Starting phenix.real_space_refine on Mon Apr 6 08:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q6z_72282/04_2026/9q6z_72282.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q6z_72282/04_2026/9q6z_72282.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 { model { file = "/net/cci-nas-00/data/ceres_data/9q6z_72282/04_2026/9q6z_72282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q6z_72282/04_2026/9q6z_72282.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q6z_72282/04_2026/9q6z_72282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q6z_72282/04_2026/9q6z_72282.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5368 2.51 5 N 1470 2.21 5 O 1650 1.98 5 H 8259 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16805 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 9224 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 560} Chain: "B" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1992 Classifications: {'peptide': 131} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1879 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "D" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1884 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1826 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Time building chain proxies: 2.93, per 1000 atoms: 0.17 Number of scatterers: 16805 At special positions: 0 Unit cell: (82.626, 113.391, 139.761, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 O 1650 8.00 N 1470 7.00 C 5368 6.00 H 8259 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.04 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.04 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.04 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 118 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 117 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 722.3 milliseconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 49.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.616A pdb=" N ASP A 37 " --> pdb=" O HIS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 55 Processing helix chain 'A' and resid 59 through 80 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 174 through 195 Processing helix chain 'A' and resid 197 through 247 Proline residue: A 204 - end of helix removed outlier: 3.717A pdb=" N LYS A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 272 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.558A pdb=" N PHE A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.501A pdb=" N CYS A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 423 removed outlier: 3.671A pdb=" N LYS A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Proline residue: A 403 - end of helix Proline residue: A 408 - end of helix removed outlier: 3.837A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 439 Processing helix chain 'A' and resid 443 through 463 removed outlier: 3.865A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 491 removed outlier: 4.400A pdb=" N MET A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 494 through 504 removed outlier: 4.572A pdb=" N SER A 504 " --> pdb=" O CYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 515 Processing helix chain 'A' and resid 534 through 540 removed outlier: 4.021A pdb=" N CYS A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 564 through 585 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.623A pdb=" N ARG C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'E' and resid 50 through 54 Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.531A pdb=" N GLU E 86 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 Processing helix chain 'E' and resid 128 through 132 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.739A pdb=" N VAL B 29 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG B 50 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA B 66 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TRP B 52 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.739A pdb=" N VAL B 29 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 136 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AA5, first strand: chain 'C' and resid 24 through 29 Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.743A pdb=" N MET C 56 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 72 " --> pdb=" O MET C 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 35 Processing sheet with id=AA8, first strand: chain 'D' and resid 28 through 29 removed outlier: 3.970A pdb=" N SER D 29 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER D 43 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 80 through 81 removed outlier: 4.126A pdb=" N TRP D 58 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR D 72 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET D 56 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 81 removed outlier: 4.126A pdb=" N TRP D 58 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR D 72 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET D 56 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AB3, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.435A pdb=" N GLY E 32 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER E 144 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA E 34 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 72 through 74 removed outlier: 6.742A pdb=" N THR E 72 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA E 79 " --> pdb=" O THR E 72 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1431 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: 4.02 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8258 1.03 - 1.23: 124 1.23 - 1.43: 3607 1.43 - 1.63: 4924 1.63 - 1.82: 71 Bond restraints: 16984 Sorted by residual: bond pdb=" N HIS B 18 " pdb=" H1 HIS B 18 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ARG B 133 " pdb=" CA ARG B 133 " ideal model delta sigma weight residual 1.461 1.450 0.011 9.20e-03 1.18e+04 1.55e+00 bond pdb=" CA THR E 50 " pdb=" C THR E 50 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.12e-02 7.97e+03 9.79e-01 bond pdb=" CA THR C 50 " pdb=" C THR C 50 " ideal model delta sigma weight residual 1.523 1.509 0.014 1.41e-02 5.03e+03 9.73e-01 bond pdb=" CA ASP A 273 " pdb=" C ASP A 273 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.10e-02 8.26e+03 9.68e-01 ... (remaining 16979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 29582 1.33 - 2.67: 929 2.67 - 4.00: 77 4.00 - 5.33: 17 5.33 - 6.66: 3 Bond angle restraints: 30608 Sorted by residual: angle pdb=" N ASN B 47 " pdb=" CA ASN B 47 " pdb=" C ASN B 47 " ideal model delta sigma weight residual 113.18 108.27 4.91 1.33e+00 5.65e-01 1.36e+01 angle pdb=" N ARG B 133 " pdb=" CA ARG B 133 " pdb=" C ARG B 133 " ideal model delta sigma weight residual 112.75 107.89 4.86 1.36e+00 5.41e-01 1.28e+01 angle pdb=" C VAL C 70 " pdb=" N GLY C 71 " pdb=" CA GLY C 71 " ideal model delta sigma weight residual 121.41 114.75 6.66 1.96e+00 2.60e-01 1.16e+01 angle pdb=" CA LEU A 38 " pdb=" C LEU A 38 " pdb=" N GLY A 39 " ideal model delta sigma weight residual 114.76 118.25 -3.49 1.14e+00 7.69e-01 9.37e+00 angle pdb=" N VAL A 493 " pdb=" CA VAL A 493 " pdb=" C VAL A 493 " ideal model delta sigma weight residual 113.71 110.87 2.84 9.50e-01 1.11e+00 8.92e+00 ... (remaining 30603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7359 18.00 - 35.99: 526 35.99 - 53.99: 160 53.99 - 71.99: 36 71.99 - 89.99: 14 Dihedral angle restraints: 8095 sinusoidal: 4337 harmonic: 3758 Sorted by residual: dihedral pdb=" CB CYS A 340 " pdb=" SG CYS A 340 " pdb=" SG CYS A 385 " pdb=" CB CYS A 385 " ideal model delta sinusoidal sigma weight residual 93.00 155.76 -62.76 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N GLY A 423 " pdb=" CA GLY A 423 " ideal model delta harmonic sigma weight residual 180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA THR A 103 " pdb=" C THR A 103 " pdb=" N LEU A 104 " pdb=" CA LEU A 104 " ideal model delta harmonic sigma weight residual -180.00 -153.42 -26.58 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 8092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 819 0.030 - 0.060: 338 0.060 - 0.090: 69 0.090 - 0.120: 42 0.120 - 0.150: 7 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA VAL B 64 " pdb=" N VAL B 64 " pdb=" C VAL B 64 " pdb=" CB VAL B 64 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA VAL C 70 " pdb=" N VAL C 70 " pdb=" C VAL C 70 " pdb=" CB VAL C 70 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL C 114 " pdb=" N VAL C 114 " pdb=" C VAL C 114 " pdb=" CB VAL C 114 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1272 not shown) Planarity restraints: 2588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 203 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 204 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO A 510 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 407 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 408 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.019 5.00e-02 4.00e+02 ... (remaining 2585 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 740 2.16 - 2.77: 33063 2.77 - 3.38: 46932 3.38 - 3.99: 59034 3.99 - 4.60: 93257 Nonbonded interactions: 233026 Sorted by model distance: nonbonded pdb=" O CYS A 538 " pdb="HH21 ARG A 545 " model vdw 1.552 2.450 nonbonded pdb=" O VAL D 34 " pdb=" H SER D 145 " model vdw 1.553 2.450 nonbonded pdb=" H LYS D 109 " pdb=" OD2 ASP D 112 " model vdw 1.554 2.450 nonbonded pdb=" OD1 ASP A 574 " pdb="HH21 ARG E 74 " model vdw 1.575 2.450 nonbonded pdb=" HZ2 LYS A 264 " pdb=" OE2 GLU A 268 " model vdw 1.578 2.450 ... (remaining 233021 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 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: 4.330 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: 0.090 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8747 Z= 0.176 Angle : 0.612 6.664 11839 Z= 0.362 Chirality : 0.037 0.150 1275 Planarity : 0.004 0.061 1540 Dihedral : 13.638 89.987 3204 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.09 % Rotamer: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1083 helix: 1.82 (0.24), residues: 455 sheet: -0.31 (0.31), residues: 264 loop : -0.83 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 67 TYR 0.020 0.001 TYR A 185 PHE 0.014 0.002 PHE A 427 TRP 0.010 0.001 TRP B 137 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8725) covalent geometry : angle 0.60954 (11795) SS BOND : bond 0.00285 ( 22) SS BOND : angle 1.02742 ( 44) hydrogen bonds : bond 0.12616 ( 498) hydrogen bonds : angle 6.79264 ( 1431) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LYS cc_start: 0.9165 (ttpt) cc_final: 0.8646 (ttmm) REVERT: B 67 ILE cc_start: 0.9225 (tt) cc_final: 0.8987 (tp) REVERT: B 71 PHE cc_start: 0.8781 (m-80) cc_final: 0.8435 (m-10) REVERT: D 102 TYR cc_start: 0.6846 (m-80) cc_final: 0.6525 (m-80) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.2788 time to fit residues: 78.3184 Evaluate side-chains 141 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.050336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037139 restraints weight = 136552.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.039668 restraints weight = 55349.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041348 restraints weight = 30855.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042447 restraints weight = 20522.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043178 restraints weight = 15426.569| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8747 Z= 0.166 Angle : 0.584 6.020 11839 Z= 0.318 Chirality : 0.037 0.166 1275 Planarity : 0.005 0.044 1540 Dihedral : 5.284 48.083 1198 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.46 % Favored : 93.44 % Rotamer: Outliers : 0.88 % Allowed : 12.18 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1083 helix: 1.99 (0.24), residues: 457 sheet: -0.45 (0.32), residues: 241 loop : -0.81 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.019 0.001 TYR A 185 PHE 0.016 0.001 PHE A 427 TRP 0.009 0.001 TRP A 238 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8725) covalent geometry : angle 0.58252 (11795) SS BOND : bond 0.00409 ( 22) SS BOND : angle 0.83719 ( 44) hydrogen bonds : bond 0.04399 ( 498) hydrogen bonds : angle 5.81942 ( 1431) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9336 (mt-10) REVERT: A 476 TYR cc_start: 0.8934 (m-80) cc_final: 0.8540 (m-10) REVERT: B 67 ILE cc_start: 0.9368 (tt) cc_final: 0.8972 (tp) REVERT: B 71 PHE cc_start: 0.9536 (m-80) cc_final: 0.9219 (m-10) REVERT: B 89 ASP cc_start: 0.9482 (t0) cc_final: 0.9139 (p0) REVERT: B 96 TYR cc_start: 0.9067 (m-80) cc_final: 0.8608 (m-80) REVERT: D 50 GLU cc_start: 0.9076 (mp0) cc_final: 0.8749 (mp0) REVERT: D 117 TYR cc_start: 0.9182 (m-80) cc_final: 0.8636 (m-80) outliers start: 8 outliers final: 7 residues processed: 143 average time/residue: 0.2498 time to fit residues: 47.0246 Evaluate side-chains 135 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 59 optimal weight: 0.0170 chunk 99 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.048890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.035688 restraints weight = 143145.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038091 restraints weight = 58238.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.039707 restraints weight = 32876.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.040782 restraints weight = 22107.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041430 restraints weight = 16759.221| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8747 Z= 0.226 Angle : 0.573 5.796 11839 Z= 0.316 Chirality : 0.037 0.164 1275 Planarity : 0.004 0.042 1540 Dihedral : 5.255 48.948 1198 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.29 % Favored : 92.61 % Rotamer: Outliers : 1.43 % Allowed : 12.29 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1083 helix: 1.93 (0.24), residues: 460 sheet: -0.51 (0.32), residues: 243 loop : -0.85 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 49 TYR 0.015 0.001 TYR A 185 PHE 0.016 0.001 PHE A 401 TRP 0.009 0.001 TRP A 238 HIS 0.004 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8725) covalent geometry : angle 0.57222 (11795) SS BOND : bond 0.00275 ( 22) SS BOND : angle 0.84726 ( 44) hydrogen bonds : bond 0.04014 ( 498) hydrogen bonds : angle 5.72854 ( 1431) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9345 (mt-10) REVERT: A 136 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9130 (tt) REVERT: A 155 GLU cc_start: 0.9347 (pm20) cc_final: 0.9101 (pm20) REVERT: A 476 TYR cc_start: 0.8961 (m-80) cc_final: 0.8580 (m-10) REVERT: B 71 PHE cc_start: 0.9508 (m-80) cc_final: 0.9306 (m-10) REVERT: B 89 ASP cc_start: 0.9470 (t0) cc_final: 0.9112 (p0) REVERT: B 96 TYR cc_start: 0.9041 (m-80) cc_final: 0.8603 (m-80) REVERT: C 56 MET cc_start: 0.7843 (mmm) cc_final: 0.7527 (mmm) REVERT: D 117 TYR cc_start: 0.9152 (m-80) cc_final: 0.8718 (m-80) outliers start: 13 outliers final: 8 residues processed: 134 average time/residue: 0.2259 time to fit residues: 40.7897 Evaluate side-chains 131 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.035429 restraints weight = 139686.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037860 restraints weight = 56728.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.039501 restraints weight = 31867.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.040587 restraints weight = 21361.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.041300 restraints weight = 16108.392| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8747 Z= 0.161 Angle : 0.535 5.279 11839 Z= 0.289 Chirality : 0.037 0.161 1275 Planarity : 0.004 0.053 1540 Dihedral : 5.109 48.297 1198 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.07 % Rotamer: Outliers : 1.98 % Allowed : 12.95 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1083 helix: 2.05 (0.24), residues: 463 sheet: -0.49 (0.32), residues: 241 loop : -0.72 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.013 0.001 TYR A 185 PHE 0.011 0.001 PHE A 401 TRP 0.016 0.001 TRP B 137 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8725) covalent geometry : angle 0.53302 (11795) SS BOND : bond 0.00439 ( 22) SS BOND : angle 0.85098 ( 44) hydrogen bonds : bond 0.03701 ( 498) hydrogen bonds : angle 5.49239 ( 1431) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.9565 (mt-10) cc_final: 0.9345 (mt-10) REVERT: A 136 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9074 (tt) REVERT: A 476 TYR cc_start: 0.8988 (m-80) cc_final: 0.8636 (m-10) REVERT: B 89 ASP cc_start: 0.9478 (t0) cc_final: 0.9174 (p0) REVERT: B 96 TYR cc_start: 0.9020 (m-80) cc_final: 0.8497 (m-10) REVERT: D 117 TYR cc_start: 0.9107 (m-80) cc_final: 0.8640 (m-80) REVERT: D 138 GLN cc_start: 0.9283 (pm20) cc_final: 0.8982 (pm20) REVERT: E 66 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8082 (pm20) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 0.2172 time to fit residues: 39.1212 Evaluate side-chains 133 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.046477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.033296 restraints weight = 146477.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.035598 restraints weight = 61445.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.037141 restraints weight = 35412.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.038164 restraints weight = 24299.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.038846 restraints weight = 18646.225| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 8747 Z= 0.341 Angle : 0.636 5.940 11839 Z= 0.356 Chirality : 0.038 0.153 1275 Planarity : 0.005 0.046 1540 Dihedral : 5.345 47.028 1198 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.87 % Rotamer: Outliers : 2.52 % Allowed : 14.16 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1083 helix: 1.45 (0.23), residues: 464 sheet: -0.74 (0.33), residues: 242 loop : -1.02 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 61 TYR 0.016 0.002 TYR A 343 PHE 0.014 0.002 PHE A 333 TRP 0.011 0.002 TRP E 58 HIS 0.006 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00670 ( 8725) covalent geometry : angle 0.63478 (11795) SS BOND : bond 0.00341 ( 22) SS BOND : angle 0.94684 ( 44) hydrogen bonds : bond 0.04083 ( 498) hydrogen bonds : angle 5.93045 ( 1431) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.9509 (tp30) cc_final: 0.9256 (mp0) REVERT: A 476 TYR cc_start: 0.9025 (m-80) cc_final: 0.8639 (m-10) REVERT: D 117 TYR cc_start: 0.9020 (m-80) cc_final: 0.8556 (m-80) REVERT: D 138 GLN cc_start: 0.9261 (pm20) cc_final: 0.8979 (pm20) REVERT: E 104 MET cc_start: 0.9287 (mpp) cc_final: 0.9031 (mpp) outliers start: 23 outliers final: 17 residues processed: 128 average time/residue: 0.2165 time to fit residues: 37.6224 Evaluate side-chains 122 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 35 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.047576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034329 restraints weight = 142121.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036730 restraints weight = 58420.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.038356 restraints weight = 33170.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.039418 restraints weight = 22421.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040117 restraints weight = 17029.004| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8747 Z= 0.165 Angle : 0.553 5.501 11839 Z= 0.296 Chirality : 0.037 0.154 1275 Planarity : 0.004 0.041 1540 Dihedral : 5.161 45.421 1198 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.07 % Rotamer: Outliers : 1.87 % Allowed : 15.26 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1083 helix: 1.94 (0.24), residues: 462 sheet: -0.65 (0.34), residues: 231 loop : -0.84 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.020 0.001 TYR A 174 PHE 0.015 0.001 PHE A 401 TRP 0.009 0.001 TRP E 58 HIS 0.002 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8725) covalent geometry : angle 0.55078 (11795) SS BOND : bond 0.00340 ( 22) SS BOND : angle 1.00783 ( 44) hydrogen bonds : bond 0.03654 ( 498) hydrogen bonds : angle 5.52821 ( 1431) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.8950 (tpt170) REVERT: A 476 TYR cc_start: 0.9005 (m-80) cc_final: 0.8645 (m-10) REVERT: B 89 ASP cc_start: 0.9378 (t0) cc_final: 0.8912 (p0) REVERT: B 96 TYR cc_start: 0.9030 (m-80) cc_final: 0.8467 (m-10) REVERT: D 50 GLU cc_start: 0.8839 (mp0) cc_final: 0.8524 (mp0) REVERT: D 98 GLU cc_start: 0.9737 (tp30) cc_final: 0.9512 (mm-30) REVERT: D 117 TYR cc_start: 0.9043 (m-80) cc_final: 0.8503 (m-80) REVERT: D 138 GLN cc_start: 0.9250 (pm20) cc_final: 0.8960 (pm20) outliers start: 17 outliers final: 14 residues processed: 128 average time/residue: 0.2218 time to fit residues: 38.5279 Evaluate side-chains 123 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035639 restraints weight = 141470.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038114 restraints weight = 57752.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039797 restraints weight = 32633.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040880 restraints weight = 21932.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041561 restraints weight = 16579.181| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8747 Z= 0.115 Angle : 0.532 5.448 11839 Z= 0.281 Chirality : 0.037 0.160 1275 Planarity : 0.004 0.037 1540 Dihedral : 4.964 44.875 1198 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.35 % Rotamer: Outliers : 1.43 % Allowed : 16.25 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 1083 helix: 2.25 (0.24), residues: 462 sheet: -0.53 (0.35), residues: 223 loop : -0.58 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.016 0.001 TYR A 174 PHE 0.014 0.001 PHE D 59 TRP 0.008 0.001 TRP A 238 HIS 0.002 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8725) covalent geometry : angle 0.52902 (11795) SS BOND : bond 0.00260 ( 22) SS BOND : angle 0.99769 ( 44) hydrogen bonds : bond 0.03400 ( 498) hydrogen bonds : angle 5.20801 ( 1431) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9018 (mm-30) REVERT: A 232 GLU cc_start: 0.8492 (pm20) cc_final: 0.8272 (pm20) REVERT: A 242 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.9144 (tpt90) REVERT: A 316 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8483 (mm-30) REVERT: A 476 TYR cc_start: 0.9027 (m-80) cc_final: 0.8690 (m-10) REVERT: B 89 ASP cc_start: 0.9346 (t0) cc_final: 0.8722 (p0) REVERT: D 50 GLU cc_start: 0.8813 (mp0) cc_final: 0.8516 (mp0) REVERT: D 117 TYR cc_start: 0.8984 (m-80) cc_final: 0.8459 (m-80) REVERT: D 138 GLN cc_start: 0.9249 (pm20) cc_final: 0.8914 (pm20) outliers start: 13 outliers final: 12 residues processed: 124 average time/residue: 0.2259 time to fit residues: 38.1990 Evaluate side-chains 126 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.048490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.035263 restraints weight = 142147.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.037692 restraints weight = 58366.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039358 restraints weight = 33151.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.040446 restraints weight = 22321.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041156 restraints weight = 16883.125| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8747 Z= 0.157 Angle : 0.535 5.310 11839 Z= 0.286 Chirality : 0.037 0.159 1275 Planarity : 0.004 0.042 1540 Dihedral : 4.931 45.342 1198 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.32 % Allowed : 16.36 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 1083 helix: 2.30 (0.24), residues: 462 sheet: -0.55 (0.35), residues: 223 loop : -0.63 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 138 TYR 0.013 0.001 TYR A 174 PHE 0.011 0.001 PHE D 59 TRP 0.018 0.001 TRP A 238 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8725) covalent geometry : angle 0.53293 (11795) SS BOND : bond 0.00264 ( 22) SS BOND : angle 0.97334 ( 44) hydrogen bonds : bond 0.03373 ( 498) hydrogen bonds : angle 5.20255 ( 1431) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8522 (mm-30) REVERT: A 476 TYR cc_start: 0.9042 (m-80) cc_final: 0.8688 (m-10) REVERT: B 89 ASP cc_start: 0.9331 (t0) cc_final: 0.8717 (p0) REVERT: D 117 TYR cc_start: 0.8988 (m-80) cc_final: 0.8488 (m-80) REVERT: D 138 GLN cc_start: 0.9235 (pm20) cc_final: 0.8931 (pm20) outliers start: 12 outliers final: 11 residues processed: 117 average time/residue: 0.2203 time to fit residues: 35.4617 Evaluate side-chains 120 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.048100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.034832 restraints weight = 141368.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.037253 restraints weight = 58029.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.038906 restraints weight = 32923.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.039933 restraints weight = 22201.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.040664 restraints weight = 17009.880| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8747 Z= 0.163 Angle : 0.543 6.151 11839 Z= 0.291 Chirality : 0.037 0.159 1275 Planarity : 0.004 0.041 1540 Dihedral : 4.909 45.063 1198 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.54 % Allowed : 16.90 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.27), residues: 1083 helix: 2.22 (0.24), residues: 468 sheet: -0.62 (0.34), residues: 223 loop : -0.66 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 138 TYR 0.012 0.001 TYR A 174 PHE 0.010 0.001 PHE D 59 TRP 0.021 0.001 TRP A 238 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8725) covalent geometry : angle 0.54054 (11795) SS BOND : bond 0.00266 ( 22) SS BOND : angle 0.96970 ( 44) hydrogen bonds : bond 0.03356 ( 498) hydrogen bonds : angle 5.17705 ( 1431) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.9562 (tp30) cc_final: 0.9338 (mm-30) REVERT: A 242 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.9104 (tpt-90) REVERT: A 476 TYR cc_start: 0.9055 (m-80) cc_final: 0.8695 (m-10) REVERT: B 89 ASP cc_start: 0.9328 (t0) cc_final: 0.8710 (p0) REVERT: D 117 TYR cc_start: 0.8963 (m-80) cc_final: 0.8452 (m-80) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.2268 time to fit residues: 37.4936 Evaluate side-chains 125 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.048350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035081 restraints weight = 140598.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037522 restraints weight = 57554.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.039182 restraints weight = 32569.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.040225 restraints weight = 21953.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.040968 restraints weight = 16775.255| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8747 Z= 0.132 Angle : 0.537 5.165 11839 Z= 0.284 Chirality : 0.037 0.161 1275 Planarity : 0.004 0.040 1540 Dihedral : 4.862 44.583 1198 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.43 % Allowed : 16.79 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 1083 helix: 2.24 (0.24), residues: 474 sheet: -0.57 (0.34), residues: 222 loop : -0.62 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 138 TYR 0.011 0.001 TYR A 174 PHE 0.010 0.001 PHE D 59 TRP 0.019 0.001 TRP A 238 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8725) covalent geometry : angle 0.53520 (11795) SS BOND : bond 0.00255 ( 22) SS BOND : angle 0.96723 ( 44) hydrogen bonds : bond 0.03280 ( 498) hydrogen bonds : angle 5.08297 ( 1431) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9094 (tpt-90) REVERT: A 476 TYR cc_start: 0.9034 (m-80) cc_final: 0.8661 (m-10) REVERT: B 89 ASP cc_start: 0.9315 (t0) cc_final: 0.8806 (p0) REVERT: B 96 TYR cc_start: 0.9027 (m-80) cc_final: 0.8508 (m-10) REVERT: D 117 TYR cc_start: 0.8963 (m-80) cc_final: 0.8445 (m-80) outliers start: 13 outliers final: 11 residues processed: 124 average time/residue: 0.2361 time to fit residues: 39.5058 Evaluate side-chains 126 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 142 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.047849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034653 restraints weight = 141621.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.037045 restraints weight = 58557.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038685 restraints weight = 33370.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.039758 restraints weight = 22533.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040487 restraints weight = 17099.516| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8747 Z= 0.214 Angle : 0.563 5.495 11839 Z= 0.304 Chirality : 0.036 0.158 1275 Planarity : 0.004 0.044 1540 Dihedral : 4.958 44.866 1198 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.43 % Allowed : 16.68 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.27), residues: 1083 helix: 2.08 (0.24), residues: 474 sheet: -0.66 (0.34), residues: 226 loop : -0.72 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 121 TYR 0.020 0.001 TYR B 127 PHE 0.010 0.001 PHE D 59 TRP 0.018 0.001 TRP A 238 HIS 0.004 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8725) covalent geometry : angle 0.56083 (11795) SS BOND : bond 0.00274 ( 22) SS BOND : angle 0.95893 ( 44) hydrogen bonds : bond 0.03410 ( 498) hydrogen bonds : angle 5.22221 ( 1431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.64 seconds wall clock time: 51 minutes 47.22 seconds (3107.22 seconds total)