Starting phenix.real_space_refine on Wed Sep 25 00:07:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/09_2024/7tuz_26136.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/09_2024/7tuz_26136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/09_2024/7tuz_26136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/09_2024/7tuz_26136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/09_2024/7tuz_26136.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuz_26136/09_2024/7tuz_26136.cif" } resolution = 3.12 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= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5681 2.51 5 N 1504 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 8910 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2214 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1823 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.45, per 1000 atoms: 0.61 Number of scatterers: 8910 At special positions: 0 Unit cell: (104.125, 119.119, 110.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1657 8.00 N 1504 7.00 C 5681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 181 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 38.0% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'R' and resid 26 through 59 removed outlier: 3.988A pdb=" N ILE R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) Proline residue: R 35 - end of helix removed outlier: 3.562A pdb=" N LEU R 51 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 88 Proline residue: R 85 - end of helix Processing helix chain 'R' and resid 102 through 134 removed outlier: 4.236A pdb=" N ILE R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR R 115 " --> pdb=" O PHE R 111 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR R 116 " --> pdb=" O TYR R 112 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER R 126 " --> pdb=" O MET R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 142 Processing helix chain 'R' and resid 144 through 168 Proline residue: R 165 - end of helix removed outlier: 3.827A pdb=" N ILE R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 188 Processing helix chain 'R' and resid 192 through 230 removed outlier: 4.620A pdb=" N LEU R 198 " --> pdb=" O PRO R 194 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY R 199 " --> pdb=" O TRP R 195 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU R 207 " --> pdb=" O ILE R 203 " (cutoff:3.500A) Proline residue: R 208 - end of helix Processing helix chain 'R' and resid 230 through 237 removed outlier: 3.647A pdb=" N GLU R 234 " --> pdb=" O ASN R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 274 removed outlier: 4.593A pdb=" N LYS R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Proline residue: R 259 - end of helix Processing helix chain 'R' and resid 281 through 312 removed outlier: 4.151A pdb=" N CYS R 295 " --> pdb=" O HIS R 291 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N CYS R 301 " --> pdb=" O MET R 297 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS R 302 " --> pdb=" O ASN R 298 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET R 303 " --> pdb=" O PHE R 299 " (cutoff:3.500A) Proline residue: R 305 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.614A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.877A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.502A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.890A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.507A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.540A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.742A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.293A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.974A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.899A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.994A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.733A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.685A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.438A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.879A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.050A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.715A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1278 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: 2.60 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1448 1.27 - 1.41: 2296 1.41 - 1.54: 5205 1.54 - 1.68: 46 1.68 - 1.82: 100 Bond restraints: 9095 Sorted by residual: bond pdb=" C05 KJX R 401 " pdb=" C06 KJX R 401 " ideal model delta sigma weight residual 1.522 1.131 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" C04 KJX R 401 " pdb=" C09 KJX R 401 " ideal model delta sigma weight residual 1.528 1.193 0.335 2.00e-02 2.50e+03 2.80e+02 bond pdb=" C06 KJX R 401 " pdb=" C14 KJX R 401 " ideal model delta sigma weight residual 1.526 1.257 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C10 KJX R 401 " pdb=" C17 KJX R 401 " ideal model delta sigma weight residual 1.519 1.251 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C09 KJX R 401 " pdb=" C12 KJX R 401 " ideal model delta sigma weight residual 1.528 1.279 0.249 2.00e-02 2.50e+03 1.55e+02 ... (remaining 9090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 12092 2.13 - 4.26: 192 4.26 - 6.39: 38 6.39 - 8.51: 7 8.51 - 10.64: 1 Bond angle restraints: 12330 Sorted by residual: angle pdb=" C ALA R 102 " pdb=" N LEU R 103 " pdb=" CA LEU R 103 " ideal model delta sigma weight residual 120.38 125.62 -5.24 1.46e+00 4.69e-01 1.29e+01 angle pdb=" C14 KJX R 401 " pdb=" C19 KJX R 401 " pdb=" C17 KJX R 401 " ideal model delta sigma weight residual 125.07 114.43 10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.08 126.65 -4.57 1.47e+00 4.63e-01 9.65e+00 angle pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 122.46 126.77 -4.31 1.41e+00 5.03e-01 9.36e+00 angle pdb=" N LEU R 84 " pdb=" CA LEU R 84 " pdb=" C LEU R 84 " ideal model delta sigma weight residual 109.81 116.39 -6.58 2.21e+00 2.05e-01 8.87e+00 ... (remaining 12325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4969 17.31 - 34.61: 416 34.61 - 51.92: 62 51.92 - 69.22: 7 69.22 - 86.53: 4 Dihedral angle restraints: 5458 sinusoidal: 2141 harmonic: 3317 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PHE R 111 " pdb=" C PHE R 111 " pdb=" N TYR R 112 " pdb=" CA TYR R 112 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ILE R 113 " pdb=" C ILE R 113 " pdb=" N ASN R 114 " pdb=" CA ASN R 114 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 1410 0.280 - 0.559: 2 0.559 - 0.839: 1 0.839 - 1.119: 0 1.119 - 1.398: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" C06 KJX R 401 " pdb=" C05 KJX R 401 " pdb=" C07 KJX R 401 " pdb=" C14 KJX R 401 " both_signs ideal model delta sigma weight residual False -2.58 -1.19 -1.40 2.00e-01 2.50e+01 4.89e+01 chirality pdb=" C04 KJX R 401 " pdb=" C05 KJX R 401 " pdb=" C08 KJX R 401 " pdb=" C09 KJX R 401 " both_signs ideal model delta sigma weight residual False -2.94 -2.15 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C08 KJX R 401 " pdb=" C04 KJX R 401 " pdb=" C13 KJX R 401 " pdb=" C15 KJX R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.98 -0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 1411 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 KJX R 401 " 0.091 2.00e-02 2.50e+03 1.23e-01 1.90e+02 pdb=" C14 KJX R 401 " -0.119 2.00e-02 2.50e+03 pdb=" C17 KJX R 401 " -0.107 2.00e-02 2.50e+03 pdb=" C19 KJX R 401 " 0.196 2.00e-02 2.50e+03 pdb=" C21 KJX R 401 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 236 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 184 " 0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO R 185 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 185 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 185 " 0.026 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 324 2.71 - 3.26: 8764 3.26 - 3.80: 14198 3.80 - 4.35: 17914 4.35 - 4.90: 30664 Nonbonded interactions: 71864 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.161 3.040 nonbonded pdb=" O THR R 123 " pdb=" OG SER R 126 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.216 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.255 3.040 ... (remaining 71859 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.520 Find NCS groups from input model: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.011 0.391 9095 Z= 0.639 Angle : 0.733 10.643 12330 Z= 0.403 Chirality : 0.066 1.398 1414 Planarity : 0.005 0.123 1554 Dihedral : 12.680 86.527 3307 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.22), residues: 1123 helix: -0.54 (0.24), residues: 406 sheet: -1.68 (0.26), residues: 309 loop : -2.09 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.012 0.001 HIS R 37 PHE 0.017 0.002 PHE B 199 TYR 0.016 0.002 TYR R 90 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7449 (mmm) cc_final: 0.6953 (mmm) REVERT: R 87 ARG cc_start: 0.6850 (tpp80) cc_final: 0.6489 (tpt-90) REVERT: R 149 LYS cc_start: 0.7782 (tppt) cc_final: 0.7109 (tptt) REVERT: R 160 PHE cc_start: 0.7758 (m-10) cc_final: 0.7489 (m-80) REVERT: R 225 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7593 (ttm110) REVERT: B 3 GLU cc_start: 0.9081 (tp30) cc_final: 0.8768 (tp30) REVERT: B 10 GLU cc_start: 0.9182 (tp30) cc_final: 0.8546 (tp30) REVERT: B 23 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8717 (tmmt) REVERT: B 217 MET cc_start: 0.8398 (ptm) cc_final: 0.8080 (ptm) REVERT: C 17 GLU cc_start: 0.8985 (tp30) cc_final: 0.8553 (tp30) REVERT: E 153 GLU cc_start: 0.8340 (pt0) cc_final: 0.7822 (pt0) REVERT: E 220 GLU cc_start: 0.8172 (mp0) cc_final: 0.7771 (mp0) REVERT: E 223 ASP cc_start: 0.8220 (m-30) cc_final: 0.7757 (m-30) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.3140 time to fit residues: 71.7407 Evaluate side-chains 131 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 chunk 33 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 244 ASN R 282 GLN ** R 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS B 88 ASN B 91 HIS B 119 ASN B 259 GLN B 293 ASN E 232 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9095 Z= 0.157 Angle : 0.533 8.803 12330 Z= 0.282 Chirality : 0.042 0.146 1414 Planarity : 0.004 0.044 1554 Dihedral : 4.853 62.986 1299 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.14 % Allowed : 8.62 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.99 (0.24), residues: 1123 helix: 0.78 (0.26), residues: 411 sheet: -1.18 (0.27), residues: 297 loop : -1.61 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 PHE 0.009 0.001 PHE B 234 TYR 0.018 0.001 TYR E 190 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 149 LYS cc_start: 0.7834 (tppt) cc_final: 0.7195 (tptt) REVERT: R 275 SER cc_start: 0.5480 (m) cc_final: 0.5267 (t) REVERT: R 287 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8531 (tm-30) REVERT: B 3 GLU cc_start: 0.9073 (tp30) cc_final: 0.8746 (tp30) REVERT: B 10 GLU cc_start: 0.9175 (tp30) cc_final: 0.8512 (tp30) REVERT: B 23 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8669 (tmmt) REVERT: B 59 TYR cc_start: 0.8935 (m-80) cc_final: 0.8600 (m-80) REVERT: B 254 ASP cc_start: 0.7893 (t70) cc_final: 0.7632 (t0) REVERT: C 17 GLU cc_start: 0.8945 (tp30) cc_final: 0.8716 (tp30) REVERT: C 20 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8396 (mttp) REVERT: E 220 GLU cc_start: 0.8104 (mp0) cc_final: 0.7693 (mp0) REVERT: E 223 ASP cc_start: 0.8418 (m-30) cc_final: 0.7809 (m-30) outliers start: 11 outliers final: 6 residues processed: 157 average time/residue: 0.2545 time to fit residues: 52.3236 Evaluate side-chains 139 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.0050 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 36 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9095 Z= 0.294 Angle : 0.549 6.254 12330 Z= 0.293 Chirality : 0.043 0.184 1414 Planarity : 0.004 0.045 1554 Dihedral : 4.903 76.439 1299 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.97 % Allowed : 11.01 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.56 (0.25), residues: 1123 helix: 1.21 (0.27), residues: 413 sheet: -0.96 (0.28), residues: 296 loop : -1.47 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.015 0.001 HIS R 37 PHE 0.010 0.001 PHE B 199 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 TYR cc_start: 0.7939 (m-80) cc_final: 0.7715 (m-80) REVERT: R 147 HIS cc_start: 0.7250 (m-70) cc_final: 0.6524 (t-170) REVERT: R 149 LYS cc_start: 0.7869 (tppt) cc_final: 0.7270 (tptt) REVERT: R 291 HIS cc_start: 0.7591 (t-90) cc_final: 0.7328 (t-90) REVERT: B 3 GLU cc_start: 0.9104 (tp30) cc_final: 0.8786 (tp30) REVERT: B 10 GLU cc_start: 0.9183 (tp30) cc_final: 0.8654 (tp30) REVERT: B 23 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8681 (tmmt) REVERT: B 254 ASP cc_start: 0.7948 (t70) cc_final: 0.7627 (t0) REVERT: C 17 GLU cc_start: 0.8974 (tp30) cc_final: 0.8650 (tp30) REVERT: E 220 GLU cc_start: 0.8072 (mp0) cc_final: 0.7606 (mp0) REVERT: E 223 ASP cc_start: 0.8397 (m-30) cc_final: 0.7350 (m-30) outliers start: 19 outliers final: 13 residues processed: 151 average time/residue: 0.2437 time to fit residues: 48.7786 Evaluate side-chains 142 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS A 204 GLN B 36 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9095 Z= 0.214 Angle : 0.522 9.024 12330 Z= 0.276 Chirality : 0.042 0.210 1414 Planarity : 0.003 0.043 1554 Dihedral : 4.784 76.834 1299 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.80 % Allowed : 12.25 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.28 (0.25), residues: 1123 helix: 1.43 (0.27), residues: 412 sheet: -0.76 (0.28), residues: 296 loop : -1.33 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 291 PHE 0.010 0.001 PHE B 199 TYR 0.015 0.001 TYR E 190 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7041 (mtm) REVERT: R 147 HIS cc_start: 0.7286 (m-70) cc_final: 0.6512 (t-170) REVERT: R 149 LYS cc_start: 0.7888 (tppt) cc_final: 0.7300 (tptt) REVERT: B 3 GLU cc_start: 0.9119 (tp30) cc_final: 0.8798 (tp30) REVERT: B 10 GLU cc_start: 0.9178 (tp30) cc_final: 0.8641 (tp30) REVERT: B 23 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8679 (tmmt) REVERT: B 254 ASP cc_start: 0.7929 (t70) cc_final: 0.7592 (t0) REVERT: C 15 LEU cc_start: 0.9128 (tp) cc_final: 0.8739 (tt) REVERT: C 17 GLU cc_start: 0.8963 (tp30) cc_final: 0.8745 (tp30) REVERT: C 20 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8454 (mttp) REVERT: E 51 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8002 (tp) REVERT: E 220 GLU cc_start: 0.8027 (mp0) cc_final: 0.7710 (mp0) REVERT: E 223 ASP cc_start: 0.8443 (m-30) cc_final: 0.7651 (m-30) outliers start: 27 outliers final: 19 residues processed: 158 average time/residue: 0.2393 time to fit residues: 50.6103 Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9095 Z= 0.193 Angle : 0.518 9.092 12330 Z= 0.273 Chirality : 0.041 0.178 1414 Planarity : 0.003 0.042 1554 Dihedral : 4.660 77.129 1299 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.70 % Allowed : 12.88 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1123 helix: 1.65 (0.27), residues: 414 sheet: -0.61 (0.29), residues: 284 loop : -1.19 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.011 0.001 HIS R 37 PHE 0.016 0.001 PHE R 154 TYR 0.015 0.001 TYR E 190 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7047 (mtm) REVERT: R 147 HIS cc_start: 0.7269 (m-70) cc_final: 0.6533 (t-170) REVERT: R 149 LYS cc_start: 0.7891 (tppt) cc_final: 0.7306 (tptt) REVERT: A 20 ASP cc_start: 0.8519 (m-30) cc_final: 0.8291 (m-30) REVERT: B 3 GLU cc_start: 0.9115 (tp30) cc_final: 0.8793 (tp30) REVERT: B 10 GLU cc_start: 0.9178 (tp30) cc_final: 0.8637 (tp30) REVERT: B 23 LYS cc_start: 0.8909 (ttpp) cc_final: 0.8672 (tmmt) REVERT: B 254 ASP cc_start: 0.7926 (t70) cc_final: 0.7590 (t0) REVERT: C 17 GLU cc_start: 0.8972 (tp30) cc_final: 0.8686 (tp30) REVERT: E 51 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8007 (tp) REVERT: E 220 GLU cc_start: 0.7989 (mp0) cc_final: 0.7704 (mp0) REVERT: E 223 ASP cc_start: 0.8436 (m-30) cc_final: 0.7642 (m-30) outliers start: 26 outliers final: 18 residues processed: 158 average time/residue: 0.2476 time to fit residues: 52.0592 Evaluate side-chains 155 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9095 Z= 0.152 Angle : 0.510 8.111 12330 Z= 0.270 Chirality : 0.041 0.178 1414 Planarity : 0.003 0.041 1554 Dihedral : 4.544 77.610 1299 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.08 % Allowed : 14.43 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.13 (0.26), residues: 1123 helix: 1.65 (0.27), residues: 420 sheet: -0.46 (0.29), residues: 285 loop : -1.09 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.009 0.001 HIS R 37 PHE 0.018 0.001 PHE R 299 TYR 0.017 0.001 TYR R 38 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 34 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7077 (mtm) REVERT: R 149 LYS cc_start: 0.7920 (tppt) cc_final: 0.7324 (tptt) REVERT: R 291 HIS cc_start: 0.7507 (t-170) cc_final: 0.7213 (t-170) REVERT: B 3 GLU cc_start: 0.9104 (tp30) cc_final: 0.8785 (tp30) REVERT: B 23 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8661 (tmmt) REVERT: B 254 ASP cc_start: 0.7851 (t70) cc_final: 0.7540 (t0) REVERT: C 15 LEU cc_start: 0.9130 (tp) cc_final: 0.8746 (tt) REVERT: C 17 GLU cc_start: 0.8951 (tp30) cc_final: 0.8737 (tp30) REVERT: C 20 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8469 (mttp) REVERT: E 51 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7962 (tp) REVERT: E 140 MET cc_start: 0.8439 (mtp) cc_final: 0.8204 (mmm) REVERT: E 220 GLU cc_start: 0.7932 (mp0) cc_final: 0.7697 (mp0) REVERT: E 223 ASP cc_start: 0.8441 (m-30) cc_final: 0.7606 (m-30) outliers start: 20 outliers final: 13 residues processed: 157 average time/residue: 0.3100 time to fit residues: 64.2685 Evaluate side-chains 154 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9095 Z= 0.151 Angle : 0.507 9.101 12330 Z= 0.268 Chirality : 0.041 0.201 1414 Planarity : 0.003 0.041 1554 Dihedral : 4.436 79.007 1299 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.70 % Allowed : 14.23 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.32 (0.26), residues: 1123 helix: 1.77 (0.27), residues: 421 sheet: -0.22 (0.30), residues: 269 loop : -1.04 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 291 PHE 0.013 0.001 PHE R 154 TYR 0.014 0.001 TYR E 190 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 HIS cc_start: 0.7224 (m-70) cc_final: 0.6513 (t-170) REVERT: R 149 LYS cc_start: 0.7923 (tppt) cc_final: 0.7327 (tptt) REVERT: R 160 PHE cc_start: 0.7546 (m-10) cc_final: 0.7230 (m-80) REVERT: A 317 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6816 (ttpt) REVERT: B 3 GLU cc_start: 0.9082 (tp30) cc_final: 0.8758 (tp30) REVERT: B 23 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8658 (tmmt) REVERT: B 146 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8527 (tt) REVERT: B 254 ASP cc_start: 0.7786 (t70) cc_final: 0.7478 (t0) REVERT: C 15 LEU cc_start: 0.9116 (tp) cc_final: 0.8722 (tt) REVERT: C 20 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8441 (mttp) REVERT: E 51 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7963 (tp) REVERT: E 223 ASP cc_start: 0.8439 (m-30) cc_final: 0.7443 (m-30) outliers start: 26 outliers final: 12 residues processed: 167 average time/residue: 0.2511 time to fit residues: 55.1876 Evaluate side-chains 159 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.0050 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9095 Z= 0.190 Angle : 0.550 14.190 12330 Z= 0.284 Chirality : 0.042 0.338 1414 Planarity : 0.003 0.041 1554 Dihedral : 4.498 78.232 1299 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.28 % Allowed : 15.06 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.45 (0.26), residues: 1123 helix: 1.88 (0.27), residues: 418 sheet: -0.15 (0.30), residues: 269 loop : -0.95 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.008 0.001 HIS R 291 PHE 0.017 0.001 PHE R 299 TYR 0.014 0.001 TYR E 190 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 147 HIS cc_start: 0.7234 (m-70) cc_final: 0.6525 (t-170) REVERT: R 149 LYS cc_start: 0.7947 (tppt) cc_final: 0.7348 (tptt) REVERT: R 160 PHE cc_start: 0.7575 (m-10) cc_final: 0.7246 (m-80) REVERT: R 291 HIS cc_start: 0.7671 (t-170) cc_final: 0.7038 (t-170) REVERT: A 317 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6928 (ttpt) REVERT: B 3 GLU cc_start: 0.9092 (tp30) cc_final: 0.8779 (tp30) REVERT: B 23 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8652 (tmmt) REVERT: B 254 ASP cc_start: 0.7807 (t70) cc_final: 0.7499 (t0) REVERT: C 15 LEU cc_start: 0.9111 (tp) cc_final: 0.8717 (tt) REVERT: E 51 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8008 (tp) REVERT: E 73 ASP cc_start: 0.7714 (t0) cc_final: 0.7392 (t0) REVERT: E 220 GLU cc_start: 0.7733 (mp0) cc_final: 0.7465 (mp0) outliers start: 22 outliers final: 15 residues processed: 162 average time/residue: 0.2421 time to fit residues: 51.4580 Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9095 Z= 0.182 Angle : 0.536 8.202 12330 Z= 0.283 Chirality : 0.041 0.218 1414 Planarity : 0.003 0.051 1554 Dihedral : 4.479 78.488 1299 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.08 % Allowed : 15.47 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.46 (0.26), residues: 1123 helix: 1.88 (0.27), residues: 419 sheet: -0.18 (0.30), residues: 270 loop : -0.90 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.007 0.001 HIS R 291 PHE 0.020 0.001 PHE R 299 TYR 0.014 0.001 TYR E 190 ARG 0.014 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: R 147 HIS cc_start: 0.7235 (m-70) cc_final: 0.6531 (t-170) REVERT: R 149 LYS cc_start: 0.7938 (tppt) cc_final: 0.7375 (tptt) REVERT: R 160 PHE cc_start: 0.7604 (m-10) cc_final: 0.7281 (m-80) REVERT: R 291 HIS cc_start: 0.7714 (t-170) cc_final: 0.7479 (t-170) REVERT: R 299 PHE cc_start: 0.8275 (t80) cc_final: 0.7777 (t80) REVERT: A 317 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6922 (ttpt) REVERT: B 3 GLU cc_start: 0.9081 (tp30) cc_final: 0.8773 (tp30) REVERT: B 23 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8652 (tmmt) REVERT: B 146 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8517 (tt) REVERT: B 254 ASP cc_start: 0.7817 (t70) cc_final: 0.7512 (t0) REVERT: C 20 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8465 (mttp) REVERT: E 51 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8051 (tp) outliers start: 20 outliers final: 14 residues processed: 158 average time/residue: 0.2577 time to fit residues: 53.5467 Evaluate side-chains 158 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9095 Z= 0.197 Angle : 0.563 7.645 12330 Z= 0.293 Chirality : 0.042 0.216 1414 Planarity : 0.003 0.058 1554 Dihedral : 4.519 78.654 1299 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.87 % Allowed : 15.58 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.52 (0.26), residues: 1123 helix: 1.96 (0.27), residues: 414 sheet: -0.10 (0.31), residues: 262 loop : -0.90 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.007 0.001 HIS R 291 PHE 0.022 0.001 PHE R 299 TYR 0.014 0.001 TYR E 190 ARG 0.014 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 147 HIS cc_start: 0.7235 (m-70) cc_final: 0.6529 (t-170) REVERT: R 149 LYS cc_start: 0.7950 (tppt) cc_final: 0.7385 (tptt) REVERT: R 160 PHE cc_start: 0.7519 (m-10) cc_final: 0.7237 (m-80) REVERT: R 299 PHE cc_start: 0.8251 (t80) cc_final: 0.7756 (t80) REVERT: A 317 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6928 (ttpt) REVERT: B 3 GLU cc_start: 0.9103 (tp30) cc_final: 0.8810 (tp30) REVERT: B 23 LYS cc_start: 0.8896 (ttpp) cc_final: 0.8658 (tmmt) REVERT: B 146 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8496 (tt) REVERT: B 254 ASP cc_start: 0.7824 (t70) cc_final: 0.7520 (t0) REVERT: C 20 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8492 (mttp) REVERT: C 58 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: E 51 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8064 (tp) outliers start: 18 outliers final: 13 residues processed: 155 average time/residue: 0.2583 time to fit residues: 53.0657 Evaluate side-chains 154 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.109838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075222 restraints weight = 16056.452| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.18 r_work: 0.2961 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9095 Z= 0.263 Angle : 0.593 8.900 12330 Z= 0.311 Chirality : 0.043 0.258 1414 Planarity : 0.004 0.059 1554 Dihedral : 4.624 78.826 1299 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.28 % Allowed : 15.26 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.39 (0.26), residues: 1123 helix: 1.85 (0.27), residues: 419 sheet: -0.26 (0.30), residues: 279 loop : -0.96 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.013 0.001 HIS R 291 PHE 0.020 0.001 PHE R 299 TYR 0.014 0.001 TYR E 190 ARG 0.014 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.26 seconds wall clock time: 41 minutes 55.15 seconds (2515.15 seconds total)