Starting phenix.real_space_refine on Sun May 11 14:20:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i97_35259/05_2025/8i97_35259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i97_35259/05_2025/8i97_35259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i97_35259/05_2025/8i97_35259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i97_35259/05_2025/8i97_35259.map" model { file = "/net/cci-nas-00/data/ceres_data/8i97_35259/05_2025/8i97_35259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i97_35259/05_2025/8i97_35259.cif" } resolution = 3.19 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= 0.032 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 54 5.16 5 C 5189 2.51 5 N 1402 2.21 5 O 1485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8130 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2046 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1565 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2427 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1689 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 5.53, per 1000 atoms: 0.68 Number of scatterers: 8130 At special positions: 0 Unit cell: (86.1111, 119.067, 122.257, 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 54 16.00 O 1485 8.00 N 1402 7.00 C 5189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 355 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.3% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'C' and resid 20 through 50 removed outlier: 3.834A pdb=" N SER C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 84 removed outlier: 3.985A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 Proline residue: C 99 - end of helix removed outlier: 5.105A pdb=" N VAL C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.537A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 153 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 333 through 363 removed outlier: 5.972A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.520A pdb=" N ARG C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 403 removed outlier: 3.819A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 435 removed outlier: 6.388A pdb=" N LEU C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.630A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.674A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.135A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.680A pdb=" N ILE A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.502A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.568A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.957A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.936A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 162 through 164 removed outlier: 3.538A pdb=" N GLU C 162 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 164 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 171 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.381A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.018A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.898A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.676A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.635A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.591A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.563A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.240A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.240A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.652A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.466A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1239 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: 2.41 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1486 1.33 - 1.45: 2164 1.45 - 1.57: 4585 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 8306 Sorted by residual: bond pdb=" N GLN C 372 " pdb=" CA GLN C 372 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.23e-02 6.61e+03 1.09e+01 bond pdb=" N PHE C 107 " pdb=" CA PHE C 107 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.33e-02 5.65e+03 9.60e+00 bond pdb=" N MET C 153 " pdb=" CA MET C 153 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 6.97e+00 bond pdb=" C PHE C 111 " pdb=" O PHE C 111 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.29e-02 6.01e+03 5.65e+00 bond pdb=" N LEU A 13 " pdb=" CA LEU A 13 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.63e+00 ... (remaining 8301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 10992 1.56 - 3.12: 266 3.12 - 4.68: 40 4.68 - 6.24: 17 6.24 - 7.81: 3 Bond angle restraints: 11318 Sorted by residual: angle pdb=" N GLU A 9 " pdb=" CA GLU A 9 " pdb=" C GLU A 9 " ideal model delta sigma weight residual 113.20 107.49 5.71 1.21e+00 6.83e-01 2.22e+01 angle pdb=" N ARG A 10 " pdb=" CA ARG A 10 " pdb=" C ARG A 10 " ideal model delta sigma weight residual 111.82 106.54 5.28 1.16e+00 7.43e-01 2.07e+01 angle pdb=" N LEU A 13 " pdb=" CA LEU A 13 " pdb=" C LEU A 13 " ideal model delta sigma weight residual 112.23 107.67 4.56 1.26e+00 6.30e-01 1.31e+01 angle pdb=" C ARG C 340 " pdb=" CA ARG C 340 " pdb=" CB ARG C 340 " ideal model delta sigma weight residual 110.96 106.21 4.75 1.54e+00 4.22e-01 9.53e+00 angle pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" O PHE C 107 " ideal model delta sigma weight residual 119.31 115.51 3.80 1.24e+00 6.50e-01 9.38e+00 ... (remaining 11313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 4429 17.06 - 34.12: 343 34.12 - 51.18: 66 51.18 - 68.25: 12 68.25 - 85.31: 1 Dihedral angle restraints: 4851 sinusoidal: 1643 harmonic: 3208 Sorted by residual: dihedral pdb=" CA PRO C 99 " pdb=" C PRO C 99 " pdb=" N SER C 100 " pdb=" CA SER C 100 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 355 " pdb=" CB CYS C 355 " ideal model delta sinusoidal sigma weight residual 93.00 126.68 -33.68 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" C PHE C 107 " pdb=" N PHE C 107 " pdb=" CA PHE C 107 " pdb=" CB PHE C 107 " ideal model delta harmonic sigma weight residual -122.60 -132.42 9.82 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 4848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1112 0.060 - 0.121: 194 0.121 - 0.181: 12 0.181 - 0.242: 3 0.242 - 0.302: 1 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA PHE C 107 " pdb=" N PHE C 107 " pdb=" C PHE C 107 " pdb=" CB PHE C 107 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ARG C 340 " pdb=" N ARG C 340 " pdb=" C ARG C 340 " pdb=" CB ARG C 340 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1319 not shown) Planarity restraints: 1442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 20 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO C 21 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 21 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 21 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO G 49 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 10 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ARG A 10 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG A 10 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 11 " -0.013 2.00e-02 2.50e+03 ... (remaining 1439 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1984 2.79 - 3.32: 7592 3.32 - 3.84: 13451 3.84 - 4.37: 15509 4.37 - 4.90: 27873 Nonbonded interactions: 66409 Sorted by model distance: nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.261 3.120 nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" OD1 ASP A 299 " model vdw 2.295 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.304 3.040 ... (remaining 66404 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.660 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.005 0.050 8310 Z= 0.216 Angle : 0.613 7.805 11326 Z= 0.340 Chirality : 0.046 0.302 1322 Planarity : 0.004 0.063 1442 Dihedral : 12.744 85.308 2769 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.13 % Allowed : 0.76 % Favored : 99.12 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.70 % 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: -0.00 (0.27), residues: 1095 helix: 1.40 (0.28), residues: 377 sheet: -0.53 (0.32), residues: 290 loop : -0.79 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.011 0.001 HIS H 232 PHE 0.011 0.001 PHE B 241 TYR 0.015 0.002 TYR B 105 ARG 0.010 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.18663 ( 429) hydrogen bonds : angle 7.62453 ( 1239) SS BOND : bond 0.00418 ( 4) SS BOND : angle 0.95553 ( 8) covalent geometry : bond 0.00477 ( 8306) covalent geometry : angle 0.61296 (11318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.797 Fit side-chains REVERT: C 372 GLN cc_start: 0.7290 (tt0) cc_final: 0.6974 (tt0) REVERT: A 254 ILE cc_start: 0.8561 (tp) cc_final: 0.8118 (tp) REVERT: H 101 TYR cc_start: 0.7875 (m-80) cc_final: 0.7597 (m-80) outliers start: 1 outliers final: 1 residues processed: 119 average time/residue: 0.1965 time to fit residues: 32.0904 Evaluate side-chains 106 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 63 optimal weight: 0.2980 chunk 98 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 295 ASN B 88 ASN B 259 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.195963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160115 restraints weight = 8742.612| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.78 r_work: 0.3684 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8310 Z= 0.147 Angle : 0.570 6.510 11326 Z= 0.301 Chirality : 0.044 0.195 1322 Planarity : 0.004 0.049 1442 Dihedral : 4.429 49.466 1185 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.26 % Allowed : 7.44 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1095 helix: 1.47 (0.28), residues: 379 sheet: -0.47 (0.32), residues: 268 loop : -0.78 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.005 0.001 HIS H 232 PHE 0.012 0.001 PHE H 29 TYR 0.012 0.001 TYR H 190 ARG 0.005 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 429) hydrogen bonds : angle 5.37362 ( 1239) SS BOND : bond 0.00457 ( 4) SS BOND : angle 1.18807 ( 8) covalent geometry : bond 0.00327 ( 8306) covalent geometry : angle 0.56964 (11318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.877 Fit side-chains REVERT: C 372 GLN cc_start: 0.7412 (tt0) cc_final: 0.7091 (tt0) REVERT: A 254 ILE cc_start: 0.8758 (tp) cc_final: 0.8214 (tp) REVERT: H 7 SER cc_start: 0.7964 (m) cc_final: 0.7608 (p) outliers start: 10 outliers final: 9 residues processed: 115 average time/residue: 0.1827 time to fit residues: 29.6124 Evaluate side-chains 114 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 0.0010 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.196489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159756 restraints weight = 8911.015| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.77 r_work: 0.3679 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8310 Z= 0.139 Angle : 0.558 7.923 11326 Z= 0.288 Chirality : 0.043 0.152 1322 Planarity : 0.004 0.050 1442 Dihedral : 4.330 49.925 1185 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.51 % Allowed : 9.84 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1095 helix: 1.49 (0.28), residues: 379 sheet: -0.50 (0.32), residues: 268 loop : -0.76 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS H 232 PHE 0.009 0.001 PHE H 29 TYR 0.012 0.001 TYR H 190 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 429) hydrogen bonds : angle 5.08088 ( 1239) SS BOND : bond 0.00411 ( 4) SS BOND : angle 1.11733 ( 8) covalent geometry : bond 0.00315 ( 8306) covalent geometry : angle 0.55731 (11318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 254 ILE cc_start: 0.8789 (tp) cc_final: 0.8215 (tp) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 0.2042 time to fit residues: 33.6963 Evaluate side-chains 116 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN B 32 GLN B 259 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.196310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158006 restraints weight = 8864.472| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.04 r_work: 0.3636 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8310 Z= 0.172 Angle : 0.572 6.801 11326 Z= 0.296 Chirality : 0.044 0.147 1322 Planarity : 0.004 0.051 1442 Dihedral : 4.185 19.639 1183 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.02 % Allowed : 12.86 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1095 helix: 1.44 (0.28), residues: 379 sheet: -0.50 (0.31), residues: 274 loop : -0.88 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS H 232 PHE 0.010 0.001 PHE A 190 TYR 0.013 0.001 TYR H 190 ARG 0.003 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 429) hydrogen bonds : angle 5.02510 ( 1239) SS BOND : bond 0.00406 ( 4) SS BOND : angle 1.18573 ( 8) covalent geometry : bond 0.00401 ( 8306) covalent geometry : angle 0.57083 (11318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.924 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 115 average time/residue: 0.1893 time to fit residues: 31.0473 Evaluate side-chains 120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 63 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.0020 chunk 29 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN B 32 GLN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.198937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.162204 restraints weight = 8731.809| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.81 r_work: 0.3699 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8310 Z= 0.120 Angle : 0.531 6.563 11326 Z= 0.274 Chirality : 0.043 0.224 1322 Planarity : 0.004 0.050 1442 Dihedral : 4.017 18.672 1183 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.02 % Allowed : 13.11 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1095 helix: 1.54 (0.28), residues: 379 sheet: -0.56 (0.31), residues: 287 loop : -0.77 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.021 0.001 PHE C 442 TYR 0.011 0.001 TYR H 190 ARG 0.008 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 429) hydrogen bonds : angle 4.83038 ( 1239) SS BOND : bond 0.00388 ( 4) SS BOND : angle 1.07163 ( 8) covalent geometry : bond 0.00267 ( 8306) covalent geometry : angle 0.53013 (11318) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: H 116 THR cc_start: 0.8254 (t) cc_final: 0.7943 (p) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.1718 time to fit residues: 31.9880 Evaluate side-chains 128 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN B 32 GLN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.197977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161394 restraints weight = 8809.590| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.91 r_work: 0.3680 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8310 Z= 0.146 Angle : 0.547 7.136 11326 Z= 0.283 Chirality : 0.043 0.193 1322 Planarity : 0.004 0.051 1442 Dihedral : 4.078 23.835 1183 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.52 % Allowed : 13.11 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.06 (0.26), residues: 1095 helix: 1.57 (0.28), residues: 378 sheet: -0.62 (0.31), residues: 287 loop : -0.78 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.009 0.001 PHE H 29 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 429) hydrogen bonds : angle 4.82546 ( 1239) SS BOND : bond 0.00391 ( 4) SS BOND : angle 1.12320 ( 8) covalent geometry : bond 0.00338 ( 8306) covalent geometry : angle 0.54642 (11318) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.954 Fit side-chains REVERT: B 234 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8733 (m-80) REVERT: H 116 THR cc_start: 0.8289 (t) cc_final: 0.7984 (p) outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 0.1854 time to fit residues: 33.2335 Evaluate side-chains 130 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 427 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.195823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157186 restraints weight = 8890.692| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.07 r_work: 0.3638 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8310 Z= 0.188 Angle : 0.579 7.711 11326 Z= 0.300 Chirality : 0.044 0.179 1322 Planarity : 0.004 0.051 1442 Dihedral : 4.223 25.599 1183 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.77 % Allowed : 13.62 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1095 helix: 1.47 (0.28), residues: 378 sheet: -0.71 (0.31), residues: 287 loop : -0.85 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 232 PHE 0.010 0.001 PHE B 241 TYR 0.013 0.002 TYR H 190 ARG 0.004 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 429) hydrogen bonds : angle 4.90183 ( 1239) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.16213 ( 8) covalent geometry : bond 0.00443 ( 8306) covalent geometry : angle 0.57860 (11318) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.922 Fit side-chains REVERT: B 111 TYR cc_start: 0.9018 (m-80) cc_final: 0.8777 (m-80) REVERT: B 234 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: G 47 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: H 116 THR cc_start: 0.8306 (t) cc_final: 0.7996 (p) outliers start: 22 outliers final: 18 residues processed: 124 average time/residue: 0.1788 time to fit residues: 31.6254 Evaluate side-chains 130 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 95 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.198221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159768 restraints weight = 8854.414| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.93 r_work: 0.3671 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8310 Z= 0.130 Angle : 0.541 9.204 11326 Z= 0.278 Chirality : 0.043 0.165 1322 Planarity : 0.004 0.051 1442 Dihedral : 4.096 26.697 1183 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.52 % Allowed : 14.12 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1095 helix: 1.57 (0.28), residues: 380 sheet: -0.72 (0.31), residues: 287 loop : -0.82 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.012 0.001 PHE H 29 TYR 0.011 0.001 TYR H 190 ARG 0.004 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 429) hydrogen bonds : angle 4.81467 ( 1239) SS BOND : bond 0.00389 ( 4) SS BOND : angle 0.99210 ( 8) covalent geometry : bond 0.00295 ( 8306) covalent geometry : angle 0.54052 (11318) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.896 Fit side-chains REVERT: B 234 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: B 338 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8681 (mm) REVERT: G 47 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: H 116 THR cc_start: 0.8192 (t) cc_final: 0.7934 (p) outliers start: 20 outliers final: 14 residues processed: 126 average time/residue: 0.1864 time to fit residues: 33.7988 Evaluate side-chains 128 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 0.3980 chunk 99 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 7 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.197198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158800 restraints weight = 8999.665| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.09 r_work: 0.3656 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8310 Z= 0.157 Angle : 0.561 11.304 11326 Z= 0.287 Chirality : 0.043 0.160 1322 Planarity : 0.004 0.051 1442 Dihedral : 4.128 24.938 1183 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.40 % Allowed : 14.75 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1095 helix: 1.52 (0.28), residues: 380 sheet: -0.73 (0.31), residues: 287 loop : -0.84 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE C 61 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 429) hydrogen bonds : angle 4.81555 ( 1239) SS BOND : bond 0.00400 ( 4) SS BOND : angle 1.03753 ( 8) covalent geometry : bond 0.00367 ( 8306) covalent geometry : angle 0.56013 (11318) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.861 Fit side-chains REVERT: C 340 ARG cc_start: 0.7103 (ptt90) cc_final: 0.6813 (ptt-90) REVERT: B 111 TYR cc_start: 0.9014 (m-80) cc_final: 0.8759 (m-80) REVERT: B 234 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8795 (m-80) REVERT: B 338 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8693 (mm) REVERT: H 116 THR cc_start: 0.8174 (t) cc_final: 0.7914 (p) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.1787 time to fit residues: 31.5019 Evaluate side-chains 126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 0.0370 chunk 74 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.197788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.159555 restraints weight = 8835.613| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.09 r_work: 0.3664 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8310 Z= 0.142 Angle : 0.554 11.908 11326 Z= 0.283 Chirality : 0.043 0.157 1322 Planarity : 0.004 0.051 1442 Dihedral : 4.104 24.740 1183 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.52 % Allowed : 15.13 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.00 (0.26), residues: 1095 helix: 1.55 (0.28), residues: 380 sheet: -0.72 (0.31), residues: 287 loop : -0.81 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 29 TYR 0.012 0.001 TYR H 190 ARG 0.005 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 429) hydrogen bonds : angle 4.80543 ( 1239) SS BOND : bond 0.00426 ( 4) SS BOND : angle 0.99406 ( 8) covalent geometry : bond 0.00328 ( 8306) covalent geometry : angle 0.55312 (11318) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.837 Fit side-chains REVERT: C 340 ARG cc_start: 0.7064 (ptt90) cc_final: 0.6834 (ptt-90) REVERT: B 234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: B 338 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8686 (mm) REVERT: H 116 THR cc_start: 0.8145 (t) cc_final: 0.7896 (p) outliers start: 20 outliers final: 17 residues processed: 121 average time/residue: 0.1753 time to fit residues: 30.4198 Evaluate side-chains 127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.196051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157464 restraints weight = 8955.868| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.05 r_work: 0.3643 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8310 Z= 0.171 Angle : 0.572 11.927 11326 Z= 0.294 Chirality : 0.044 0.158 1322 Planarity : 0.004 0.051 1442 Dihedral : 4.192 24.459 1183 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.52 % Allowed : 14.88 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.06 (0.26), residues: 1095 helix: 1.49 (0.28), residues: 380 sheet: -0.75 (0.31), residues: 287 loop : -0.84 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE A 190 TYR 0.013 0.001 TYR H 190 ARG 0.004 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 429) hydrogen bonds : angle 4.87319 ( 1239) SS BOND : bond 0.00414 ( 4) SS BOND : angle 1.05337 ( 8) covalent geometry : bond 0.00401 ( 8306) covalent geometry : angle 0.57195 (11318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5001.84 seconds wall clock time: 87 minutes 6.74 seconds (5226.74 seconds total)