Starting phenix.real_space_refine on Tue Feb 11 13:31:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgk_41239/02_2025/8tgk_41239_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgk_41239/02_2025/8tgk_41239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tgk_41239/02_2025/8tgk_41239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgk_41239/02_2025/8tgk_41239.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgk_41239/02_2025/8tgk_41239_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgk_41239/02_2025/8tgk_41239_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 57 5.16 5 C 3837 2.51 5 N 900 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5772 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2864 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2856 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.35, per 1000 atoms: 0.75 Number of scatterers: 5772 At special positions: 0 Unit cell: (72.5973, 63.744, 114.208, 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 57 16.00 O 978 8.00 N 900 7.00 C 3837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 91.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.839A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.789A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.550A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.502A pdb=" N MET A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 159 through 165 removed outlier: 4.030A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 194 through 219 Processing helix chain 'A' and resid 221 through 255 removed outlier: 4.126A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix removed outlier: 3.926A pdb=" N GLY A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 278 removed outlier: 4.246A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 299 through 331 removed outlier: 3.990A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 336 through 342 removed outlier: 4.209A pdb=" N LEU A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 5.086A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 422 Proline residue: A 412 - end of helix removed outlier: 4.145A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.677A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 5.337A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.585A pdb=" N TYR A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A 480 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 54 removed outlier: 4.071A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Proline residue: B 46 - end of helix removed outlier: 3.689A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 154 removed outlier: 4.443A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.947A pdb=" N LEU B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.541A pdb=" N MET B 170 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.690A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 250 removed outlier: 4.128A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.808A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.547A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 318 removed outlier: 4.212A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 331 removed outlier: 4.208A pdb=" N THR B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 364 removed outlier: 3.619A pdb=" N SER B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 421 Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.522A pdb=" N ALA B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.829A pdb=" N GLY B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 3.900A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 445 hydrogen bonds defined for protein. 1308 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: 1.75 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 861 1.31 - 1.44: 1567 1.44 - 1.56: 3386 1.56 - 1.69: 2 1.69 - 1.81: 100 Bond restraints: 5916 Sorted by residual: bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.402 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C17 YHR B 601 " pdb=" O19 YHR B 601 " ideal model delta sigma weight residual 1.325 1.396 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CG HSM A 601 " pdb=" ND1 HSM A 601 " ideal model delta sigma weight residual 1.383 1.314 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CD2 HSM A 601 " pdb=" NE2 HSM A 601 " ideal model delta sigma weight residual 1.376 1.313 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" N ILE B 136 " pdb=" CA ILE B 136 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.88e+00 ... (remaining 5911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 8007 4.16 - 8.32: 45 8.32 - 12.49: 4 12.49 - 16.65: 1 16.65 - 20.81: 1 Bond angle restraints: 8058 Sorted by residual: angle pdb=" N PHE B 131 " pdb=" CA PHE B 131 " pdb=" C PHE B 131 " ideal model delta sigma weight residual 112.92 99.68 13.24 1.23e+00 6.61e-01 1.16e+02 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 132.70 -20.81 3.00e+00 1.11e-01 4.81e+01 angle pdb=" N GLY B 243 " pdb=" CA GLY B 243 " pdb=" C GLY B 243 " ideal model delta sigma weight residual 112.50 118.55 -6.05 1.16e+00 7.43e-01 2.72e+01 angle pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta sigma weight residual 103.25 97.80 5.45 1.05e+00 9.07e-01 2.69e+01 angle pdb=" C GLN B 21 " pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 ... (remaining 8053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 3104 23.33 - 46.65: 326 46.65 - 69.97: 40 69.97 - 93.30: 2 93.30 - 116.62: 3 Dihedral angle restraints: 3475 sinusoidal: 1320 harmonic: 2155 Sorted by residual: dihedral pdb=" CA PRO A 43 " pdb=" C PRO A 43 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 57.66 -58.96 116.62 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C PRO B 482 " pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta harmonic sigma weight residual -120.70 -111.15 -9.55 0 2.50e+00 1.60e-01 1.46e+01 ... (remaining 3472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 873 0.076 - 0.152: 88 0.152 - 0.228: 5 0.228 - 0.305: 1 0.305 - 0.381: 1 Chirality restraints: 968 Sorted by residual: chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.67 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA PHE B 131 " pdb=" N PHE B 131 " pdb=" C PHE B 131 " pdb=" CB PHE B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C3 YHR B 601 " pdb=" C16 YHR B 601 " pdb=" C4 YHR B 601 " pdb=" O2 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.58 2.37 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 965 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " 0.090 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO A 473 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 20 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ARG B 20 " 0.062 2.00e-02 2.50e+03 pdb=" O ARG B 20 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 21 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 42 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B 43 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " -0.039 5.00e-02 4.00e+02 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 571 2.74 - 3.28: 5993 3.28 - 3.82: 9617 3.82 - 4.36: 10439 4.36 - 4.90: 18960 Nonbonded interactions: 45580 Sorted by model distance: nonbonded pdb=" O ALA B 442 " pdb=" OG SER B 446 " model vdw 2.204 3.040 nonbonded pdb=" O GLY B 140 " pdb=" N PHE B 143 " model vdw 2.262 3.120 nonbonded pdb=" O SER A 424 " pdb=" OG SER A 424 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 333 " pdb=" OE1 GLN A 337 " model vdw 2.293 3.040 nonbonded pdb=" O GLN B 21 " pdb=" N LEU B 24 " model vdw 2.303 3.120 ... (remaining 45575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 278 or resid 288 through 483)) selection = (chain 'B' and (resid 19 through 51 or resid 135 through 483)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.640 Find NCS groups from input model: 0.240 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 0.076 5916 Z= 0.346 Angle : 0.870 20.810 8058 Z= 0.488 Chirality : 0.047 0.381 968 Planarity : 0.009 0.134 982 Dihedral : 17.763 116.624 2105 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 1.72 % Favored : 97.62 % Rotamer: Outliers : 0.81 % Allowed : 34.47 % Favored : 64.72 % Cbeta Deviations : 0.15 % 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 (0.29), residues: 756 helix: 1.03 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 326 HIS 0.003 0.001 HIS B 416 PHE 0.039 0.002 PHE B 48 TYR 0.009 0.001 TYR A 251 ARG 0.005 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.622 Fit side-chains REVERT: A 160 LEU cc_start: 0.8559 (tp) cc_final: 0.8290 (tt) REVERT: A 414 MET cc_start: 0.7811 (mmm) cc_final: 0.7286 (mmm) REVERT: B 132 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6711 (mm) REVERT: B 135 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: B 250 MET cc_start: 0.7854 (ttp) cc_final: 0.6951 (ppp) REVERT: B 291 THR cc_start: 0.8024 (m) cc_final: 0.7745 (p) REVERT: B 355 LEU cc_start: 0.7929 (tp) cc_final: 0.7649 (tt) outliers start: 5 outliers final: 2 residues processed: 137 average time/residue: 0.1484 time to fit residues: 27.5885 Evaluate side-chains 129 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 482 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.0010 chunk 31 optimal weight: 0.2980 chunk 19 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 59 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103747 restraints weight = 8938.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106489 restraints weight = 4764.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108309 restraints weight = 2997.599| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5916 Z= 0.214 Angle : 0.674 7.898 8058 Z= 0.337 Chirality : 0.043 0.139 968 Planarity : 0.005 0.041 982 Dihedral : 7.704 58.490 882 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.23 % Allowed : 29.27 % Favored : 66.50 % 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: 1.49 (0.31), residues: 756 helix: 1.67 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -1.63 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.025 0.001 PHE A 356 TYR 0.011 0.001 TYR A 476 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.565 Fit side-chains REVERT: A 153 VAL cc_start: 0.8328 (t) cc_final: 0.8121 (t) REVERT: A 157 VAL cc_start: 0.8546 (t) cc_final: 0.8325 (p) REVERT: A 212 LEU cc_start: 0.6516 (mt) cc_final: 0.6236 (mp) REVERT: B 153 VAL cc_start: 0.8441 (t) cc_final: 0.8230 (p) REVERT: B 355 LEU cc_start: 0.7864 (tp) cc_final: 0.7539 (tt) REVERT: B 405 MET cc_start: 0.6865 (ttp) cc_final: 0.6623 (ttp) REVERT: B 439 MET cc_start: 0.7324 (mmm) cc_final: 0.7069 (mmm) outliers start: 26 outliers final: 13 residues processed: 149 average time/residue: 0.1500 time to fit residues: 30.4650 Evaluate side-chains 149 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094824 restraints weight = 9118.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097517 restraints weight = 4809.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099239 restraints weight = 3011.547| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 5916 Z= 0.357 Angle : 0.706 8.012 8058 Z= 0.356 Chirality : 0.047 0.189 968 Planarity : 0.005 0.043 982 Dihedral : 6.548 49.631 874 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.69 % Allowed : 27.80 % Favored : 66.50 % 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: 1.36 (0.32), residues: 756 helix: 1.65 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -2.12 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 336 HIS 0.004 0.001 HIS B 422 PHE 0.028 0.002 PHE A 356 TYR 0.016 0.002 TYR A 251 ARG 0.002 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.637 Fit side-chains REVERT: A 41 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8208 (p) REVERT: A 153 VAL cc_start: 0.8281 (t) cc_final: 0.8075 (t) REVERT: A 254 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7598 (p) REVERT: B 131 PHE cc_start: 0.6683 (p90) cc_final: 0.5694 (p90) REVERT: B 135 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6206 (mp0) REVERT: B 355 LEU cc_start: 0.7778 (tp) cc_final: 0.7532 (tt) REVERT: B 405 MET cc_start: 0.6979 (ttp) cc_final: 0.6774 (ttm) REVERT: B 409 SER cc_start: 0.7959 (m) cc_final: 0.7692 (p) REVERT: B 417 LEU cc_start: 0.8003 (mt) cc_final: 0.7564 (mp) REVERT: B 439 MET cc_start: 0.7444 (mmm) cc_final: 0.7210 (mmm) outliers start: 35 outliers final: 19 residues processed: 159 average time/residue: 0.1463 time to fit residues: 31.8529 Evaluate side-chains 157 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 480 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097110 restraints weight = 9167.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100224 restraints weight = 4554.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102204 restraints weight = 2733.404| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5916 Z= 0.264 Angle : 0.676 7.373 8058 Z= 0.337 Chirality : 0.044 0.158 968 Planarity : 0.005 0.045 982 Dihedral : 5.860 48.762 874 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.02 % Allowed : 27.15 % Favored : 66.83 % 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: 1.52 (0.32), residues: 756 helix: 1.77 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.08 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.003 0.001 HIS B 422 PHE 0.026 0.001 PHE A 38 TYR 0.012 0.002 TYR A 251 ARG 0.006 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.616 Fit side-chains REVERT: A 41 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 411 MET cc_start: 0.8230 (mmt) cc_final: 0.7980 (mmp) REVERT: B 135 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: B 250 MET cc_start: 0.7077 (ttp) cc_final: 0.6806 (tmm) REVERT: B 296 LEU cc_start: 0.7782 (tp) cc_final: 0.7548 (tt) REVERT: B 355 LEU cc_start: 0.7815 (tp) cc_final: 0.7557 (tt) REVERT: B 411 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7218 (mpp) REVERT: B 417 LEU cc_start: 0.8029 (mt) cc_final: 0.7624 (mp) REVERT: B 439 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7174 (mmm) outliers start: 37 outliers final: 19 residues processed: 151 average time/residue: 0.1488 time to fit residues: 30.8100 Evaluate side-chains 154 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 44 optimal weight: 0.0060 chunk 28 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098528 restraints weight = 9074.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101641 restraints weight = 4522.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103667 restraints weight = 2717.536| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5916 Z= 0.211 Angle : 0.641 7.500 8058 Z= 0.319 Chirality : 0.043 0.132 968 Planarity : 0.005 0.045 982 Dihedral : 5.518 49.632 874 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.04 % Allowed : 28.13 % Favored : 66.83 % 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: 1.72 (0.32), residues: 756 helix: 1.91 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.05 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.000 HIS A 167 PHE 0.023 0.001 PHE A 38 TYR 0.010 0.001 TYR A 251 ARG 0.008 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.641 Fit side-chains REVERT: A 41 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (p) REVERT: A 313 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6765 (m-40) REVERT: A 411 MET cc_start: 0.8161 (mmt) cc_final: 0.7910 (mmp) REVERT: B 135 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: B 250 MET cc_start: 0.7146 (ttp) cc_final: 0.6831 (tmm) REVERT: B 296 LEU cc_start: 0.7768 (tp) cc_final: 0.7551 (tt) REVERT: B 355 LEU cc_start: 0.7765 (tp) cc_final: 0.7520 (tt) REVERT: B 410 MET cc_start: 0.7902 (tpp) cc_final: 0.7361 (tpp) REVERT: B 411 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7206 (mpp) REVERT: B 417 LEU cc_start: 0.8037 (mt) cc_final: 0.7629 (mp) REVERT: B 439 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7164 (mmm) outliers start: 31 outliers final: 17 residues processed: 156 average time/residue: 0.1423 time to fit residues: 30.6974 Evaluate side-chains 156 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096070 restraints weight = 9014.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099093 restraints weight = 4502.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101056 restraints weight = 2715.019| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5916 Z= 0.307 Angle : 0.677 7.651 8058 Z= 0.339 Chirality : 0.045 0.173 968 Planarity : 0.005 0.056 982 Dihedral : 5.502 48.490 874 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.85 % Allowed : 27.48 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.32), residues: 756 helix: 1.83 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -2.10 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS B 422 PHE 0.023 0.002 PHE A 38 TYR 0.015 0.002 TYR A 476 ARG 0.004 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.571 Fit side-chains REVERT: A 41 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 160 LEU cc_start: 0.8630 (tp) cc_final: 0.8359 (tt) REVERT: A 313 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.6977 (m-40) REVERT: B 135 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: B 296 LEU cc_start: 0.7761 (tp) cc_final: 0.7525 (tt) REVERT: B 316 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7644 (m) REVERT: B 355 LEU cc_start: 0.7719 (tp) cc_final: 0.7494 (tt) REVERT: B 363 MET cc_start: 0.7796 (ppp) cc_final: 0.7152 (ptt) REVERT: B 411 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7235 (mpp) REVERT: B 417 LEU cc_start: 0.8037 (mt) cc_final: 0.7634 (mp) REVERT: B 439 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7199 (mmm) outliers start: 36 outliers final: 23 residues processed: 152 average time/residue: 0.1532 time to fit residues: 31.4771 Evaluate side-chains 160 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.097216 restraints weight = 9028.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100209 restraints weight = 4595.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102146 restraints weight = 2791.552| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5916 Z= 0.253 Angle : 0.653 8.366 8058 Z= 0.328 Chirality : 0.043 0.133 968 Planarity : 0.005 0.055 982 Dihedral : 5.429 48.317 874 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.37 % Allowed : 28.62 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.32), residues: 756 helix: 1.89 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -1.99 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.002 0.001 HIS B 422 PHE 0.020 0.001 PHE A 38 TYR 0.012 0.001 TYR A 476 ARG 0.006 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.695 Fit side-chains REVERT: A 36 MET cc_start: 0.7488 (tpp) cc_final: 0.7238 (tpp) REVERT: A 41 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8148 (p) REVERT: A 160 LEU cc_start: 0.8632 (tp) cc_final: 0.8344 (tt) REVERT: A 254 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7795 (p) REVERT: A 313 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.6868 (m-40) REVERT: A 410 MET cc_start: 0.7132 (mmp) cc_final: 0.6901 (mmp) REVERT: B 135 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: B 153 VAL cc_start: 0.8380 (t) cc_final: 0.8122 (p) REVERT: B 296 LEU cc_start: 0.7767 (tp) cc_final: 0.7527 (tt) REVERT: B 316 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7645 (m) REVERT: B 355 LEU cc_start: 0.7712 (tp) cc_final: 0.7485 (tt) REVERT: B 363 MET cc_start: 0.7785 (ppp) cc_final: 0.7242 (ptt) REVERT: B 371 ILE cc_start: 0.7547 (mm) cc_final: 0.7306 (mt) REVERT: B 411 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7265 (mpp) REVERT: B 417 LEU cc_start: 0.8056 (mt) cc_final: 0.7651 (mp) REVERT: B 439 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7171 (mmm) outliers start: 33 outliers final: 22 residues processed: 148 average time/residue: 0.1617 time to fit residues: 32.5476 Evaluate side-chains 158 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100650 restraints weight = 8736.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103345 restraints weight = 4789.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105168 restraints weight = 3070.229| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5916 Z= 0.208 Angle : 0.636 9.002 8058 Z= 0.318 Chirality : 0.042 0.130 968 Planarity : 0.005 0.052 982 Dihedral : 5.373 47.901 874 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.72 % Allowed : 28.94 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.32), residues: 756 helix: 2.00 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -1.96 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.002 0.000 HIS A 167 PHE 0.019 0.001 PHE B 356 TYR 0.009 0.001 TYR A 349 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.606 Fit side-chains REVERT: A 36 MET cc_start: 0.7361 (tpp) cc_final: 0.7130 (tpp) REVERT: A 41 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 160 LEU cc_start: 0.8644 (tp) cc_final: 0.8342 (tt) REVERT: A 254 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 313 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6749 (m110) REVERT: A 410 MET cc_start: 0.7167 (mmp) cc_final: 0.6952 (mmp) REVERT: B 135 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6462 (mp0) REVERT: B 250 MET cc_start: 0.7035 (ttp) cc_final: 0.6769 (tmm) REVERT: B 296 LEU cc_start: 0.7772 (tp) cc_final: 0.7564 (tt) REVERT: B 316 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7676 (m) REVERT: B 355 LEU cc_start: 0.7717 (tp) cc_final: 0.7491 (tt) REVERT: B 363 MET cc_start: 0.7743 (ppp) cc_final: 0.7240 (ptt) REVERT: B 371 ILE cc_start: 0.7476 (mm) cc_final: 0.7272 (mt) REVERT: B 410 MET cc_start: 0.7790 (tpp) cc_final: 0.7114 (tpp) REVERT: B 411 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: B 417 LEU cc_start: 0.8115 (mt) cc_final: 0.7696 (mp) REVERT: B 439 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7120 (mmm) outliers start: 29 outliers final: 20 residues processed: 149 average time/residue: 0.1450 time to fit residues: 29.7396 Evaluate side-chains 161 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 0.0770 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 63 optimal weight: 0.0030 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.2548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102760 restraints weight = 8865.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105470 restraints weight = 4826.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107315 restraints weight = 3087.801| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5916 Z= 0.187 Angle : 0.635 9.435 8058 Z= 0.318 Chirality : 0.042 0.131 968 Planarity : 0.005 0.051 982 Dihedral : 5.333 47.138 874 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.88 % Allowed : 28.94 % Favored : 66.18 % 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: 1.92 (0.32), residues: 756 helix: 2.04 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.94 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.001 0.000 HIS A 167 PHE 0.018 0.001 PHE B 356 TYR 0.008 0.001 TYR A 251 ARG 0.004 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.632 Fit side-chains REVERT: A 36 MET cc_start: 0.7347 (tpp) cc_final: 0.7113 (tpp) REVERT: A 41 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 160 LEU cc_start: 0.8651 (tp) cc_final: 0.8342 (tt) REVERT: A 177 MET cc_start: 0.7276 (ttp) cc_final: 0.7066 (tmm) REVERT: A 313 ASN cc_start: 0.7272 (OUTLIER) cc_final: 0.6812 (m110) REVERT: A 414 MET cc_start: 0.7406 (mmm) cc_final: 0.6971 (mmm) REVERT: B 135 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: B 316 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7679 (m) REVERT: B 363 MET cc_start: 0.7753 (ppp) cc_final: 0.7266 (ptt) REVERT: B 410 MET cc_start: 0.7778 (tpp) cc_final: 0.7090 (tpp) REVERT: B 439 MET cc_start: 0.7291 (mmm) cc_final: 0.7076 (mmm) outliers start: 30 outliers final: 18 residues processed: 149 average time/residue: 0.1468 time to fit residues: 29.9499 Evaluate side-chains 154 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 0.0060 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098443 restraints weight = 8895.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101090 restraints weight = 4815.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102893 restraints weight = 3059.943| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5916 Z= 0.286 Angle : 0.700 10.363 8058 Z= 0.346 Chirality : 0.044 0.154 968 Planarity : 0.005 0.060 982 Dihedral : 5.399 47.274 874 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.90 % Allowed : 30.24 % Favored : 65.85 % 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: 1.73 (0.32), residues: 756 helix: 1.89 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.93 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.003 0.001 HIS A 167 PHE 0.023 0.002 PHE B 246 TYR 0.013 0.002 TYR A 476 ARG 0.003 0.000 ARG A 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.527 Fit side-chains REVERT: A 36 MET cc_start: 0.7350 (tpp) cc_final: 0.7142 (tpp) REVERT: A 41 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 160 LEU cc_start: 0.8694 (tp) cc_final: 0.8378 (tt) REVERT: A 313 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.6936 (m-40) REVERT: B 149 MET cc_start: 0.7580 (tpp) cc_final: 0.7279 (tpp) REVERT: B 316 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7708 (m) REVERT: B 363 MET cc_start: 0.7754 (ppp) cc_final: 0.7269 (ptt) REVERT: B 371 ILE cc_start: 0.7515 (mm) cc_final: 0.7314 (mp) REVERT: B 410 MET cc_start: 0.7783 (tpp) cc_final: 0.7123 (tpp) REVERT: B 411 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7248 (mpp) REVERT: B 417 LEU cc_start: 0.8066 (mt) cc_final: 0.7657 (mp) REVERT: B 439 MET cc_start: 0.7345 (mmm) cc_final: 0.7132 (mmm) outliers start: 24 outliers final: 19 residues processed: 148 average time/residue: 0.1418 time to fit residues: 28.7847 Evaluate side-chains 160 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 411 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097984 restraints weight = 8937.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100637 restraints weight = 4818.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102474 restraints weight = 3046.185| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 5916 Z= 0.330 Angle : 1.124 59.189 8058 Z= 0.653 Chirality : 0.043 0.149 968 Planarity : 0.005 0.061 982 Dihedral : 5.165 47.335 871 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.90 % Allowed : 30.24 % Favored : 65.85 % Cbeta Deviations : 0.15 % 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: 1.73 (0.32), residues: 756 helix: 1.88 (0.22), residues: 603 sheet: None (None), residues: 0 loop : -1.93 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.003 0.001 HIS A 167 PHE 0.035 0.002 PHE B 246 TYR 0.012 0.001 TYR A 476 ARG 0.003 0.000 ARG A 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.04 seconds wall clock time: 33 minutes 45.29 seconds (2025.29 seconds total)