Starting phenix.real_space_refine on Tue Aug 4 22:34:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j14_61067/08_2026/9j14_61067.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j14_61067/08_2026/9j14_61067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j14_61067/08_2026/9j14_61067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j14_61067/08_2026/9j14_61067.map" model { file = "/net/cci-nas-00/data/ceres_data/9j14_61067/08_2026/9j14_61067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j14_61067/08_2026/9j14_61067.cif" } resolution = 3.49 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= 0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 4686 2.51 5 N 1160 2.21 5 O 1318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 7218 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3593 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain: "B" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3593 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.25 Number of scatterers: 7218 At special positions: 0 Unit cell: (73.7, 115.5, 88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1318 8.00 N 1160 7.00 C 4686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 242 " distance=2.02 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: 0.58 Conformation dependent library (CDL) restraints added in 364.5 milliseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 66.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.506A pdb=" N HIS A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 39 through 55 Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.568A pdb=" N VAL A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.532A pdb=" N CYS A 77 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.250A pdb=" N CYS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 95 through 127 removed outlier: 3.693A pdb=" N VAL A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 removed outlier: 4.104A pdb=" N TYR A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.511A pdb=" N MET A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 190 through 209 removed outlier: 3.658A pdb=" N ARG A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.542A pdb=" N TRP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 334 through 360 removed outlier: 4.101A pdb=" N GLY A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 406 removed outlier: 3.872A pdb=" N LEU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 removed outlier: 3.522A pdb=" N ALA A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.954A pdb=" N ASN A 432 " --> pdb=" O PRO A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 Processing helix chain 'A' and resid 438 through 451 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.551A pdb=" N ILE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 3.884A pdb=" N THR A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix Processing helix chain 'A' and resid 479 through 495 removed outlier: 4.046A pdb=" N GLY A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 removed outlier: 3.526A pdb=" N LEU B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 39 through 55 Processing helix chain 'B' and resid 56 through 67 removed outlier: 3.569A pdb=" N VAL B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.531A pdb=" N CYS B 77 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.251A pdb=" N CYS B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 91' Processing helix chain 'B' and resid 95 through 127 removed outlier: 3.693A pdb=" N VAL B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 removed outlier: 4.104A pdb=" N TYR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 179 removed outlier: 3.511A pdb=" N MET B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 190 through 209 removed outlier: 3.658A pdb=" N ARG B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.542A pdb=" N TRP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 334 through 360 removed outlier: 4.101A pdb=" N GLY B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 358 " --> pdb=" O TYR B 354 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 399 through 406 removed outlier: 3.873A pdb=" N LEU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 removed outlier: 3.522A pdb=" N ALA B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.954A pdb=" N ASN B 432 " --> pdb=" O PRO B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 Processing helix chain 'B' and resid 438 through 451 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.552A pdb=" N ILE B 456 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 478 removed outlier: 3.885A pdb=" N THR B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Proline residue: B 475 - end of helix Processing helix chain 'B' and resid 479 through 495 removed outlier: 4.045A pdb=" N GLY B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.131A pdb=" N ALA A 135 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 394 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135 removed outlier: 4.133A pdb=" N ALA B 135 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 394 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 221 380 hydrogen bonds defined for protein. 1122 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: 1.10 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1193 1.33 - 1.45: 1917 1.45 - 1.57: 4164 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 7366 Sorted by residual: bond pdb=" C4 ZEA A 601 " pdb=" C5 ZEA A 601 " ideal model delta sigma weight residual 1.387 1.456 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 ZEA B 601 " pdb=" C5 ZEA B 601 " ideal model delta sigma weight residual 1.387 1.455 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C5 ZEA B 601 " pdb=" C6 ZEA B 601 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C5 ZEA A 601 " pdb=" C6 ZEA A 601 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C PHE B 396 " pdb=" O PHE B 396 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.21e-02 6.83e+03 6.89e+00 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 9893 3.11 - 6.21: 89 6.21 - 9.32: 20 9.32 - 12.43: 2 12.43 - 15.54: 2 Bond angle restraints: 10006 Sorted by residual: angle pdb=" N GLU A 234 " pdb=" CA GLU A 234 " pdb=" C GLU A 234 " ideal model delta sigma weight residual 109.59 94.05 15.54 1.47e+00 4.63e-01 1.12e+02 angle pdb=" N GLU B 234 " pdb=" CA GLU B 234 " pdb=" C GLU B 234 " ideal model delta sigma weight residual 109.59 94.08 15.51 1.47e+00 4.63e-01 1.11e+02 angle pdb=" N THR B 235 " pdb=" CA THR B 235 " pdb=" CB THR B 235 " ideal model delta sigma weight residual 110.77 122.89 -12.12 1.63e+00 3.76e-01 5.53e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" CB THR A 235 " ideal model delta sigma weight residual 110.77 122.81 -12.04 1.63e+00 3.76e-01 5.46e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" C THR A 235 " ideal model delta sigma weight residual 108.26 99.58 8.68 1.66e+00 3.63e-01 2.74e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3681 17.54 - 35.09: 479 35.09 - 52.63: 106 52.63 - 70.18: 12 70.18 - 87.72: 8 Dihedral angle restraints: 4286 sinusoidal: 1558 harmonic: 2728 Sorted by residual: dihedral pdb=" CA ILE A 144 " pdb=" C ILE A 144 " pdb=" N ALA A 145 " pdb=" CA ALA A 145 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ILE B 144 " pdb=" C ILE B 144 " pdb=" N ALA B 145 " pdb=" CA ALA B 145 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA PHE B 420 " pdb=" C PHE B 420 " pdb=" N LEU B 421 " pdb=" CA LEU B 421 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 858 0.043 - 0.086: 274 0.086 - 0.129: 59 0.129 - 0.172: 9 0.172 - 0.214: 4 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CA GLU B 234 " pdb=" N GLU B 234 " pdb=" C GLU B 234 " pdb=" CB GLU B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 234 " pdb=" N GLU A 234 " pdb=" C GLU A 234 " pdb=" CB GLU A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA THR A 71 " pdb=" N THR A 71 " pdb=" C THR A 71 " pdb=" CB THR A 71 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1201 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 439 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 440 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 439 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 440 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 144 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ILE A 144 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 144 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 145 " 0.009 2.00e-02 2.50e+03 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 11 2.32 - 2.96: 3592 2.96 - 3.61: 10586 3.61 - 4.25: 14875 4.25 - 4.90: 26011 Nonbonded interactions: 55075 Sorted by model distance: nonbonded pdb=" CE MET A 450 " pdb=" CH2 TRP B 458 " model vdw 1.674 3.760 nonbonded pdb=" CH2 TRP A 458 " pdb=" CE MET B 450 " model vdw 1.683 3.760 nonbonded pdb=" CE MET A 450 " pdb=" CZ3 TRP B 458 " model vdw 2.133 3.760 nonbonded pdb=" CZ3 TRP A 458 " pdb=" CE MET B 450 " model vdw 2.143 3.760 nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.251 3.040 ... (remaining 55070 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 7372 Z= 0.192 Angle : 0.812 15.537 10018 Z= 0.452 Chirality : 0.044 0.214 1204 Planarity : 0.004 0.040 1232 Dihedral : 16.002 87.724 2540 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.26 % Allowed : 27.02 % Favored : 72.72 % 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: -0.73 (0.27), residues: 966 helix: 0.85 (0.23), residues: 572 sheet: None (None), residues: 0 loop : -2.62 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 104 TYR 0.008 0.001 TYR B 143 PHE 0.024 0.001 PHE B 295 TRP 0.003 0.001 TRP A 286 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 ( 7366) covalent geometry : angle 0.81043 / 0.45 (10006) SS BOND : bond 0.00378 / 0.17 ( 6) SS BOND : angle 1.71785 / 0.91 ( 12) hydrogen bonds : bond 0.16226 / 10.60 ( 380) hydrogen bonds : angle 5.33571 / 3.90 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.259 Fit side-chains REVERT: A 16 LYS cc_start: 0.8467 (tttm) cc_final: 0.7905 (mmmt) REVERT: A 152 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8016 (mtt-85) REVERT: A 184 LYS cc_start: 0.6743 (ttpt) cc_final: 0.6043 (tmtt) REVERT: A 331 LYS cc_start: 0.7062 (mtpp) cc_final: 0.6861 (ptpp) REVERT: A 346 LEU cc_start: 0.8841 (tp) cc_final: 0.8631 (tp) REVERT: A 371 GLU cc_start: 0.7323 (tp30) cc_final: 0.6759 (pt0) REVERT: A 435 ARG cc_start: 0.8291 (ttp80) cc_final: 0.8026 (ptt-90) REVERT: A 448 MET cc_start: 0.7979 (mmm) cc_final: 0.7760 (mmp) REVERT: B 16 LYS cc_start: 0.8462 (tttm) cc_final: 0.7906 (mmmt) REVERT: B 152 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8042 (mtt-85) REVERT: B 184 LYS cc_start: 0.6693 (ttpt) cc_final: 0.5991 (tmtt) REVERT: B 331 LYS cc_start: 0.7012 (mtpp) cc_final: 0.6810 (ptpp) REVERT: B 346 LEU cc_start: 0.8850 (tp) cc_final: 0.8637 (tp) REVERT: B 371 GLU cc_start: 0.7315 (tp30) cc_final: 0.6765 (pt0) REVERT: B 435 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8132 (ptt-90) REVERT: B 448 MET cc_start: 0.8020 (mmm) cc_final: 0.7813 (mmp) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.0865 time to fit residues: 18.6896 Evaluate side-chains 123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 211 GLN B 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.149345 restraints weight = 9340.596| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.48 r_work: 0.3494 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7372 Z= 0.120 Angle : 0.596 6.451 10018 Z= 0.313 Chirality : 0.042 0.163 1204 Planarity : 0.004 0.042 1232 Dihedral : 4.823 29.246 1030 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 6.01 % Allowed : 22.19 % Favored : 71.80 % 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: -0.45 (0.27), residues: 966 helix: 1.12 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.54 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.011 0.001 TYR A 143 PHE 0.007 0.001 PHE B 51 TRP 0.008 0.001 TRP B 458 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7366) covalent geometry : angle 0.59265 / 0.31 (10006) SS BOND : bond 0.00089 / 0.04 ( 6) SS BOND : angle 2.00199 / 1.05 ( 12) hydrogen bonds : bond 0.03740 / 2.48 ( 380) hydrogen bonds : angle 4.07722 / 2.95 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8365 (tttm) cc_final: 0.7882 (mmmt) REVERT: A 33 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7246 (mt) REVERT: A 104 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.6914 (mtm180) REVERT: A 124 MET cc_start: 0.8622 (tpt) cc_final: 0.8080 (tpp) REVERT: A 152 ARG cc_start: 0.8733 (mtt180) cc_final: 0.8339 (mtt-85) REVERT: A 171 CYS cc_start: 0.8454 (m) cc_final: 0.8003 (t) REVERT: A 184 LYS cc_start: 0.6909 (ttpt) cc_final: 0.5820 (tmtt) REVERT: A 234 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7049 (tp30) REVERT: A 330 ARG cc_start: 0.4776 (mpt180) cc_final: 0.3389 (tmm160) REVERT: A 356 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6276 (tpt) REVERT: A 371 GLU cc_start: 0.7016 (tp30) cc_final: 0.6669 (pt0) REVERT: A 435 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8254 (ptt-90) REVERT: A 448 MET cc_start: 0.8611 (mmm) cc_final: 0.8142 (mmp) REVERT: A 450 MET cc_start: 0.8833 (ttp) cc_final: 0.8615 (tmm) REVERT: A 460 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: B 16 LYS cc_start: 0.8387 (tttm) cc_final: 0.7893 (mmmt) REVERT: B 33 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7270 (mt) REVERT: B 104 ARG cc_start: 0.7315 (ttp-110) cc_final: 0.6901 (mtm180) REVERT: B 124 MET cc_start: 0.8624 (tpt) cc_final: 0.8077 (tpp) REVERT: B 152 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8274 (mtt-85) REVERT: B 171 CYS cc_start: 0.8472 (m) cc_final: 0.8007 (t) REVERT: B 184 LYS cc_start: 0.6904 (ttpt) cc_final: 0.5801 (tmtt) REVERT: B 226 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8684 (mt) REVERT: B 234 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7053 (tp30) REVERT: B 330 ARG cc_start: 0.4779 (mpt180) cc_final: 0.3363 (tmm160) REVERT: B 356 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6197 (tpt) REVERT: B 371 GLU cc_start: 0.7028 (tp30) cc_final: 0.6775 (pt0) REVERT: B 448 MET cc_start: 0.8597 (mmm) cc_final: 0.8122 (mmp) REVERT: B 450 MET cc_start: 0.8792 (ttp) cc_final: 0.8584 (tmm) REVERT: B 460 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7785 (mt-10) outliers start: 46 outliers final: 18 residues processed: 178 average time/residue: 0.0991 time to fit residues: 22.9524 Evaluate side-chains 147 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 86 optimal weight: 0.0170 chunk 83 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.0030 chunk 54 optimal weight: 0.0070 overall best weight: 0.3648 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.182574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151053 restraints weight = 9238.385| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.43 r_work: 0.3347 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7372 Z= 0.105 Angle : 0.565 6.009 10018 Z= 0.294 Chirality : 0.041 0.196 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.563 30.271 1030 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 5.35 % Allowed : 21.80 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.20 (0.27), residues: 966 helix: 1.33 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.44 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.008 0.001 TYR B 143 PHE 0.009 0.001 PHE B 368 TRP 0.003 0.001 TRP A 253 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 7366) covalent geometry : angle 0.56263 / 0.29 (10006) SS BOND : bond 0.00166 / 0.08 ( 6) SS BOND : angle 1.72536 / 0.91 ( 12) hydrogen bonds : bond 0.03124 / 2.08 ( 380) hydrogen bonds : angle 3.98802 / 2.88 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.254 Fit side-chains REVERT: A 16 LYS cc_start: 0.8341 (tttm) cc_final: 0.7790 (mmmt) REVERT: A 104 ARG cc_start: 0.7461 (ttp-110) cc_final: 0.7015 (mtm180) REVERT: A 124 MET cc_start: 0.8670 (tpt) cc_final: 0.8133 (tpp) REVERT: A 152 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8368 (mtt-85) REVERT: A 171 CYS cc_start: 0.8635 (m) cc_final: 0.8154 (t) REVERT: A 179 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7405 (pp) REVERT: A 184 LYS cc_start: 0.6791 (ttpt) cc_final: 0.5632 (tmtt) REVERT: A 234 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7188 (tp30) REVERT: A 330 ARG cc_start: 0.4591 (mpt180) cc_final: 0.3110 (ttp-170) REVERT: A 450 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8860 (tmm) REVERT: B 16 LYS cc_start: 0.8332 (tttm) cc_final: 0.7790 (mmmt) REVERT: B 104 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.6998 (mtm180) REVERT: B 124 MET cc_start: 0.8669 (tpt) cc_final: 0.8120 (tpp) REVERT: B 152 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8364 (mtt-85) REVERT: B 171 CYS cc_start: 0.8618 (m) cc_final: 0.8126 (t) REVERT: B 179 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7382 (pp) REVERT: B 234 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7215 (tp30) REVERT: B 330 ARG cc_start: 0.4488 (mpt180) cc_final: 0.3106 (ttp-170) REVERT: B 356 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5826 (tpt) REVERT: B 448 MET cc_start: 0.8759 (mmm) cc_final: 0.8546 (mmm) REVERT: B 450 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8858 (tmm) outliers start: 41 outliers final: 12 residues processed: 154 average time/residue: 0.0854 time to fit residues: 17.7735 Evaluate side-chains 130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 0.0040 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 0.0370 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151100 restraints weight = 9470.023| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.48 r_work: 0.3551 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7372 Z= 0.107 Angle : 0.566 5.820 10018 Z= 0.296 Chirality : 0.041 0.233 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.514 29.855 1030 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 5.87 % Allowed : 21.15 % Favored : 72.98 % 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: -0.15 (0.27), residues: 966 helix: 1.40 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.47 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.009 0.001 TYR A 343 PHE 0.010 0.001 PHE B 368 TRP 0.003 0.001 TRP B 253 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7366) covalent geometry : angle 0.56200 / 0.29 (10006) SS BOND : bond 0.00509 / 0.25 ( 6) SS BOND : angle 2.06344 / 1.02 ( 12) hydrogen bonds : bond 0.02896 / 1.91 ( 380) hydrogen bonds : angle 3.94828 / 2.86 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.270 Fit side-chains REVERT: A 16 LYS cc_start: 0.8279 (tttm) cc_final: 0.7854 (mmmt) REVERT: A 76 ASP cc_start: 0.8124 (m-30) cc_final: 0.7882 (t0) REVERT: A 124 MET cc_start: 0.8563 (tpt) cc_final: 0.8037 (tpp) REVERT: A 152 ARG cc_start: 0.8688 (mtt180) cc_final: 0.8227 (mtt-85) REVERT: A 171 CYS cc_start: 0.8467 (m) cc_final: 0.8036 (t) REVERT: A 179 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7378 (pp) REVERT: A 330 ARG cc_start: 0.4411 (mpt180) cc_final: 0.3278 (ttp-170) REVERT: A 448 MET cc_start: 0.8471 (mmm) cc_final: 0.8112 (mmp) REVERT: A 450 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8624 (tmm) REVERT: B 16 LYS cc_start: 0.8283 (tttm) cc_final: 0.7864 (mmmt) REVERT: B 33 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7200 (mt) REVERT: B 76 ASP cc_start: 0.8134 (m-30) cc_final: 0.7896 (t0) REVERT: B 124 MET cc_start: 0.8553 (tpt) cc_final: 0.8028 (tpp) REVERT: B 152 ARG cc_start: 0.8660 (mtt180) cc_final: 0.8198 (mtt-85) REVERT: B 171 CYS cc_start: 0.8482 (m) cc_final: 0.8039 (t) REVERT: B 179 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7361 (pp) REVERT: B 330 ARG cc_start: 0.4345 (mpt180) cc_final: 0.3246 (ttp-170) REVERT: B 450 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8628 (tmm) outliers start: 45 outliers final: 24 residues processed: 149 average time/residue: 0.0840 time to fit residues: 16.8808 Evaluate side-chains 138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.177598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145987 restraints weight = 9502.480| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.46 r_work: 0.3485 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7372 Z= 0.121 Angle : 0.587 6.131 10018 Z= 0.308 Chirality : 0.042 0.251 1204 Planarity : 0.004 0.042 1232 Dihedral : 4.618 30.191 1030 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 6.27 % Allowed : 20.63 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.07 (0.28), residues: 966 helix: 1.53 (0.23), residues: 566 sheet: None (None), residues: 0 loop : -2.55 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.010 0.001 TYR A 343 PHE 0.008 0.001 PHE B 368 TRP 0.003 0.001 TRP B 286 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7366) covalent geometry : angle 0.58225 / 0.31 (10006) SS BOND : bond 0.00226 / 0.11 ( 6) SS BOND : angle 2.15084 / 1.09 ( 12) hydrogen bonds : bond 0.03495 / 2.32 ( 380) hydrogen bonds : angle 3.98821 / 2.89 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.282 Fit side-chains REVERT: A 16 LYS cc_start: 0.8372 (tttm) cc_final: 0.7879 (mmmt) REVERT: A 33 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7324 (mt) REVERT: A 124 MET cc_start: 0.8665 (tpt) cc_final: 0.8128 (tpp) REVERT: A 179 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7524 (pp) REVERT: A 182 ARG cc_start: 0.7480 (ttp80) cc_final: 0.7257 (ttp80) REVERT: A 184 LYS cc_start: 0.6857 (ttpt) cc_final: 0.5674 (tmtt) REVERT: A 330 ARG cc_start: 0.4614 (mpt180) cc_final: 0.3184 (ttp-170) REVERT: A 448 MET cc_start: 0.8639 (mmm) cc_final: 0.8249 (mmp) REVERT: A 450 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8366 (tmm) REVERT: B 16 LYS cc_start: 0.8373 (tttm) cc_final: 0.7883 (mmmt) REVERT: B 33 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 124 MET cc_start: 0.8636 (tpt) cc_final: 0.8104 (tpp) REVERT: B 152 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8331 (mtt-85) REVERT: B 179 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7512 (pp) REVERT: B 182 ARG cc_start: 0.7465 (ttp80) cc_final: 0.7209 (ttp80) REVERT: B 330 ARG cc_start: 0.4553 (mpt180) cc_final: 0.3127 (ttp-170) REVERT: B 448 MET cc_start: 0.8696 (mmm) cc_final: 0.8311 (mmp) REVERT: B 450 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8381 (tmm) outliers start: 48 outliers final: 32 residues processed: 161 average time/residue: 0.0651 time to fit residues: 14.9419 Evaluate side-chains 148 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 9 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.2908 > 50:) chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.173474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141837 restraints weight = 9501.749| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.45 r_work: 0.3393 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7372 Z= 0.157 Angle : 0.625 6.327 10018 Z= 0.330 Chirality : 0.043 0.247 1204 Planarity : 0.004 0.042 1232 Dihedral : 4.901 29.969 1030 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 5.22 % Allowed : 22.19 % Favored : 72.58 % 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: -0.21 (0.28), residues: 966 helix: 1.40 (0.23), residues: 568 sheet: None (None), residues: 0 loop : -2.59 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.011 0.001 TYR B 343 PHE 0.010 0.001 PHE B 207 TRP 0.005 0.001 TRP B 286 HIS 0.002 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 7366) covalent geometry : angle 0.62110 / 0.33 (10006) SS BOND : bond 0.00441 / 0.20 ( 6) SS BOND : angle 2.20266 / 1.12 ( 12) hydrogen bonds : bond 0.04155 / 2.76 ( 380) hydrogen bonds : angle 4.15556 / 3.02 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.171 Fit side-chains REVERT: A 16 LYS cc_start: 0.8338 (tttm) cc_final: 0.7890 (mmmt) REVERT: A 124 MET cc_start: 0.8672 (tpt) cc_final: 0.8172 (tpp) REVERT: A 179 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7559 (pp) REVERT: A 184 LYS cc_start: 0.6944 (ttpt) cc_final: 0.5752 (tmtt) REVERT: A 324 ILE cc_start: 0.8296 (mm) cc_final: 0.8093 (mm) REVERT: A 328 GLU cc_start: 0.7942 (tp30) cc_final: 0.7443 (tp30) REVERT: A 330 ARG cc_start: 0.4612 (mpt180) cc_final: 0.3313 (ttp-170) REVERT: A 448 MET cc_start: 0.8509 (mmm) cc_final: 0.8115 (mmp) REVERT: A 450 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8681 (ttt) REVERT: B 16 LYS cc_start: 0.8340 (tttm) cc_final: 0.7901 (mmmt) REVERT: B 33 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7750 (mt) REVERT: B 124 MET cc_start: 0.8632 (tpt) cc_final: 0.8117 (tpp) REVERT: B 179 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7526 (pp) REVERT: B 184 LYS cc_start: 0.6934 (ttpt) cc_final: 0.5751 (tmtt) REVERT: B 328 GLU cc_start: 0.7898 (tp30) cc_final: 0.7295 (tp30) REVERT: B 330 ARG cc_start: 0.4540 (mpt180) cc_final: 0.3230 (ttp-170) REVERT: B 448 MET cc_start: 0.8513 (mmm) cc_final: 0.8125 (mmp) REVERT: B 450 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8673 (ttt) outliers start: 40 outliers final: 29 residues processed: 143 average time/residue: 0.0718 time to fit residues: 14.4817 Evaluate side-chains 143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 0.0010 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.177061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.145272 restraints weight = 9471.045| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.47 r_work: 0.3449 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7372 Z= 0.116 Angle : 0.587 6.457 10018 Z= 0.310 Chirality : 0.041 0.241 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.702 30.327 1030 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 4.83 % Allowed : 22.45 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.19 (0.28), residues: 966 helix: 1.41 (0.23), residues: 568 sheet: None (None), residues: 0 loop : -2.59 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.009 0.001 TYR A 343 PHE 0.008 0.001 PHE B 368 TRP 0.005 0.001 TRP A 253 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7366) covalent geometry : angle 0.58426 / 0.31 (10006) SS BOND : bond 0.00338 / 0.15 ( 6) SS BOND : angle 1.86817 / 0.96 ( 12) hydrogen bonds : bond 0.03255 / 2.17 ( 380) hydrogen bonds : angle 4.07430 / 2.97 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.170 Fit side-chains REVERT: A 16 LYS cc_start: 0.8312 (tttm) cc_final: 0.7878 (mmmt) REVERT: A 124 MET cc_start: 0.8617 (tpt) cc_final: 0.8105 (tpp) REVERT: A 152 ARG cc_start: 0.8659 (mtt180) cc_final: 0.8238 (mtt-85) REVERT: A 179 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7498 (pp) REVERT: A 184 LYS cc_start: 0.6902 (ttpt) cc_final: 0.5739 (tmtt) REVERT: A 328 GLU cc_start: 0.7972 (tp30) cc_final: 0.7481 (tp30) REVERT: A 330 ARG cc_start: 0.4384 (mpt180) cc_final: 0.3253 (ttp-170) REVERT: A 448 MET cc_start: 0.8517 (mmm) cc_final: 0.8089 (mmp) REVERT: A 450 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8239 (tmm) REVERT: B 16 LYS cc_start: 0.8310 (tttm) cc_final: 0.7885 (mmmt) REVERT: B 33 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7485 (mt) REVERT: B 124 MET cc_start: 0.8577 (tpt) cc_final: 0.8036 (tpp) REVERT: B 152 ARG cc_start: 0.8645 (mtt180) cc_final: 0.8223 (mtt-85) REVERT: B 179 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7477 (pp) REVERT: B 184 LYS cc_start: 0.6902 (ttpt) cc_final: 0.5742 (tmtt) REVERT: B 328 GLU cc_start: 0.7904 (tp30) cc_final: 0.7255 (tp30) REVERT: B 330 ARG cc_start: 0.4380 (mpt180) cc_final: 0.3224 (ttp-170) REVERT: B 448 MET cc_start: 0.8453 (mmm) cc_final: 0.8058 (mmp) REVERT: B 450 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8249 (tmm) outliers start: 37 outliers final: 22 residues processed: 135 average time/residue: 0.0876 time to fit residues: 15.7755 Evaluate side-chains 130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.176129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144321 restraints weight = 9552.487| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.47 r_work: 0.3430 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7372 Z= 0.131 Angle : 0.611 6.424 10018 Z= 0.323 Chirality : 0.042 0.227 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.720 30.145 1030 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 4.31 % Allowed : 21.28 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.21 (0.28), residues: 966 helix: 1.42 (0.23), residues: 566 sheet: None (None), residues: 0 loop : -2.61 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 182 TYR 0.026 0.001 TYR B 375 PHE 0.008 0.001 PHE B 51 TRP 0.003 0.001 TRP A 253 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7366) covalent geometry : angle 0.60820 / 0.32 (10006) SS BOND : bond 0.00277 / 0.13 ( 6) SS BOND : angle 1.69425 / 0.86 ( 12) hydrogen bonds : bond 0.03532 / 2.35 ( 380) hydrogen bonds : angle 4.07728 / 2.97 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.247 Fit side-chains REVERT: A 16 LYS cc_start: 0.8308 (tttm) cc_final: 0.7878 (mmmt) REVERT: A 124 MET cc_start: 0.8591 (tpt) cc_final: 0.8049 (tpp) REVERT: A 152 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8253 (mtt-85) REVERT: A 179 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7501 (pp) REVERT: A 324 ILE cc_start: 0.8154 (mm) cc_final: 0.7867 (mm) REVERT: A 328 GLU cc_start: 0.7998 (tp30) cc_final: 0.7653 (mt-10) REVERT: A 330 ARG cc_start: 0.4414 (mpt180) cc_final: 0.3302 (ttp-170) REVERT: A 448 MET cc_start: 0.8540 (mmm) cc_final: 0.8116 (mmp) REVERT: A 450 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8232 (tmm) REVERT: B 16 LYS cc_start: 0.8305 (tttm) cc_final: 0.7877 (mmmt) REVERT: B 33 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7468 (mt) REVERT: B 124 MET cc_start: 0.8566 (tpt) cc_final: 0.8013 (tpp) REVERT: B 152 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8237 (mtt-85) REVERT: B 179 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7472 (pp) REVERT: B 328 GLU cc_start: 0.7944 (tp30) cc_final: 0.7277 (tp30) REVERT: B 330 ARG cc_start: 0.4393 (mpt180) cc_final: 0.3244 (ttp-170) REVERT: B 448 MET cc_start: 0.8506 (mmm) cc_final: 0.8102 (mmp) REVERT: B 450 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8230 (tmm) outliers start: 33 outliers final: 22 residues processed: 130 average time/residue: 0.0705 time to fit residues: 12.7699 Evaluate side-chains 126 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 ASN B 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.178403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146637 restraints weight = 9333.547| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.45 r_work: 0.3359 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7372 Z= 0.115 Angle : 0.594 8.243 10018 Z= 0.313 Chirality : 0.041 0.218 1204 Planarity : 0.005 0.072 1232 Dihedral : 4.592 30.162 1030 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 3.79 % Allowed : 21.93 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.19 (0.28), residues: 966 helix: 1.36 (0.23), residues: 576 sheet: None (None), residues: 0 loop : -2.57 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 288 TYR 0.009 0.001 TYR A 343 PHE 0.008 0.001 PHE B 368 TRP 0.005 0.001 TRP A 253 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7366) covalent geometry : angle 0.59244 / 0.31 (10006) SS BOND : bond 0.00261 / 0.12 ( 6) SS BOND : angle 1.52269 / 0.78 ( 12) hydrogen bonds : bond 0.03098 / 2.06 ( 380) hydrogen bonds : angle 4.01107 / 2.91 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8307 (tttm) cc_final: 0.7822 (mmmt) REVERT: A 124 MET cc_start: 0.8659 (tpt) cc_final: 0.8074 (tpp) REVERT: A 152 ARG cc_start: 0.8714 (mtt180) cc_final: 0.8290 (mtt-85) REVERT: A 179 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7700 (pp) REVERT: A 218 LEU cc_start: 0.9187 (tp) cc_final: 0.8887 (tp) REVERT: A 328 GLU cc_start: 0.8185 (tp30) cc_final: 0.7708 (mt-10) REVERT: A 330 ARG cc_start: 0.4486 (mpt180) cc_final: 0.3207 (ttp-170) REVERT: A 448 MET cc_start: 0.8608 (mmm) cc_final: 0.8187 (mmp) REVERT: A 450 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8308 (tmm) REVERT: B 16 LYS cc_start: 0.8315 (tttm) cc_final: 0.7834 (mmmt) REVERT: B 33 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7220 (mt) REVERT: B 124 MET cc_start: 0.8664 (tpt) cc_final: 0.8084 (tpp) REVERT: B 152 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8290 (mtt-85) REVERT: B 179 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7541 (pp) REVERT: B 182 ARG cc_start: 0.6639 (ttp80) cc_final: 0.6372 (ttp-110) REVERT: B 328 GLU cc_start: 0.8147 (tp30) cc_final: 0.7499 (tp30) REVERT: B 330 ARG cc_start: 0.4334 (mpt180) cc_final: 0.3081 (ttp-170) REVERT: B 448 MET cc_start: 0.8638 (mmm) cc_final: 0.8236 (mmp) REVERT: B 450 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8867 (tmm) outliers start: 29 outliers final: 21 residues processed: 128 average time/residue: 0.0770 time to fit residues: 13.6942 Evaluate side-chains 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.175652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143711 restraints weight = 9402.941| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.47 r_work: 0.3245 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7372 Z= 0.130 Angle : 0.594 9.517 10018 Z= 0.311 Chirality : 0.041 0.240 1204 Planarity : 0.005 0.088 1232 Dihedral : 4.685 30.287 1030 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 3.66 % Allowed : 22.58 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.20 (0.28), residues: 966 helix: 1.43 (0.23), residues: 566 sheet: None (None), residues: 0 loop : -2.60 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.009 0.001 TYR A 343 PHE 0.009 0.001 PHE B 368 TRP 0.003 0.001 TRP A 253 HIS 0.002 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7366) covalent geometry : angle 0.59199 / 0.31 (10006) SS BOND : bond 0.00235 / 0.11 ( 6) SS BOND : angle 1.52403 / 0.77 ( 12) hydrogen bonds : bond 0.03576 / 2.38 ( 380) hydrogen bonds : angle 4.03425 / 2.93 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8329 (tttm) cc_final: 0.7879 (mmmt) REVERT: A 152 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8325 (mtt-85) REVERT: A 179 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7569 (pp) REVERT: A 218 LEU cc_start: 0.9198 (tp) cc_final: 0.8876 (tp) REVERT: A 328 GLU cc_start: 0.8220 (tp30) cc_final: 0.7762 (mt-10) REVERT: A 330 ARG cc_start: 0.4521 (mpt180) cc_final: 0.3214 (ttp-170) REVERT: A 448 MET cc_start: 0.8736 (mmm) cc_final: 0.8310 (mmp) REVERT: A 450 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8327 (tmm) REVERT: B 16 LYS cc_start: 0.8349 (tttm) cc_final: 0.7896 (mmmt) REVERT: B 33 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7293 (mt) REVERT: B 124 MET cc_start: 0.8704 (tpt) cc_final: 0.8126 (tpp) REVERT: B 152 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8354 (mtt-85) REVERT: B 179 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 218 LEU cc_start: 0.9215 (tp) cc_final: 0.8943 (tp) REVERT: B 328 GLU cc_start: 0.8159 (tp30) cc_final: 0.7529 (tp30) REVERT: B 330 ARG cc_start: 0.4569 (mpt180) cc_final: 0.3175 (ttp-170) REVERT: B 448 MET cc_start: 0.8724 (mmm) cc_final: 0.8314 (mmp) REVERT: B 450 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8330 (tmm) outliers start: 28 outliers final: 22 residues processed: 127 average time/residue: 0.0765 time to fit residues: 13.2934 Evaluate side-chains 126 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 1.9990 chunk 35 optimal weight: 0.0020 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.177274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145708 restraints weight = 9423.784| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.44 r_work: 0.3449 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7372 Z= 0.120 Angle : 0.611 10.022 10018 Z= 0.320 Chirality : 0.041 0.238 1204 Planarity : 0.005 0.094 1232 Dihedral : 4.614 30.243 1030 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 3.79 % Allowed : 22.72 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.21 (0.28), residues: 966 helix: 1.37 (0.23), residues: 574 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 182 TYR 0.009 0.001 TYR A 343 PHE 0.008 0.001 PHE A 368 TRP 0.004 0.001 TRP A 253 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7366) covalent geometry : angle 0.60879 / 0.32 (10006) SS BOND : bond 0.00281 / 0.13 ( 6) SS BOND : angle 1.46825 / 0.75 ( 12) hydrogen bonds : bond 0.03242 / 2.16 ( 380) hydrogen bonds : angle 4.01931 / 2.92 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.26 seconds wall clock time: 26 minutes 17.70 seconds (1577.70 seconds total)