Starting phenix.real_space_refine on Wed Aug 5 00:28:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w01_65488/08_2026/9w01_65488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w01_65488/08_2026/9w01_65488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w01_65488/08_2026/9w01_65488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w01_65488/08_2026/9w01_65488.map" model { file = "/net/cci-nas-00/data/ceres_data/9w01_65488/08_2026/9w01_65488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w01_65488/08_2026/9w01_65488.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4842 2.51 5 N 1262 2.21 5 O 1364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7509 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 865 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 6644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6644 Classifications: {'peptide': 809} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 765} Time building chain proxies: 1.93, per 1000 atoms: 0.26 Number of scatterers: 7509 At special positions: 0 Unit cell: (69.1956, 108.379, 130.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1364 8.00 N 1262 7.00 C 4842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 455.5 milliseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 40.5% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 1097 through 1102 Processing helix chain 'A' and resid 1150 through 1154 Processing helix chain 'B' and resid 10 through 25 removed outlier: 4.054A pdb=" N GLU B 16 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 55 through 75 removed outlier: 3.622A pdb=" N VAL B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 101 removed outlier: 3.709A pdb=" N ILE B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.567A pdb=" N VAL B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 138 removed outlier: 3.706A pdb=" N VAL B 124 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 removed outlier: 3.519A pdb=" N MET B 156 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.766A pdb=" N THR B 229 " --> pdb=" O THR B 226 " (cutoff:3.500A) Proline residue: B 231 - end of helix Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.583A pdb=" N LEU B 263 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER B 264 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 265 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 266 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.859A pdb=" N ASP B 272 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 303 removed outlier: 3.620A pdb=" N CYS B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 301 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.531A pdb=" N TYR B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 422 through 431 removed outlier: 4.143A pdb=" N ARG B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.695A pdb=" N LYS B 450 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.862A pdb=" N GLU B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 530 removed outlier: 3.548A pdb=" N GLU B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 547 through 551 removed outlier: 3.582A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 removed outlier: 3.902A pdb=" N ARG B 565 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 578 removed outlier: 3.639A pdb=" N LEU B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 641 through 650 removed outlier: 4.065A pdb=" N VAL B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 674 removed outlier: 3.741A pdb=" N TRP B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 713 Processing helix chain 'B' and resid 715 through 733 removed outlier: 4.267A pdb=" N VAL B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) Proline residue: B 721 - end of helix removed outlier: 3.610A pdb=" N VAL B 724 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 727 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP B 728 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 731 " --> pdb=" O VAL B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 748 through 769 removed outlier: 3.784A pdb=" N THR B 757 " --> pdb=" O MET B 753 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 785 removed outlier: 3.707A pdb=" N THR B 777 " --> pdb=" O THR B 773 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 804 removed outlier: 3.568A pdb=" N TYR B 803 " --> pdb=" O SER B 800 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1083 through 1086 removed outlier: 8.591A pdb=" N ILE A1171 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER A1070 " --> pdb=" O ILE A1171 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR A1173 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL A1072 " --> pdb=" O TYR A1173 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR A1170 " --> pdb=" O PHE A1118 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE A1118 " --> pdb=" O THR A1170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1146 through 1148 removed outlier: 4.072A pdb=" N VAL A1146 " --> pdb=" O THR A1159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.846A pdb=" N THR B 187 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 275 through 279 removed outlier: 6.972A pdb=" N LYS B 246 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG B 278 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR B 244 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B 257 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 221 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 207 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL B 389 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 209 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 387 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 306 through 309 removed outlier: 3.782A pdb=" N VAL B 236 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 235 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 434 through 436 removed outlier: 6.399A pdb=" N TYR B 434 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B 589 " --> pdb=" O TYR B 434 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 436 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE B 557 " --> pdb=" O ILE B 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 458 through 459 Processing sheet with id=AA9, first strand: chain 'B' and resid 478 through 480 Processing sheet with id=AB1, first strand: chain 'B' and resid 593 through 594 255 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2294 1.34 - 1.46: 1493 1.46 - 1.58: 3854 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 7705 Sorted by residual: bond pdb=" C VAL B 720 " pdb=" N PRO B 721 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 3.96e+00 bond pdb=" N TYR B 116 " pdb=" CA TYR B 116 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.58e-02 4.01e+03 3.44e+00 bond pdb=" CG1 ILE A1172 " pdb=" CD1 ILE A1172 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.06e+00 bond pdb=" CB THR B 570 " pdb=" CG2 THR B 570 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.04e+00 bond pdb=" CB TRP B 160 " pdb=" CG TRP B 160 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.79e+00 ... (remaining 7700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9991 1.99 - 3.97: 401 3.97 - 5.96: 46 5.96 - 7.94: 12 7.94 - 9.93: 4 Bond angle restraints: 10454 Sorted by residual: angle pdb=" C SER B 532 " pdb=" N MET B 533 " pdb=" CA MET B 533 " ideal model delta sigma weight residual 120.09 126.24 -6.15 1.25e+00 6.40e-01 2.42e+01 angle pdb=" C GLU B 115 " pdb=" N TYR B 116 " pdb=" CA TYR B 116 " ideal model delta sigma weight residual 123.93 130.51 -6.58 1.54e+00 4.22e-01 1.83e+01 angle pdb=" C ASP A1150 " pdb=" N LEU A1151 " pdb=" CA LEU A1151 " ideal model delta sigma weight residual 120.38 125.99 -5.61 1.46e+00 4.69e-01 1.47e+01 angle pdb=" N TYR B 116 " pdb=" CA TYR B 116 " pdb=" C TYR B 116 " ideal model delta sigma weight residual 113.40 108.65 4.75 1.47e+00 4.63e-01 1.04e+01 angle pdb=" CA TRP B 455 " pdb=" CB TRP B 455 " pdb=" CG TRP B 455 " ideal model delta sigma weight residual 113.60 119.46 -5.86 1.90e+00 2.77e-01 9.51e+00 ... (remaining 10449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 4124 18.04 - 36.08: 408 36.08 - 54.12: 55 54.12 - 72.16: 13 72.16 - 90.20: 8 Dihedral angle restraints: 4608 sinusoidal: 1908 harmonic: 2700 Sorted by residual: dihedral pdb=" CA GLY A1124 " pdb=" C GLY A1124 " pdb=" N PRO A1125 " pdb=" CA PRO A1125 " ideal model delta harmonic sigma weight residual 180.00 153.73 26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA TYR B 116 " pdb=" C TYR B 116 " pdb=" N ASN B 117 " pdb=" CA ASN B 117 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLU B 130 " pdb=" C GLU B 130 " pdb=" N TRP B 131 " pdb=" CA TRP B 131 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 4605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 921 0.074 - 0.147: 198 0.147 - 0.220: 13 0.220 - 0.294: 1 0.294 - 0.367: 1 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CB VAL B 720 " pdb=" CA VAL B 720 " pdb=" CG1 VAL B 720 " pdb=" CG2 VAL B 720 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE B 257 " pdb=" CA ILE B 257 " pdb=" CG1 ILE B 257 " pdb=" CG2 ILE B 257 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA VAL B 720 " pdb=" N VAL B 720 " pdb=" C VAL B 720 " pdb=" CB VAL B 720 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1131 not shown) Planarity restraints: 1337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 131 " -0.029 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP B 131 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP B 131 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP B 131 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 131 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 131 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 131 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 131 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 131 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 131 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 104 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO B 105 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B 105 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 105 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 412 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO B 413 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.044 5.00e-02 4.00e+02 ... (remaining 1334 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1873 2.80 - 3.32: 6110 3.32 - 3.85: 11349 3.85 - 4.37: 13254 4.37 - 4.90: 23790 Nonbonded interactions: 56376 Sorted by model distance: nonbonded pdb=" OH TYR B 173 " pdb=" OD2 ASP B 454 " model vdw 2.273 3.040 nonbonded pdb=" NZ LYS B 164 " pdb=" OD2 ASP B 168 " model vdw 2.333 3.120 nonbonded pdb=" OG1 THR B 465 " pdb=" OE2 GLU B 529 " model vdw 2.352 3.040 nonbonded pdb=" O PHE A1081 " pdb=" OH TYR A1173 " model vdw 2.355 3.040 nonbonded pdb=" ND1 HIS B 539 " pdb=" OE2 GLU B 543 " model vdw 2.369 3.120 ... (remaining 56371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.840 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.007 0.082 7705 Z= 0.279 Angle : 0.906 9.930 10454 Z= 0.505 Chirality : 0.058 0.367 1134 Planarity : 0.009 0.105 1337 Dihedral : 14.512 90.203 2866 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.25), residues: 914 helix: -1.97 (0.24), residues: 321 sheet: -1.68 (0.37), residues: 156 loop : -1.75 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1099 TYR 0.038 0.002 TYR B 94 PHE 0.025 0.003 PHE B 524 TRP 0.074 0.004 TRP B 131 HIS 0.010 0.002 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.28 ( 7705) covalent geometry : angle 0.90568 / 0.50 (10454) hydrogen bonds : bond 0.19677 / 13.87 ( 255) hydrogen bonds : angle 7.33986 / 5.29 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.214 Fit side-chains REVERT: B 686 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.7268 (mtm110) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0825 time to fit residues: 13.3415 Evaluate side-chains 100 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS B 324 GLN B 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135157 restraints weight = 8980.058| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.36 r_work: 0.3368 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7705 Z= 0.104 Angle : 0.506 6.589 10454 Z= 0.271 Chirality : 0.044 0.150 1134 Planarity : 0.006 0.072 1337 Dihedral : 4.639 21.609 1014 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.48 % Allowed : 6.75 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.27), residues: 914 helix: -0.42 (0.29), residues: 322 sheet: -1.58 (0.37), residues: 153 loop : -1.30 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1099 TYR 0.010 0.001 TYR B 569 PHE 0.010 0.001 PHE B 524 TRP 0.018 0.001 TRP B 656 HIS 0.005 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 7705) covalent geometry : angle 0.50646 / 0.27 (10454) hydrogen bonds : bond 0.04465 / 3.18 ( 255) hydrogen bonds : angle 5.02903 / 3.61 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 1112 LYS cc_start: 0.6889 (mmpt) cc_final: 0.6374 (tptt) REVERT: B 243 GLN cc_start: 0.7075 (tt0) cc_final: 0.6705 (tt0) REVERT: B 289 TYR cc_start: 0.7339 (p90) cc_final: 0.6899 (p90) REVERT: B 529 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 672 LYS cc_start: 0.8387 (tptt) cc_final: 0.8117 (tptt) REVERT: B 686 ARG cc_start: 0.7610 (mtp-110) cc_final: 0.7335 (mtm110) REVERT: B 718 THR cc_start: 0.8364 (m) cc_final: 0.7985 (p) REVERT: B 746 ASN cc_start: 0.7443 (t0) cc_final: 0.7128 (t0) outliers start: 4 outliers final: 2 residues processed: 115 average time/residue: 0.0882 time to fit residues: 13.4821 Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 652 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.0060 chunk 78 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1089 GLN A1148 ASN B 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132913 restraints weight = 8920.583| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.34 r_work: 0.3339 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7705 Z= 0.128 Angle : 0.516 6.529 10454 Z= 0.274 Chirality : 0.045 0.149 1134 Planarity : 0.005 0.059 1337 Dihedral : 4.380 22.032 1014 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.84 % Allowed : 8.92 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.28), residues: 914 helix: 0.12 (0.31), residues: 321 sheet: -1.50 (0.38), residues: 146 loop : -1.13 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1098 TYR 0.012 0.001 TYR B 660 PHE 0.014 0.001 PHE B 524 TRP 0.013 0.001 TRP B 85 HIS 0.005 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7705) covalent geometry : angle 0.51624 / 0.27 (10454) hydrogen bonds : bond 0.04736 / 3.36 ( 255) hydrogen bonds : angle 4.74357 / 3.39 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.290 Fit side-chains REVERT: B 243 GLN cc_start: 0.7232 (tt0) cc_final: 0.6924 (tt0) REVERT: B 260 GLU cc_start: 0.7492 (pm20) cc_final: 0.6991 (pm20) REVERT: B 289 TYR cc_start: 0.7553 (p90) cc_final: 0.6893 (p90) REVERT: B 686 ARG cc_start: 0.7604 (mtp-110) cc_final: 0.7388 (mtm110) REVERT: B 746 ASN cc_start: 0.7426 (t0) cc_final: 0.7087 (t0) outliers start: 7 outliers final: 5 residues processed: 118 average time/residue: 0.0880 time to fit residues: 13.9823 Evaluate side-chains 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 720 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.173764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133411 restraints weight = 9154.210| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.37 r_work: 0.3369 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7705 Z= 0.113 Angle : 0.489 6.559 10454 Z= 0.260 Chirality : 0.044 0.153 1134 Planarity : 0.005 0.052 1337 Dihedral : 4.169 21.233 1014 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.33 % Allowed : 10.84 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.93 (0.28), residues: 914 helix: 0.41 (0.31), residues: 321 sheet: -1.36 (0.39), residues: 147 loop : -1.05 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1098 TYR 0.010 0.001 TYR B 660 PHE 0.011 0.001 PHE B 524 TRP 0.013 0.001 TRP B 85 HIS 0.005 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 7705) covalent geometry : angle 0.48943 / 0.26 (10454) hydrogen bonds : bond 0.04173 / 2.97 ( 255) hydrogen bonds : angle 4.57095 / 3.27 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.291 Fit side-chains REVERT: B 636 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: B 733 TRP cc_start: 0.6064 (t-100) cc_final: 0.5792 (t-100) REVERT: B 746 ASN cc_start: 0.7471 (t0) cc_final: 0.7134 (t0) outliers start: 11 outliers final: 8 residues processed: 114 average time/residue: 0.0938 time to fit residues: 14.3902 Evaluate side-chains 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 728 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 0.0050 chunk 8 optimal weight: 2.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.172333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131919 restraints weight = 9073.703| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.35 r_work: 0.3431 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7705 Z= 0.145 Angle : 0.520 6.686 10454 Z= 0.277 Chirality : 0.045 0.152 1134 Planarity : 0.005 0.054 1337 Dihedral : 4.234 22.549 1014 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.69 % Allowed : 11.57 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.87 (0.28), residues: 914 helix: 0.49 (0.31), residues: 321 sheet: -1.35 (0.39), residues: 147 loop : -1.04 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1098 TYR 0.012 0.001 TYR B 660 PHE 0.014 0.002 PHE B 524 TRP 0.014 0.001 TRP B 85 HIS 0.005 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 7705) covalent geometry : angle 0.52039 / 0.28 (10454) hydrogen bonds : bond 0.04728 / 3.36 ( 255) hydrogen bonds : angle 4.63649 / 3.29 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.222 Fit side-chains REVERT: B 243 GLN cc_start: 0.7362 (tt0) cc_final: 0.7144 (tt0) REVERT: B 260 GLU cc_start: 0.7555 (pm20) cc_final: 0.7256 (pm20) REVERT: B 636 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: B 686 ARG cc_start: 0.7574 (mtm110) cc_final: 0.6672 (ptp90) REVERT: B 769 MET cc_start: 0.8597 (mmm) cc_final: 0.8353 (mmm) outliers start: 14 outliers final: 11 residues processed: 114 average time/residue: 0.0789 time to fit residues: 12.0561 Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain B residue 761 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 0.0020 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 20 optimal weight: 0.0470 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.178104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138683 restraints weight = 9078.968| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.32 r_work: 0.3492 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7705 Z= 0.087 Angle : 0.459 6.663 10454 Z= 0.242 Chirality : 0.043 0.151 1134 Planarity : 0.004 0.047 1337 Dihedral : 3.873 20.231 1014 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.33 % Allowed : 12.77 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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 (0.29), residues: 914 helix: 0.86 (0.31), residues: 322 sheet: -1.31 (0.40), residues: 145 loop : -0.91 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1098 TYR 0.010 0.001 TYR B 289 PHE 0.009 0.001 PHE B 707 TRP 0.012 0.001 TRP B 85 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 ( 7705) covalent geometry : angle 0.45885 / 0.24 (10454) hydrogen bonds : bond 0.03508 / 2.49 ( 255) hydrogen bonds : angle 4.37821 / 3.14 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: B 636 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: B 672 LYS cc_start: 0.8347 (tptt) cc_final: 0.8131 (tptt) REVERT: B 686 ARG cc_start: 0.7557 (mtm110) cc_final: 0.6668 (ptp90) REVERT: B 746 ASN cc_start: 0.7592 (t0) cc_final: 0.7244 (t0) outliers start: 11 outliers final: 8 residues processed: 119 average time/residue: 0.0632 time to fit residues: 10.3983 Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 720 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.0070 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 64 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138683 restraints weight = 9045.511| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.31 r_work: 0.3402 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7705 Z= 0.098 Angle : 0.478 7.062 10454 Z= 0.251 Chirality : 0.043 0.149 1134 Planarity : 0.004 0.047 1337 Dihedral : 3.783 20.526 1014 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.69 % Allowed : 13.61 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.39 (0.29), residues: 914 helix: 1.05 (0.31), residues: 322 sheet: -1.24 (0.41), residues: 145 loop : -0.83 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1098 TYR 0.009 0.001 TYR B 660 PHE 0.010 0.001 PHE B 21 TRP 0.015 0.001 TRP B 85 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 7705) covalent geometry : angle 0.47789 / 0.25 (10454) hydrogen bonds : bond 0.03657 / 2.60 ( 255) hydrogen bonds : angle 4.32325 / 3.10 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 202 GLN cc_start: 0.7139 (tt0) cc_final: 0.6806 (tt0) REVERT: B 636 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: B 672 LYS cc_start: 0.8337 (tptt) cc_final: 0.8121 (tptt) REVERT: B 686 ARG cc_start: 0.7542 (mtm110) cc_final: 0.6726 (ptp90) REVERT: B 746 ASN cc_start: 0.7560 (t0) cc_final: 0.7199 (t0) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.0745 time to fit residues: 12.2111 Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 720 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.174306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134255 restraints weight = 9099.708| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.33 r_work: 0.3487 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7705 Z= 0.102 Angle : 0.481 6.773 10454 Z= 0.253 Chirality : 0.043 0.148 1134 Planarity : 0.004 0.047 1337 Dihedral : 3.750 20.196 1014 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.69 % Allowed : 13.86 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.30 (0.29), residues: 914 helix: 1.16 (0.31), residues: 322 sheet: -1.26 (0.41), residues: 145 loop : -0.80 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1098 TYR 0.010 0.001 TYR B 289 PHE 0.009 0.001 PHE B 21 TRP 0.017 0.001 TRP B 85 HIS 0.003 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 7705) covalent geometry : angle 0.48125 / 0.25 (10454) hydrogen bonds : bond 0.03714 / 2.64 ( 255) hydrogen bonds : angle 4.30743 / 3.07 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 202 GLN cc_start: 0.7120 (tt0) cc_final: 0.6800 (tt0) REVERT: B 289 TYR cc_start: 0.7851 (p90) cc_final: 0.7460 (p90) REVERT: B 636 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: B 672 LYS cc_start: 0.8324 (tptt) cc_final: 0.8105 (tptt) REVERT: B 686 ARG cc_start: 0.7559 (mtm110) cc_final: 0.6779 (ptp90) REVERT: B 746 ASN cc_start: 0.7581 (t0) cc_final: 0.7214 (t0) REVERT: B 769 MET cc_start: 0.8593 (mmm) cc_final: 0.8325 (mmm) outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 0.0783 time to fit residues: 12.7488 Evaluate side-chains 120 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 720 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134578 restraints weight = 8948.478| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.32 r_work: 0.3471 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7705 Z= 0.115 Angle : 0.500 6.884 10454 Z= 0.262 Chirality : 0.044 0.148 1134 Planarity : 0.005 0.047 1337 Dihedral : 3.822 21.002 1014 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.57 % Allowed : 14.46 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.27 (0.29), residues: 914 helix: 1.18 (0.31), residues: 322 sheet: -1.19 (0.41), residues: 140 loop : -0.80 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1098 TYR 0.018 0.001 TYR B 608 PHE 0.010 0.001 PHE B 393 TRP 0.019 0.001 TRP B 85 HIS 0.004 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7705) covalent geometry : angle 0.50032 / 0.26 (10454) hydrogen bonds : bond 0.03976 / 2.82 ( 255) hydrogen bonds : angle 4.35804 / 3.10 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: B 202 GLN cc_start: 0.7121 (tt0) cc_final: 0.6829 (tt0) REVERT: B 636 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: B 672 LYS cc_start: 0.8373 (tptt) cc_final: 0.8151 (tptt) REVERT: B 686 ARG cc_start: 0.7541 (mtm110) cc_final: 0.6795 (ptp90) REVERT: B 769 MET cc_start: 0.8567 (mmm) cc_final: 0.8321 (mmm) outliers start: 13 outliers final: 11 residues processed: 117 average time/residue: 0.0910 time to fit residues: 14.8578 Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 720 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132735 restraints weight = 8982.262| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.32 r_work: 0.3323 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7705 Z= 0.140 Angle : 0.534 6.896 10454 Z= 0.280 Chirality : 0.045 0.150 1134 Planarity : 0.005 0.047 1337 Dihedral : 4.004 21.718 1014 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.69 % Allowed : 14.82 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.37 (0.29), residues: 914 helix: 1.04 (0.31), residues: 323 sheet: -1.24 (0.41), residues: 139 loop : -0.82 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1098 TYR 0.017 0.001 TYR B 608 PHE 0.012 0.001 PHE B 393 TRP 0.021 0.001 TRP B 85 HIS 0.005 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 7705) covalent geometry : angle 0.53398 / 0.28 (10454) hydrogen bonds : bond 0.04445 / 3.16 ( 255) hydrogen bonds : angle 4.49586 / 3.19 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 202 GLN cc_start: 0.7104 (tt0) cc_final: 0.6786 (tt0) REVERT: B 270 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5226 (tp30) REVERT: B 636 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: B 672 LYS cc_start: 0.8376 (tptt) cc_final: 0.8097 (tptt) REVERT: B 686 ARG cc_start: 0.7518 (mtm110) cc_final: 0.6746 (ptp90) REVERT: B 769 MET cc_start: 0.8630 (mmm) cc_final: 0.8392 (mmm) outliers start: 14 outliers final: 10 residues processed: 116 average time/residue: 0.0902 time to fit residues: 14.1036 Evaluate side-chains 115 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 652 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 12 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136048 restraints weight = 8981.263| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.32 r_work: 0.3354 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7705 Z= 0.096 Angle : 0.486 7.168 10454 Z= 0.253 Chirality : 0.043 0.149 1134 Planarity : 0.004 0.047 1337 Dihedral : 3.776 20.442 1014 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.57 % Allowed : 14.82 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.16 (0.29), residues: 914 helix: 1.34 (0.31), residues: 322 sheet: -1.21 (0.41), residues: 140 loop : -0.77 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1098 TYR 0.017 0.001 TYR B 608 PHE 0.009 0.001 PHE B 21 TRP 0.015 0.001 TRP B 85 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 7705) covalent geometry : angle 0.48569 / 0.25 (10454) hydrogen bonds : bond 0.03518 / 2.49 ( 255) hydrogen bonds : angle 4.26069 / 3.05 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.07 seconds wall clock time: 31 minutes 57.23 seconds (1917.23 seconds total)