Starting phenix.real_space_refine on Sun Apr 5 02:06:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x9c_33071/04_2026/7x9c_33071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x9c_33071/04_2026/7x9c_33071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x9c_33071/04_2026/7x9c_33071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x9c_33071/04_2026/7x9c_33071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x9c_33071/04_2026/7x9c_33071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x9c_33071/04_2026/7x9c_33071.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 139 atoms to isotropic. 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 62 5.16 5 C 4615 2.51 5 N 1240 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7219 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2358 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1691 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2503 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 383 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 284 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 30} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.64, per 1000 atoms: 0.23 Number of scatterers: 7219 At special positions: 0 Unit cell: (123.31, 119.13, 84.645, 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 62 16.00 O 1302 8.00 N 1240 7.00 C 4615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 201 " distance=2.03 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: 0.73 Conformation dependent library (CDL) restraints added in 269.8 milliseconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 47.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'R' and resid 38 through 68 removed outlier: 3.955A pdb=" N VAL R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 103 removed outlier: 3.908A pdb=" N LEU R 78 " --> pdb=" O ASN R 74 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 110 through 144 Processing helix chain 'R' and resid 152 through 172 Processing helix chain 'R' and resid 172 through 177 removed outlier: 3.612A pdb=" N ALA R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 223 removed outlier: 3.898A pdb=" N ILE R 213 " --> pdb=" O HIS R 209 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR R 214 " --> pdb=" O HIS R 210 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 248 removed outlier: 3.580A pdb=" N VAL R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 277 Processing helix chain 'R' and resid 278 through 291 removed outlier: 3.746A pdb=" N HIS R 282 " --> pdb=" O TRP R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 313 Processing helix chain 'R' and resid 313 through 323 Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 326 through 330 removed outlier: 3.671A pdb=" N LYS R 330 " --> pdb=" O THR R 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 341 removed outlier: 3.663A pdb=" N ALA R 335 " --> pdb=" O LYS R 331 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL R 337 " --> pdb=" O ILE R 333 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.628A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.080A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.822A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.203A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.634A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.515A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.786A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.653A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.841A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 10 through 20 removed outlier: 3.812A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.575A 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 'P' and resid 13 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.885A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.470A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.715A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.890A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.824A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 7.105A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 7.096A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 371 hydrogen bonds defined for protein. 1074 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: 0.74 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1161 1.31 - 1.43: 1987 1.43 - 1.56: 4130 1.56 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 7366 Sorted by residual: bond pdb=" C TYC P 36 " pdb=" NXT TYC P 36 " ideal model delta sigma weight residual 1.340 1.449 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" CA LYS R 190 " pdb=" C LYS R 190 " ideal model delta sigma weight residual 1.522 1.583 -0.060 1.20e-02 6.94e+03 2.54e+01 bond pdb=" N LEU R 192 " pdb=" CA LEU R 192 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.26e-02 6.30e+03 7.20e+00 bond pdb=" N GLN R 121 " pdb=" CA GLN R 121 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.28e+00 bond pdb=" CZ TYC P 36 " pdb=" OH TYC P 36 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.09e+00 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9866 1.68 - 3.36: 122 3.36 - 5.03: 21 5.03 - 6.71: 5 6.71 - 8.39: 1 Bond angle restraints: 10015 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 109.46 4.01 1.01e+00 9.80e-01 1.58e+01 angle pdb=" C GLN R 121 " pdb=" CA GLN R 121 " pdb=" CB GLN R 121 " ideal model delta sigma weight residual 110.85 115.85 -5.00 1.70e+00 3.46e-01 8.65e+00 angle pdb=" C ILE R 144 " pdb=" N ASN R 145 " pdb=" CA ASN R 145 " ideal model delta sigma weight residual 121.80 128.47 -6.67 2.44e+00 1.68e-01 7.48e+00 angle pdb=" CA LEU R 172 " pdb=" CB LEU R 172 " pdb=" CG LEU R 172 " ideal model delta sigma weight residual 116.30 124.69 -8.39 3.50e+00 8.16e-02 5.75e+00 angle pdb=" CA GLN R 121 " pdb=" C GLN R 121 " pdb=" O GLN R 121 " ideal model delta sigma weight residual 120.42 117.91 2.51 1.06e+00 8.90e-01 5.61e+00 ... (remaining 10010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 4097 15.95 - 31.89: 212 31.89 - 47.84: 46 47.84 - 63.78: 8 63.78 - 79.73: 1 Dihedral angle restraints: 4364 sinusoidal: 1602 harmonic: 2762 Sorted by residual: dihedral pdb=" CA TYR B 85 " pdb=" C TYR B 85 " pdb=" N THR B 86 " pdb=" CA THR B 86 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 dihedral pdb=" C GLN R 121 " pdb=" N GLN R 121 " pdb=" CA GLN R 121 " pdb=" CB GLN R 121 " ideal model delta harmonic sigma weight residual -122.60 -130.21 7.61 0 2.50e+00 1.60e-01 9.27e+00 dihedral pdb=" CB GLU R 181 " pdb=" CG GLU R 181 " pdb=" CD GLU R 181 " pdb=" OE1 GLU R 181 " ideal model delta sinusoidal sigma weight residual 0.00 79.73 -79.73 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 4361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 848 0.037 - 0.073: 257 0.073 - 0.110: 61 0.110 - 0.147: 15 0.147 - 0.183: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA GLN R 121 " pdb=" N GLN R 121 " pdb=" C GLN R 121 " pdb=" CB GLN R 121 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA HIS R 188 " pdb=" N HIS R 188 " pdb=" C HIS R 188 " pdb=" CB HIS R 188 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1179 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 225 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO R 226 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 226 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 226 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 172 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO R 173 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 173 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO B 194 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.015 5.00e-02 4.00e+02 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 734 2.75 - 3.28: 7402 3.28 - 3.82: 12388 3.82 - 4.36: 14451 4.36 - 4.90: 24900 Nonbonded interactions: 59875 Sorted by model distance: nonbonded pdb=" OH TYR R 48 " pdb=" O LEU R 305 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OE1 GLU A 298 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR R 52 " pdb=" OE1 GLN R 95 " model vdw 2.329 3.040 ... (remaining 59870 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.003 0.109 7367 Z= 0.151 Angle : 0.510 8.390 10017 Z= 0.287 Chirality : 0.038 0.183 1182 Planarity : 0.003 0.031 1260 Dihedral : 10.402 79.725 2563 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.24), residues: 928 helix: -1.03 (0.24), residues: 392 sheet: -1.64 (0.36), residues: 183 loop : -2.20 (0.28), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 52 TYR 0.014 0.001 TYR R 48 PHE 0.010 0.001 PHE B 253 TRP 0.014 0.001 TRP R 205 HIS 0.005 0.000 HIS R 188 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7366) covalent geometry : angle 0.50961 (10015) SS BOND : bond 0.00448 ( 1) SS BOND : angle 0.77455 ( 2) hydrogen bonds : bond 0.15688 ( 371) hydrogen bonds : angle 5.98886 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: R 109 PHE cc_start: 0.7654 (m-80) cc_final: 0.7426 (m-80) REVERT: R 115 LYS cc_start: 0.5513 (mtpp) cc_final: 0.5241 (mmpt) REVERT: A 35 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7903 (mtmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.4055 time to fit residues: 69.4370 Evaluate side-chains 112 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0270 chunk 74 optimal weight: 2.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 306 GLN A 322 HIS B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134916 restraints weight = 8088.683| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.79 r_work: 0.3466 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7367 Z= 0.150 Angle : 0.580 9.159 10017 Z= 0.297 Chirality : 0.041 0.140 1182 Planarity : 0.003 0.028 1260 Dihedral : 5.248 59.936 1013 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.99 % Allowed : 11.69 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.26), residues: 928 helix: 0.18 (0.26), residues: 407 sheet: -1.33 (0.36), residues: 178 loop : -1.89 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.014 0.002 TYR R 234 PHE 0.013 0.001 PHE A 274 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS R 185 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7366) covalent geometry : angle 0.57992 (10015) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.90410 ( 2) hydrogen bonds : bond 0.03581 ( 371) hydrogen bonds : angle 4.42668 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: R 115 LYS cc_start: 0.5539 (mtpp) cc_final: 0.5033 (mmpt) REVERT: A 35 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8083 (mtmm) REVERT: A 198 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7296 (mpt) REVERT: A 258 TRP cc_start: 0.8080 (m-90) cc_final: 0.7754 (m-10) REVERT: B 259 GLN cc_start: 0.7456 (tp40) cc_final: 0.7102 (tp40) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.4275 time to fit residues: 61.5878 Evaluate side-chains 120 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN ** R 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.173628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132118 restraints weight = 8026.091| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.40 r_work: 0.3381 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7367 Z= 0.152 Angle : 0.572 10.469 10017 Z= 0.292 Chirality : 0.041 0.183 1182 Planarity : 0.003 0.029 1260 Dihedral : 5.342 59.041 1013 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.85 % Allowed : 13.81 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.27), residues: 928 helix: 0.61 (0.26), residues: 414 sheet: -1.19 (0.36), residues: 177 loop : -1.68 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.019 0.002 TYR A 230 PHE 0.025 0.002 PHE R 284 TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7366) covalent geometry : angle 0.57205 (10015) SS BOND : bond 0.00095 ( 1) SS BOND : angle 1.04179 ( 2) hydrogen bonds : bond 0.03668 ( 371) hydrogen bonds : angle 4.31934 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.264 Fit side-chains REVERT: R 48 TYR cc_start: 0.6441 (m-80) cc_final: 0.6061 (m-80) REVERT: R 115 LYS cc_start: 0.5350 (mtpp) cc_final: 0.4794 (mmpt) REVERT: R 185 HIS cc_start: 0.6817 (m90) cc_final: 0.6592 (m170) REVERT: R 260 MET cc_start: 0.6195 (mmp) cc_final: 0.5963 (tpp) REVERT: R 327 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7654 (m) REVERT: A 22 ASN cc_start: 0.8073 (m110) cc_final: 0.7849 (m110) REVERT: A 198 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7548 (mpt) REVERT: B 259 GLN cc_start: 0.7544 (tp40) cc_final: 0.7215 (tp40) outliers start: 29 outliers final: 12 residues processed: 138 average time/residue: 0.4421 time to fit residues: 65.3832 Evaluate side-chains 131 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 PHE Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 188 HIS R 222 GLN B 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.170811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129295 restraints weight = 8108.936| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.38 r_work: 0.3355 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7367 Z= 0.160 Angle : 0.582 10.858 10017 Z= 0.293 Chirality : 0.041 0.126 1182 Planarity : 0.003 0.029 1260 Dihedral : 5.329 57.897 1013 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.05 % Allowed : 16.60 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.27), residues: 928 helix: 0.86 (0.26), residues: 413 sheet: -1.23 (0.36), residues: 180 loop : -1.48 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 35 TYR 0.022 0.001 TYR A 230 PHE 0.014 0.001 PHE B 253 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7366) covalent geometry : angle 0.58129 (10015) SS BOND : bond 0.00066 ( 1) SS BOND : angle 1.31661 ( 2) hydrogen bonds : bond 0.03618 ( 371) hydrogen bonds : angle 4.34207 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.257 Fit side-chains REVERT: R 115 LYS cc_start: 0.5499 (mtpp) cc_final: 0.4879 (mmpt) REVERT: R 185 HIS cc_start: 0.6984 (m90) cc_final: 0.6771 (m170) REVERT: R 327 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7708 (m) REVERT: A 22 ASN cc_start: 0.8046 (m110) cc_final: 0.7831 (m110) REVERT: A 28 GLU cc_start: 0.7488 (pt0) cc_final: 0.7250 (pt0) REVERT: A 197 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8371 (mtpp) REVERT: A 198 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7586 (mpt) REVERT: B 127 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7514 (mmtp) REVERT: B 259 GLN cc_start: 0.7651 (tp40) cc_final: 0.7334 (tp40) REVERT: B 262 MET cc_start: 0.7416 (ttp) cc_final: 0.7087 (ttp) REVERT: B 336 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8349 (tt) outliers start: 23 outliers final: 11 residues processed: 133 average time/residue: 0.4561 time to fit residues: 64.6885 Evaluate side-chains 129 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 222 GLN R 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128470 restraints weight = 8104.344| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.49 r_work: 0.3365 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7367 Z= 0.142 Angle : 0.581 11.068 10017 Z= 0.290 Chirality : 0.040 0.132 1182 Planarity : 0.003 0.031 1260 Dihedral : 5.397 59.994 1013 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.72 % Allowed : 17.53 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.27), residues: 928 helix: 1.04 (0.27), residues: 411 sheet: -1.24 (0.35), residues: 180 loop : -1.47 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.022 0.001 TYR A 230 PHE 0.017 0.001 PHE R 284 TRP 0.009 0.001 TRP B 339 HIS 0.007 0.001 HIS R 188 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7366) covalent geometry : angle 0.58064 (10015) SS BOND : bond 0.00017 ( 1) SS BOND : angle 1.07687 ( 2) hydrogen bonds : bond 0.03475 ( 371) hydrogen bonds : angle 4.30188 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: R 115 LYS cc_start: 0.5247 (mtpp) cc_final: 0.4652 (mmpt) REVERT: R 327 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7757 (m) REVERT: A 22 ASN cc_start: 0.7997 (m110) cc_final: 0.7773 (m110) REVERT: A 28 GLU cc_start: 0.7493 (pt0) cc_final: 0.7271 (pt0) REVERT: A 198 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7569 (mpt) REVERT: B 145 TYR cc_start: 0.8816 (p90) cc_final: 0.8506 (p90) REVERT: B 259 GLN cc_start: 0.7455 (tp40) cc_final: 0.7176 (tp40) REVERT: B 336 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8283 (tt) outliers start: 28 outliers final: 12 residues processed: 133 average time/residue: 0.4390 time to fit residues: 62.4684 Evaluate side-chains 127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.169963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126510 restraints weight = 8070.328| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.59 r_work: 0.3351 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7367 Z= 0.158 Angle : 0.598 11.233 10017 Z= 0.301 Chirality : 0.041 0.133 1182 Planarity : 0.003 0.031 1260 Dihedral : 5.534 59.725 1013 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.85 % Allowed : 18.06 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.27), residues: 928 helix: 1.13 (0.26), residues: 406 sheet: -1.25 (0.35), residues: 179 loop : -1.40 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.021 0.001 TYR A 230 PHE 0.013 0.001 PHE B 253 TRP 0.010 0.001 TRP A 258 HIS 0.007 0.001 HIS R 188 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7366) covalent geometry : angle 0.59833 (10015) SS BOND : bond 0.00021 ( 1) SS BOND : angle 1.14909 ( 2) hydrogen bonds : bond 0.03555 ( 371) hydrogen bonds : angle 4.34288 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: R 327 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7813 (m) REVERT: A 22 ASN cc_start: 0.8038 (m110) cc_final: 0.7803 (m110) REVERT: A 28 GLU cc_start: 0.7499 (pt0) cc_final: 0.7255 (pt0) REVERT: A 198 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7599 (mpt) REVERT: A 308 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 145 TYR cc_start: 0.8829 (p90) cc_final: 0.8508 (p90) REVERT: B 259 GLN cc_start: 0.7555 (tp40) cc_final: 0.7281 (tp40) REVERT: B 336 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8355 (tt) outliers start: 29 outliers final: 16 residues processed: 131 average time/residue: 0.4459 time to fit residues: 62.5172 Evaluate side-chains 131 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS R 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.170076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126660 restraints weight = 8114.203| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.53 r_work: 0.3354 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7367 Z= 0.149 Angle : 0.608 11.411 10017 Z= 0.304 Chirality : 0.041 0.146 1182 Planarity : 0.003 0.032 1260 Dihedral : 5.511 59.201 1013 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.98 % Allowed : 18.19 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 928 helix: 1.18 (0.27), residues: 408 sheet: -1.22 (0.36), residues: 178 loop : -1.36 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.020 0.001 TYR A 230 PHE 0.013 0.001 PHE R 88 TRP 0.011 0.001 TRP A 258 HIS 0.007 0.001 HIS R 188 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7366) covalent geometry : angle 0.60741 (10015) SS BOND : bond 0.00053 ( 1) SS BOND : angle 1.08358 ( 2) hydrogen bonds : bond 0.03580 ( 371) hydrogen bonds : angle 4.35208 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.290 Fit side-chains REVERT: R 185 HIS cc_start: 0.6704 (OUTLIER) cc_final: 0.6058 (m90) REVERT: R 327 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7814 (m) REVERT: A 22 ASN cc_start: 0.8031 (m110) cc_final: 0.7812 (m110) REVERT: A 28 GLU cc_start: 0.7508 (pt0) cc_final: 0.7259 (pt0) REVERT: A 198 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7494 (mpt) REVERT: A 308 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: B 145 TYR cc_start: 0.8802 (p90) cc_final: 0.8508 (p90) REVERT: B 259 GLN cc_start: 0.7403 (tp40) cc_final: 0.7195 (tp40) REVERT: B 336 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8342 (tt) outliers start: 30 outliers final: 16 residues processed: 129 average time/residue: 0.4436 time to fit residues: 61.1177 Evaluate side-chains 135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121692 restraints weight = 8257.696| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.34 r_work: 0.3268 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7367 Z= 0.263 Angle : 0.703 11.771 10017 Z= 0.358 Chirality : 0.045 0.175 1182 Planarity : 0.004 0.032 1260 Dihedral : 5.897 59.303 1013 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.45 % Allowed : 20.19 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.27), residues: 928 helix: 0.89 (0.26), residues: 406 sheet: -1.33 (0.37), residues: 174 loop : -1.38 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 35 TYR 0.022 0.002 TYR A 230 PHE 0.017 0.002 PHE B 253 TRP 0.015 0.002 TRP A 258 HIS 0.009 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 7366) covalent geometry : angle 0.70270 (10015) SS BOND : bond 0.00271 ( 1) SS BOND : angle 2.04342 ( 2) hydrogen bonds : bond 0.04270 ( 371) hydrogen bonds : angle 4.71522 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.237 Fit side-chains REVERT: R 185 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.6059 (m90) REVERT: R 261 LYS cc_start: 0.7175 (tptt) cc_final: 0.6823 (tppt) REVERT: A 22 ASN cc_start: 0.8146 (m110) cc_final: 0.7905 (m110) REVERT: A 28 GLU cc_start: 0.7485 (pt0) cc_final: 0.7244 (pt0) REVERT: A 198 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7629 (mpt) REVERT: A 308 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: B 259 GLN cc_start: 0.7802 (tp40) cc_final: 0.7538 (tp40) REVERT: B 262 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7790 (ptp) REVERT: B 336 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8610 (tt) outliers start: 26 outliers final: 13 residues processed: 145 average time/residue: 0.4970 time to fit residues: 76.3216 Evaluate side-chains 144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS R 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123446 restraints weight = 8067.689| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.44 r_work: 0.3327 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7367 Z= 0.159 Angle : 0.649 11.646 10017 Z= 0.327 Chirality : 0.042 0.228 1182 Planarity : 0.003 0.033 1260 Dihedral : 5.738 58.982 1013 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.05 % Allowed : 21.78 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.27), residues: 928 helix: 0.99 (0.26), residues: 406 sheet: -1.37 (0.37), residues: 169 loop : -1.22 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 243 TYR 0.019 0.002 TYR A 230 PHE 0.014 0.001 PHE R 88 TRP 0.012 0.001 TRP A 258 HIS 0.010 0.001 HIS R 185 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7366) covalent geometry : angle 0.64909 (10015) SS BOND : bond 0.00036 ( 1) SS BOND : angle 1.28596 ( 2) hydrogen bonds : bond 0.03867 ( 371) hydrogen bonds : angle 4.54850 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: R 185 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6016 (m90) REVERT: R 305 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7526 (mm) REVERT: R 327 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8142 (m) REVERT: A 22 ASN cc_start: 0.8049 (m110) cc_final: 0.7805 (m110) REVERT: A 198 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7532 (mpt) REVERT: A 308 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: B 325 MET cc_start: 0.7333 (tpp) cc_final: 0.7094 (tpp) REVERT: B 336 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8407 (tt) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 0.4349 time to fit residues: 60.5055 Evaluate side-chains 133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS B 239 ASN B 259 GLN C 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124787 restraints weight = 8222.147| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.38 r_work: 0.3303 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7367 Z= 0.174 Angle : 0.665 11.785 10017 Z= 0.335 Chirality : 0.042 0.211 1182 Planarity : 0.003 0.034 1260 Dihedral : 5.739 59.078 1013 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.19 % Allowed : 22.18 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 928 helix: 1.03 (0.26), residues: 402 sheet: -1.34 (0.38), residues: 169 loop : -1.24 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 243 TYR 0.018 0.002 TYR A 230 PHE 0.015 0.002 PHE R 88 TRP 0.016 0.001 TRP A 258 HIS 0.008 0.001 HIS R 185 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7366) covalent geometry : angle 0.66487 (10015) SS BOND : bond 0.00007 ( 1) SS BOND : angle 1.33460 ( 2) hydrogen bonds : bond 0.03860 ( 371) hydrogen bonds : angle 4.57875 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: R 185 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.6113 (m90) REVERT: R 305 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7652 (mm) REVERT: R 327 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8157 (m) REVERT: A 198 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7510 (mpt) REVERT: A 205 ARG cc_start: 0.6913 (mmp80) cc_final: 0.6701 (mmp80) REVERT: A 308 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: B 259 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7580 (tp40) REVERT: B 325 MET cc_start: 0.7468 (tpp) cc_final: 0.7166 (tpp) REVERT: B 336 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8449 (tt) outliers start: 24 outliers final: 13 residues processed: 127 average time/residue: 0.4654 time to fit residues: 63.0029 Evaluate side-chains 135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS R 222 GLN A 22 ASN B 259 GLN C 44 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121398 restraints weight = 8169.305| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.47 r_work: 0.3333 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7367 Z= 0.157 Angle : 0.659 11.704 10017 Z= 0.331 Chirality : 0.042 0.219 1182 Planarity : 0.003 0.035 1260 Dihedral : 5.732 59.627 1013 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.79 % Allowed : 22.31 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.28), residues: 928 helix: 1.08 (0.27), residues: 402 sheet: -1.31 (0.38), residues: 169 loop : -1.21 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 243 TYR 0.016 0.002 TYR A 230 PHE 0.014 0.001 PHE R 88 TRP 0.014 0.001 TRP A 258 HIS 0.007 0.001 HIS R 185 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7366) covalent geometry : angle 0.65900 (10015) SS BOND : bond 0.00082 ( 1) SS BOND : angle 1.21993 ( 2) hydrogen bonds : bond 0.03787 ( 371) hydrogen bonds : angle 4.53149 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2355.98 seconds wall clock time: 40 minutes 57.54 seconds (2457.54 seconds total)