Starting phenix.real_space_refine on Sun Dec 29 02:46:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnk_34914/12_2024/8hnk_34914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnk_34914/12_2024/8hnk_34914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnk_34914/12_2024/8hnk_34914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnk_34914/12_2024/8hnk_34914.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnk_34914/12_2024/8hnk_34914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnk_34914/12_2024/8hnk_34914.cif" } resolution = 3.01 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= 1.000 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 70 5.16 5 C 6050 2.51 5 N 1635 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9492 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "R" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2316 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain: "L" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.84, per 1000 atoms: 0.62 Number of scatterers: 9492 At special positions: 0 Unit cell: (94.35, 121.55, 147.05, 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 70 16.00 O 1737 8.00 N 1635 7.00 C 6050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 290 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 36 " distance=2.03 Simple disulfide: pdb=" SG CYS L 11 " - pdb=" SG CYS L 53 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 37.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.663A 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 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.078A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.558A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.560A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing helix chain 'R' and resid 45 through 81 removed outlier: 3.598A pdb=" N LEU R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) Proline residue: R 57 - end of helix removed outlier: 3.968A pdb=" N ARG R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 115 Proline residue: R 107 - end of helix Processing helix chain 'R' and resid 121 through 154 Processing helix chain 'R' and resid 155 through 163 Processing helix chain 'R' and resid 166 through 190 removed outlier: 3.590A pdb=" N LEU R 170 " --> pdb=" O ALA R 166 " (cutoff:3.500A) Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 208 through 245 removed outlier: 5.748A pdb=" N LEU R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 249 through 284 Proline residue: R 270 - end of helix Processing helix chain 'R' and resid 289 through 319 Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 322 through 334 Processing helix chain 'L' and resid 46 through 49 Processing helix chain 'L' and resid 58 through 72 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.558A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.041A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.654A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.137A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.325A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.507A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.903A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.831A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.932A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.621A 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 234 removed outlier: 5.928A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.795A 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 removed outlier: 3.680A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 191 through 195 removed outlier: 4.171A pdb=" N ALA R 200 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 27 through 30 removed outlier: 4.246A pdb=" N VAL L 41 " --> pdb=" O LEU L 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.951A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.951A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.561A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1383 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: 2.94 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3071 1.34 - 1.46: 2206 1.46 - 1.58: 4309 1.58 - 1.70: 1 1.70 - 1.82: 99 Bond restraints: 9686 Sorted by residual: bond pdb=" N ASP R 282 " pdb=" CA ASP R 282 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.35e+00 bond pdb=" CB PRO S 148 " pdb=" CG PRO S 148 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.21e+00 bond pdb=" N ARG L 6 " pdb=" CA ARG L 6 " ideal model delta sigma weight residual 1.455 1.473 -0.019 1.27e-02 6.20e+03 2.16e+00 bond pdb=" CB CYS B 114 " pdb=" SG CYS B 114 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" C3 CLR R 601 " pdb=" O1 CLR R 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 9681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12809 1.62 - 3.25: 252 3.25 - 4.87: 40 4.87 - 6.50: 14 6.50 - 8.12: 4 Bond angle restraints: 13119 Sorted by residual: angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 107.10 6.80 1.80e+00 3.09e-01 1.43e+01 angle pdb=" C LYS L 46 " pdb=" N GLU L 47 " pdb=" CA GLU L 47 " ideal model delta sigma weight residual 122.61 126.75 -4.14 1.56e+00 4.11e-01 7.05e+00 angle pdb=" C MET L 30 " pdb=" N TYR L 31 " pdb=" CA TYR L 31 " ideal model delta sigma weight residual 121.03 125.15 -4.12 1.60e+00 3.91e-01 6.65e+00 angle pdb=" CA ARG L 6 " pdb=" C ARG L 6 " pdb=" O ARG L 6 " ideal model delta sigma weight residual 121.33 118.56 2.77 1.08e+00 8.57e-01 6.57e+00 angle pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" C TYR S 235 " ideal model delta sigma weight residual 109.81 115.21 -5.40 2.21e+00 2.05e-01 5.98e+00 ... (remaining 13114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5333 17.93 - 35.86: 461 35.86 - 53.79: 79 53.79 - 71.72: 12 71.72 - 89.65: 5 Dihedral angle restraints: 5890 sinusoidal: 2392 harmonic: 3498 Sorted by residual: dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 290 " pdb=" CB CYS R 290 " ideal model delta sinusoidal sigma weight residual 93.00 172.22 -79.22 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta harmonic sigma weight residual -180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1112 0.044 - 0.088: 289 0.088 - 0.132: 88 0.132 - 0.176: 7 0.176 - 0.220: 3 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CA ILE L 29 " pdb=" N ILE L 29 " pdb=" C ILE L 29 " pdb=" CB ILE L 29 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA LEU R 56 " pdb=" N LEU R 56 " pdb=" C LEU R 56 " pdb=" CB LEU R 56 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 1496 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO S 75 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO S 236 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " 0.025 2.00e-02 2.50e+03 1.52e-02 4.64e+00 pdb=" CG TYR S 235 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " 0.005 2.00e-02 2.50e+03 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 417 2.72 - 3.27: 9334 3.27 - 3.81: 14931 3.81 - 4.36: 18645 4.36 - 4.90: 33054 Nonbonded interactions: 76381 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.176 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.220 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.262 3.040 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.265 3.120 ... (remaining 76376 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: 1.190 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9686 Z= 0.246 Angle : 0.609 8.121 13119 Z= 0.341 Chirality : 0.044 0.220 1499 Planarity : 0.004 0.063 1651 Dihedral : 13.488 89.649 3614 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1192 helix: 1.50 (0.26), residues: 407 sheet: 0.10 (0.31), residues: 287 loop : -1.05 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 237 PHE 0.015 0.001 PHE R 207 TYR 0.034 0.002 TYR S 235 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.102 Fit side-chains REVERT: R 331 MET cc_start: 0.7491 (ttm) cc_final: 0.7207 (tmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2623 time to fit residues: 52.9216 Evaluate side-chains 129 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 0.0060 chunk 49 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9686 Z= 0.184 Angle : 0.569 7.551 13119 Z= 0.296 Chirality : 0.043 0.213 1499 Planarity : 0.004 0.059 1651 Dihedral : 5.479 64.867 1441 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.88 % Allowed : 7.89 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1192 helix: 1.69 (0.26), residues: 418 sheet: 0.34 (0.31), residues: 289 loop : -0.89 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.017 0.001 PHE R 47 TYR 0.032 0.001 TYR S 235 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.171 Fit side-chains REVERT: G 51 LEU cc_start: 0.9047 (tp) cc_final: 0.8762 (tp) REVERT: R 68 LEU cc_start: 0.8733 (mm) cc_final: 0.8329 (mm) REVERT: R 281 MET cc_start: 0.6951 (tmm) cc_final: 0.6734 (tmm) REVERT: S 6 GLU cc_start: 0.8054 (mp0) cc_final: 0.7534 (mt-10) outliers start: 9 outliers final: 7 residues processed: 135 average time/residue: 0.2577 time to fit residues: 47.1821 Evaluate side-chains 131 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.0470 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9686 Z= 0.164 Angle : 0.526 6.864 13119 Z= 0.275 Chirality : 0.042 0.205 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.084 62.338 1441 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.36 % Allowed : 9.16 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1192 helix: 1.87 (0.26), residues: 418 sheet: 0.55 (0.31), residues: 273 loop : -0.85 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.015 0.001 PHE R 47 TYR 0.029 0.001 TYR S 235 ARG 0.002 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.112 Fit side-chains REVERT: G 51 LEU cc_start: 0.9061 (tp) cc_final: 0.8779 (tp) REVERT: R 68 LEU cc_start: 0.8766 (mm) cc_final: 0.8356 (mm) REVERT: R 281 MET cc_start: 0.6788 (tmm) cc_final: 0.6529 (tmm) REVERT: S 6 GLU cc_start: 0.8041 (mp0) cc_final: 0.7548 (mt-10) outliers start: 14 outliers final: 9 residues processed: 134 average time/residue: 0.2552 time to fit residues: 46.2574 Evaluate side-chains 128 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9686 Z= 0.248 Angle : 0.561 9.007 13119 Z= 0.291 Chirality : 0.044 0.247 1499 Planarity : 0.004 0.059 1651 Dihedral : 5.183 63.454 1441 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.75 % Allowed : 10.14 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1192 helix: 1.91 (0.26), residues: 416 sheet: 0.43 (0.31), residues: 282 loop : -0.78 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE A 189 TYR 0.038 0.002 TYR S 235 ARG 0.003 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.105 Fit side-chains REVERT: G 51 LEU cc_start: 0.9077 (tp) cc_final: 0.8802 (tp) REVERT: R 68 LEU cc_start: 0.8778 (mm) cc_final: 0.8372 (mm) REVERT: R 281 MET cc_start: 0.6805 (tmm) cc_final: 0.6534 (tmm) REVERT: S 201 ASP cc_start: 0.8043 (t70) cc_final: 0.7805 (t0) REVERT: S 235 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6763 (t80) outliers start: 18 outliers final: 13 residues processed: 133 average time/residue: 0.2494 time to fit residues: 45.3480 Evaluate side-chains 131 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9686 Z= 0.210 Angle : 0.542 8.393 13119 Z= 0.283 Chirality : 0.043 0.229 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.121 62.812 1441 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.05 % Allowed : 11.21 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1192 helix: 1.99 (0.26), residues: 416 sheet: 0.51 (0.31), residues: 278 loop : -0.79 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE R 47 TYR 0.035 0.001 TYR S 235 ARG 0.001 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.157 Fit side-chains REVERT: G 51 LEU cc_start: 0.9074 (tp) cc_final: 0.8808 (tp) REVERT: R 68 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8385 (mm) REVERT: R 334 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.6028 (tp) REVERT: S 235 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6708 (t80) outliers start: 21 outliers final: 17 residues processed: 139 average time/residue: 0.2259 time to fit residues: 43.8869 Evaluate side-chains 139 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9686 Z= 0.227 Angle : 0.560 9.279 13119 Z= 0.290 Chirality : 0.043 0.238 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.145 63.091 1441 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.73 % Allowed : 11.31 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1192 helix: 1.96 (0.26), residues: 417 sheet: 0.45 (0.31), residues: 280 loop : -0.75 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.038 0.002 TYR S 235 ARG 0.002 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.115 Fit side-chains REVERT: G 36 ASP cc_start: 0.8148 (m-30) cc_final: 0.7686 (m-30) REVERT: G 51 LEU cc_start: 0.9084 (tp) cc_final: 0.8811 (tp) REVERT: R 68 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8384 (mm) REVERT: R 334 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6114 (tp) REVERT: S 235 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6773 (t80) outliers start: 28 outliers final: 18 residues processed: 138 average time/residue: 0.2208 time to fit residues: 43.0570 Evaluate side-chains 137 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9686 Z= 0.239 Angle : 0.566 11.891 13119 Z= 0.291 Chirality : 0.043 0.236 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.162 63.323 1441 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.63 % Allowed : 12.48 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1192 helix: 1.95 (0.26), residues: 417 sheet: 0.45 (0.31), residues: 282 loop : -0.74 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 47 TYR 0.038 0.002 TYR S 235 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.107 Fit side-chains REVERT: G 36 ASP cc_start: 0.8146 (m-30) cc_final: 0.7684 (m-30) REVERT: G 51 LEU cc_start: 0.9088 (tp) cc_final: 0.8843 (tp) REVERT: R 68 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8364 (mm) REVERT: R 334 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6216 (tp) REVERT: S 235 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6753 (t80) outliers start: 27 outliers final: 18 residues processed: 137 average time/residue: 0.2090 time to fit residues: 40.4796 Evaluate side-chains 139 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9686 Z= 0.234 Angle : 0.569 11.437 13119 Z= 0.292 Chirality : 0.043 0.234 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.157 63.290 1441 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.34 % Allowed : 12.96 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1192 helix: 1.97 (0.26), residues: 417 sheet: 0.42 (0.31), residues: 282 loop : -0.75 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE R 47 TYR 0.038 0.002 TYR S 235 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.153 Fit side-chains REVERT: G 36 ASP cc_start: 0.8146 (m-30) cc_final: 0.7686 (m-30) REVERT: G 51 LEU cc_start: 0.9091 (tp) cc_final: 0.8838 (tp) REVERT: G 58 GLU cc_start: 0.8028 (pm20) cc_final: 0.7677 (pm20) REVERT: R 68 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8369 (mm) REVERT: R 281 MET cc_start: 0.6587 (tmm) cc_final: 0.6034 (tmm) REVERT: R 334 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6238 (tp) REVERT: S 235 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6741 (t80) outliers start: 24 outliers final: 18 residues processed: 135 average time/residue: 0.2218 time to fit residues: 42.1086 Evaluate side-chains 135 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 0.0570 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9686 Z= 0.140 Angle : 0.522 10.958 13119 Z= 0.268 Chirality : 0.041 0.180 1499 Planarity : 0.004 0.057 1651 Dihedral : 4.963 60.474 1441 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.85 % Allowed : 13.74 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1192 helix: 2.23 (0.26), residues: 412 sheet: 0.53 (0.31), residues: 284 loop : -0.73 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.000 HIS R 272 PHE 0.018 0.001 PHE R 47 TYR 0.025 0.001 TYR S 235 ARG 0.002 0.000 ARG S 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.186 Fit side-chains REVERT: B 12 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6916 (pt0) REVERT: G 51 LEU cc_start: 0.9029 (tp) cc_final: 0.8744 (tp) REVERT: G 58 GLU cc_start: 0.7918 (pm20) cc_final: 0.7593 (pm20) REVERT: R 68 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8392 (mm) REVERT: S 192 MET cc_start: 0.8558 (ttp) cc_final: 0.8355 (tmm) REVERT: S 235 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6348 (t80) outliers start: 19 outliers final: 12 residues processed: 129 average time/residue: 0.2292 time to fit residues: 41.3947 Evaluate side-chains 122 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9686 Z= 0.254 Angle : 0.580 11.200 13119 Z= 0.296 Chirality : 0.044 0.240 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.091 62.514 1441 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.56 % Allowed : 14.23 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1192 helix: 2.03 (0.26), residues: 417 sheet: 0.42 (0.31), residues: 285 loop : -0.75 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 47 TYR 0.041 0.002 TYR S 235 ARG 0.002 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.197 Fit side-chains REVERT: G 51 LEU cc_start: 0.9094 (tp) cc_final: 0.8841 (tp) REVERT: G 58 GLU cc_start: 0.7981 (pm20) cc_final: 0.7647 (pm20) REVERT: R 68 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8403 (mm) REVERT: S 235 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6848 (t80) outliers start: 16 outliers final: 13 residues processed: 122 average time/residue: 0.2259 time to fit residues: 38.6403 Evaluate side-chains 125 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.092094 restraints weight = 13496.274| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.38 r_work: 0.3096 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 9686 Z= 0.277 Angle : 1.014 59.117 13119 Z= 0.614 Chirality : 0.047 0.645 1499 Planarity : 0.006 0.155 1651 Dihedral : 5.245 62.474 1441 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 1.46 % Allowed : 14.33 % Favored : 84.21 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.75 (0.25), residues: 1192 helix: 2.00 (0.26), residues: 418 sheet: 0.45 (0.31), residues: 280 loop : -0.79 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE R 47 TYR 0.041 0.002 TYR S 235 ARG 0.002 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.52 seconds wall clock time: 42 minutes 28.16 seconds (2548.16 seconds total)