 (m-30) REVERT: F 104 THR cc_start: 0.8983 (p) cc_final: 0.8676 (t) REVERT: F 111 LEU cc_start: 0.9173 (tp) cc_final: 0.8906 (tt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1664 time to fit residues: 71.7690 Evaluate side-chains 240 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 169 ASN ** E 99 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: 0.7959 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9077 Z= 0.287 Angle : 0.762 8.492 12407 Z= 0.371 Chirality : 0.045 0.225 1458 Planarity : 0.005 0.043 1526 Dihedral : 6.309 63.996 1248 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 0.27 (0.26), residues: 1118 helix: 0.97 (0.20), residues: 690 sheet: -1.59 (0.70), residues: 48 loop : -0.95 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 66 HIS 0.005 0.001 HIS F 17 PHE 0.025 0.002 PHE F 15 TYR 0.013 0.002 TYR C 71 ARG 0.010 0.001 ARG D 48 *********************** 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 280 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7997 (ppp) cc_final: 0.7541 (ppp) REVERT: A 47 LEU cc_start: 0.8621 (mt) cc_final: 0.8417 (mt) REVERT: A 85 ILE cc_start: 0.6157 (pt) cc_final: 0.5840 (pt) REVERT: A 99 HIS cc_start: 0.8209 (t-90) cc_final: 0.7935 (t-170) REVERT: A 109 GLU cc_start: 0.9572 (tt0) cc_final: 0.9322 (tm-30) REVERT: B 5 ARG cc_start: 0.8809 (mtm180) cc_final: 0.8107 (mtp180) REVERT: B 10 GLU cc_start: 0.8936 (mp0) cc_final: 0.8660 (mp0) REVERT: B 29 LEU cc_start: 0.9526 (tp) cc_final: 0.9320 (tp) REVERT: B 73 ASP cc_start: 0.8132 (m-30) cc_final: 0.7912 (m-30) REVERT: B 84 LEU cc_start: 0.8410 (tp) cc_final: 0.8204 (tp) REVERT: B 175 PHE cc_start: 0.9085 (m-10) cc_final: 0.8795 (m-80) REVERT: C 86 MET cc_start: 0.8196 (mmm) cc_final: 0.7947 (mmm) REVERT: C 87 LYS cc_start: 0.9040 (mttp) cc_final: 0.6984 (tptt) REVERT: C 90 ASN cc_start: 0.8920 (m-40) cc_final: 0.8568 (m-40) REVERT: C 91 LEU cc_start: 0.9253 (tp) cc_final: 0.9026 (tp) REVERT: C 118 MET cc_start: 0.8061 (ptp) cc_final: 0.6274 (ptp) REVERT: C 119 TRP cc_start: 0.7830 (m100) cc_final: 0.7291 (m100) REVERT: C 228 MET cc_start: 0.8679 (ttm) cc_final: 0.8252 (tmm) REVERT: D 27 MET cc_start: 0.9145 (tpp) cc_final: 0.8717 (tpp) REVERT: E 6 GLU cc_start: 0.8053 (pp20) cc_final: 0.7730 (pp20) REVERT: E 7 LEU cc_start: 0.9177 (tp) cc_final: 0.8954 (tp) REVERT: E 93 GLU cc_start: 0.8793 (mp0) cc_final: 0.8532 (mp0) REVERT: F 15 PHE cc_start: 0.8025 (m-80) cc_final: 0.7748 (m-80) REVERT: F 73 ASP cc_start: 0.8473 (m-30) cc_final: 0.8090 (m-30) REVERT: F 209 PHE cc_start: 0.7256 (t80) cc_final: 0.7001 (t80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1656 time to fit residues: 67.2977 Evaluate side-chains 231 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 2.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9077 Z= 0.207 Angle : 0.735 8.395 12407 Z= 0.351 Chirality : 0.045 0.212 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.259 67.248 1248 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % 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: 0.29 (0.26), residues: 1118 helix: 1.05 (0.20), residues: 692 sheet: -1.62 (0.69), residues: 48 loop : -1.08 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 66 HIS 0.006 0.001 HIS F 17 PHE 0.020 0.002 PHE F 15 TYR 0.011 0.001 TYR D 17 ARG 0.010 0.001 ARG F 68 *********************** 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 291 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 0.871 Fit side-chains REVERT: A 1 MET cc_start: 0.7975 (ppp) cc_final: 0.7677 (ppp) REVERT: A 47 LEU cc_start: 0.8635 (mt) cc_final: 0.8430 (mt) REVERT: A 85 ILE cc_start: 0.6000 (pt) cc_final: 0.5663 (pt) REVERT: A 99 HIS cc_start: 0.8235 (t-90) cc_final: 0.7990 (t-170) REVERT: A 109 GLU cc_start: 0.9551 (tt0) cc_final: 0.9321 (tm-30) REVERT: B 5 ARG cc_start: 0.8763 (mtm180) cc_final: 0.8115 (mtp180) REVERT: B 84 LEU cc_start: 0.8380 (tp) cc_final: 0.8045 (tp) REVERT: B 133 LEU cc_start: 0.9592 (tp) cc_final: 0.9384 (tp) REVERT: B 175 PHE cc_start: 0.9102 (m-10) cc_final: 0.8802 (m-80) REVERT: C 86 MET cc_start: 0.8328 (mmm) cc_final: 0.8043 (mmm) REVERT: C 87 LYS cc_start: 0.9003 (mttp) cc_final: 0.8760 (mttm) REVERT: C 90 ASN cc_start: 0.8861 (m-40) cc_final: 0.8554 (m-40) REVERT: C 91 LEU cc_start: 0.9196 (tp) cc_final: 0.8954 (tp) REVERT: C 228 MET cc_start: 0.8659 (ttm) cc_final: 0.8244 (tmm) REVERT: D 27 MET cc_start: 0.9173 (tpp) cc_final: 0.8614 (tpp) REVERT: E 1 MET cc_start: 0.8102 (pmm) cc_final: 0.7772 (pmm) REVERT: E 6 GLU cc_start: 0.7936 (pp20) cc_final: 0.7648 (pp20) REVERT: E 93 GLU cc_start: 0.8839 (mp0) cc_final: 0.8432 (mp0) REVERT: F 11 LEU cc_start: 0.9174 (mt) cc_final: 0.8845 (mm) REVERT: F 15 PHE cc_start: 0.8035 (m-80) cc_final: 0.7783 (m-80) REVERT: F 73 ASP cc_start: 0.8484 (m-30) cc_final: 0.8094 (m-30) REVERT: F 111 LEU cc_start: 0.9223 (tp) cc_final: 0.8939 (tt) REVERT: F 168 LEU cc_start: 0.9471 (mt) cc_final: 0.9198 (mt) REVERT: F 209 PHE cc_start: 0.7148 (t80) cc_final: 0.6830 (t80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1678 time to fit residues: 70.0678 Evaluate side-chains 242 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 0.0570 chunk 103 optimal weight: 5.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** E 99 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: 0.7874 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9077 Z= 0.215 Angle : 0.754 9.545 12407 Z= 0.360 Chirality : 0.045 0.232 1458 Planarity : 0.005 0.046 1526 Dihedral : 6.177 66.925 1248 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 0.22 (0.25), residues: 1118 helix: 0.99 (0.20), residues: 691 sheet: -1.61 (0.70), residues: 48 loop : -1.10 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 66 HIS 0.005 0.001 HIS F 17 PHE 0.023 0.002 PHE C 103 TYR 0.015 0.001 TYR C 71 ARG 0.020 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 286 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7958 (ppp) cc_final: 0.7659 (ppp) REVERT: A 35 SER cc_start: 0.7855 (m) cc_final: 0.7653 (t) REVERT: A 47 LEU cc_start: 0.8636 (mt) cc_final: 0.8435 (mt) REVERT: A 85 ILE cc_start: 0.6030 (pt) cc_final: 0.5700 (pt) REVERT: A 99 HIS cc_start: 0.8214 (t-90) cc_final: 0.7977 (t-170) REVERT: A 109 GLU cc_start: 0.9549 (tt0) cc_final: 0.9308 (tm-30) REVERT: B 5 ARG cc_start: 0.8701 (mtm180) cc_final: 0.8009 (mtp180) REVERT: B 10 GLU cc_start: 0.8926 (mp0) cc_final: 0.8611 (mp0) REVERT: B 133 LEU cc_start: 0.9601 (tp) cc_final: 0.9396 (tp) REVERT: B 175 PHE cc_start: 0.9089 (m-10) cc_final: 0.8781 (m-80) REVERT: C 86 MET cc_start: 0.8301 (mmm) cc_final: 0.8064 (mmm) REVERT: C 87 LYS cc_start: 0.9050 (mttp) cc_final: 0.8840 (mttm) REVERT: C 90 ASN cc_start: 0.8824 (m-40) cc_final: 0.8338 (m-40) REVERT: C 91 LEU cc_start: 0.9156 (tp) cc_final: 0.8938 (tp) REVERT: C 118 MET cc_start: 0.8380 (ptp) cc_final: 0.7634 (ptp) REVERT: C 228 MET cc_start: 0.8643 (ttm) cc_final: 0.8230 (tmm) REVERT: D 27 MET cc_start: 0.9115 (tpp) cc_final: 0.8606 (tpp) REVERT: E 1 MET cc_start: 0.8085 (pmm) cc_final: 0.7711 (pmm) REVERT: E 6 GLU cc_start: 0.7906 (pp20) cc_final: 0.7703 (pp20) REVERT: E 7 LEU cc_start: 0.9117 (tp) cc_final: 0.8897 (tp) REVERT: E 93 GLU cc_start: 0.8812 (mp0) cc_final: 0.8437 (mp0) REVERT: F 1 MET cc_start: 0.6570 (ppp) cc_final: 0.5439 (ptp) REVERT: F 11 LEU cc_start: 0.9177 (mt) cc_final: 0.8860 (mm) REVERT: F 15 PHE cc_start: 0.7981 (m-80) cc_final: 0.7777 (m-80) REVERT: F 73 ASP cc_start: 0.8536 (m-30) cc_final: 0.8134 (m-30) REVERT: F 111 LEU cc_start: 0.9182 (tp) cc_final: 0.8902 (tt) REVERT: F 209 PHE cc_start: 0.7101 (t80) cc_final: 0.6797 (t80) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1720 time to fit residues: 70.4199 Evaluate side-chains 248 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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: 0.7980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9077 Z= 0.215 Angle : 0.748 8.705 12407 Z= 0.359 Chirality : 0.045 0.234 1458 Planarity : 0.005 0.051 1526 Dihedral : 6.145 65.974 1248 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % 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: 0.30 (0.25), residues: 1118 helix: 1.11 (0.20), residues: 683 sheet: -1.57 (0.70), residues: 48 loop : -1.16 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 66 HIS 0.004 0.001 HIS A 96 PHE 0.019 0.002 PHE B 27 TYR 0.017 0.001 TYR C 71 ARG 0.012 0.001 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 287 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7932 (ppp) cc_final: 0.7613 (ppp) REVERT: A 85 ILE cc_start: 0.6059 (pt) cc_final: 0.5757 (pt) REVERT: A 99 HIS cc_start: 0.8218 (t-90) cc_final: 0.7988 (t-170) REVERT: A 109 GLU cc_start: 0.9546 (tt0) cc_final: 0.9314 (tm-30) REVERT: B 5 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8120 (mtp180) REVERT: B 10 GLU cc_start: 0.8903 (mp0) cc_final: 0.8627 (mp0) REVERT: B 44 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 68 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8016 (tmm160) REVERT: B 133 LEU cc_start: 0.9595 (tp) cc_final: 0.9393 (tp) REVERT: B 175 PHE cc_start: 0.9096 (m-10) cc_final: 0.8786 (m-80) REVERT: C 86 MET cc_start: 0.8291 (mmm) cc_final: 0.8019 (mmm) REVERT: C 87 LYS cc_start: 0.9121 (mttp) cc_final: 0.8894 (mttm) REVERT: C 90 ASN cc_start: 0.8829 (m-40) cc_final: 0.8353 (m-40) REVERT: C 91 LEU cc_start: 0.9171 (tp) cc_final: 0.8942 (tp) REVERT: C 118 MET cc_start: 0.7954 (ptp) cc_final: 0.6320 (ptp) REVERT: C 119 TRP cc_start: 0.7838 (m100) cc_final: 0.7461 (m100) REVERT: C 146 TRP cc_start: 0.8599 (t60) cc_final: 0.8374 (t60) REVERT: C 228 MET cc_start: 0.8635 (ttm) cc_final: 0.8240 (tmm) REVERT: D 27 MET cc_start: 0.9108 (tpp) cc_final: 0.8613 (tpp) REVERT: E 1 MET cc_start: 0.8190 (pmm) cc_final: 0.7664 (pmm) REVERT: E 6 GLU cc_start: 0.7971 (pp20) cc_final: 0.7726 (pp20) REVERT: E 93 GLU cc_start: 0.8875 (mp0) cc_final: 0.8453 (mp0) REVERT: F 1 MET cc_start: 0.6474 (ppp) cc_final: 0.5260 (ptp) REVERT: F 11 LEU cc_start: 0.9189 (mt) cc_final: 0.8877 (mm) REVERT: F 73 ASP cc_start: 0.8508 (m-30) cc_final: 0.8116 (m-30) REVERT: F 111 LEU cc_start: 0.9180 (tp) cc_final: 0.8900 (tt) REVERT: F 209 PHE cc_start: 0.7053 (t80) cc_final: 0.6742 (t80) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1696 time to fit residues: 69.7772 Evaluate side-chains 242 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN C 169 ASN E 171 GLN F 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9077 Z= 0.213 Angle : 0.763 10.152 12407 Z= 0.363 Chirality : 0.045 0.231 1458 Planarity : 0.005 0.046 1526 Dihedral : 6.113 65.499 1248 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 0.26 (0.25), residues: 1118 helix: 1.01 (0.20), residues: 690 sheet: -1.51 (0.70), residues: 48 loop : -1.07 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 66 HIS 0.009 0.001 HIS F 17 PHE 0.029 0.002 PHE F 15 TYR 0.015 0.001 TYR C 71 ARG 0.010 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 279 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7884 (ppp) cc_final: 0.7553 (ppp) REVERT: A 85 ILE cc_start: 0.6088 (pt) cc_final: 0.5770 (pt) REVERT: A 99 HIS cc_start: 0.8241 (t-90) cc_final: 0.8013 (t-170) REVERT: A 109 GLU cc_start: 0.9543 (tt0) cc_final: 0.9308 (tm-30) REVERT: B 5 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8090 (mtp180) REVERT: B 10 GLU cc_start: 0.8951 (mp0) cc_final: 0.8622 (mp0) REVERT: B 44 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 68 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7526 (mmm160) REVERT: B 133 LEU cc_start: 0.9611 (tp) cc_final: 0.9402 (tp) REVERT: B 175 PHE cc_start: 0.9120 (m-10) cc_final: 0.8796 (m-80) REVERT: C 86 MET cc_start: 0.8231 (mmm) cc_final: 0.7968 (mmm) REVERT: C 87 LYS cc_start: 0.9131 (mttp) cc_final: 0.8596 (mttm) REVERT: C 90 ASN cc_start: 0.8798 (m-40) cc_final: 0.8501 (m-40) REVERT: C 91 LEU cc_start: 0.9166 (tp) cc_final: 0.8944 (tp) REVERT: C 118 MET cc_start: 0.8032 (ptp) cc_final: 0.6410 (ptp) REVERT: C 119 TRP cc_start: 0.7926 (m100) cc_final: 0.7567 (m100) REVERT: C 228 MET cc_start: 0.8630 (ttm) cc_final: 0.8256 (tmm) REVERT: D 27 MET cc_start: 0.9092 (tpp) cc_final: 0.8612 (tpp) REVERT: E 1 MET cc_start: 0.8155 (pmm) cc_final: 0.7716 (pmm) REVERT: E 6 GLU cc_start: 0.8001 (pp20) cc_final: 0.7767 (pp20) REVERT: E 7 LEU cc_start: 0.9061 (tp) cc_final: 0.8839 (tp) REVERT: E 93 GLU cc_start: 0.8869 (mp0) cc_final: 0.8413 (mp0) REVERT: F 1 MET cc_start: 0.6386 (ppp) cc_final: 0.5136 (ptp) REVERT: F 73 ASP cc_start: 0.8546 (m-30) cc_final: 0.8131 (m-30) REVERT: F 111 LEU cc_start: 0.9172 (tp) cc_final: 0.8878 (tt) REVERT: F 143 LEU cc_start: 0.9350 (tp) cc_final: 0.9142 (tp) REVERT: F 177 THR cc_start: 0.8923 (m) cc_final: 0.8712 (t) REVERT: F 209 PHE cc_start: 0.7052 (t80) cc_final: 0.6743 (t80) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1790 time to fit residues: 72.1373 Evaluate side-chains 242 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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: 0.0170 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN E 171 GLN F 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.100015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.080946 restraints weight = 31523.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.083279 restraints weight = 17955.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.084901 restraints weight = 12037.281| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9077 Z= 0.244 Angle : 0.771 8.712 12407 Z= 0.368 Chirality : 0.046 0.304 1458 Planarity : 0.005 0.045 1526 Dihedral : 6.148 64.072 1248 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % 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: 0.33 (0.26), residues: 1118 helix: 1.13 (0.20), residues: 683 sheet: -1.37 (0.70), residues: 48 loop : -1.17 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 66 HIS 0.016 0.001 HIS A 96 PHE 0.025 0.002 PHE F 15 TYR 0.015 0.002 TYR C 71 ARG 0.013 0.001 ARG F 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.31 seconds wall clock time: 38 minutes 27.21 seconds (2307.21 seconds total)