Starting phenix.real_space_refine on Fri Jul 3 10:17:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j90_36083/07_2026/8j90_36083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j90_36083/07_2026/8j90_36083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j90_36083/07_2026/8j90_36083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j90_36083/07_2026/8j90_36083.map" model { file = "/net/cci-nas-00/data/ceres_data/8j90_36083/07_2026/8j90_36083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j90_36083/07_2026/8j90_36083.cif" } resolution = 4.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 222 5.49 5 S 33 5.16 5 C 8093 2.51 5 N 2543 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13881 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 598 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 676 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "D" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "E" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 621 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 676 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 635 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "H" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "I" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2260 Classifications: {'DNA': 111} Link IDs: {'rna3p': 110} Chain: "J" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2291 Classifications: {'DNA': 111} Link IDs: {'rna3p': 110} Chain: "K" Number of atoms: 4082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4082 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 19, 'TRANS': 484} Chain breaks: 4 Time building chain proxies: 2.95, per 1000 atoms: 0.21 Number of scatterers: 13881 At special positions: 0 Unit cell: (118.72, 130.38, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 222 15.00 O 2990 8.00 N 2543 7.00 C 8093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 474.0 milliseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 11 sheets defined 69.1% alpha, 4.6% beta 109 base pairs and 181 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.789A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.501A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.787A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 35 through 47 Processing helix chain 'C' and resid 55 through 82 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 109 Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 128 through 149 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.405A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.591A pdb=" N ASN F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 35 through 47 Processing helix chain 'G' and resid 55 through 83 Processing helix chain 'G' and resid 88 through 99 Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 Processing helix chain 'H' and resid 115 through 127 Processing helix chain 'H' and resid 128 through 149 Processing helix chain 'K' and resid 185 through 193 Processing helix chain 'K' and resid 203 through 219 Processing helix chain 'K' and resid 233 through 247 removed outlier: 4.005A pdb=" N HIS K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU K 244 " --> pdb=" O PHE K 240 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS K 245 " --> pdb=" O LEU K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 260 No H-bonds generated for 'chain 'K' and resid 258 through 260' Processing helix chain 'K' and resid 261 through 273 Processing helix chain 'K' and resid 284 through 295 Processing helix chain 'K' and resid 311 through 317 Processing helix chain 'K' and resid 317 through 323 removed outlier: 3.816A pdb=" N ARG K 323 " --> pdb=" O LYS K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 338 removed outlier: 3.532A pdb=" N LEU K 338 " --> pdb=" O GLY K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 350 removed outlier: 3.641A pdb=" N ARG K 347 " --> pdb=" O CYS K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 380 Processing helix chain 'K' and resid 389 through 394 removed outlier: 3.946A pdb=" N SER K 392 " --> pdb=" O GLU K 389 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP K 393 " --> pdb=" O PHE K 390 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE K 394 " --> pdb=" O GLU K 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 389 through 394' Processing helix chain 'K' and resid 408 through 420 removed outlier: 4.301A pdb=" N ALA K 414 " --> pdb=" O GLU K 410 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU K 420 " --> pdb=" O VAL K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 428 Proline residue: K 426 - end of helix Processing helix chain 'K' and resid 453 through 465 removed outlier: 3.868A pdb=" N ASN K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 476 Processing helix chain 'K' and resid 488 through 499 Processing helix chain 'K' and resid 500 through 508 removed outlier: 3.849A pdb=" N GLN K 504 " --> pdb=" O PRO K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 523 removed outlier: 3.899A pdb=" N ILE K 519 " --> pdb=" O PRO K 515 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS K 523 " --> pdb=" O ILE K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 540 removed outlier: 3.523A pdb=" N ARG K 527 " --> pdb=" O CYS K 523 " (cutoff:3.500A) Processing helix chain 'K' and resid 549 through 563 removed outlier: 4.293A pdb=" N ILE K 555 " --> pdb=" O LYS K 551 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 588 Processing helix chain 'K' and resid 601 through 606 removed outlier: 3.550A pdb=" N GLY K 604 " --> pdb=" O ARG K 601 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU K 605 " --> pdb=" O ALA K 602 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY K 606 " --> pdb=" O GLY K 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 601 through 606' Processing helix chain 'K' and resid 623 through 636 removed outlier: 4.744A pdb=" N CYS K 634 " --> pdb=" O ALA K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 674 removed outlier: 3.845A pdb=" N ARG K 657 " --> pdb=" O SER K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 714 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.719A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.494A pdb=" N ARG C 51 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 110 through 111 removed outlier: 7.084A pdb=" N THR C 110 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 86 through 87 Processing sheet with id=AA8, first strand: chain 'K' and resid 223 through 225 Processing sheet with id=AA9, first strand: chain 'K' and resid 278 through 281 removed outlier: 4.029A pdb=" N SER K 310 " --> pdb=" O TYR K 281 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 644 through 647 removed outlier: 3.923A pdb=" N VAL K 645 " --> pdb=" O LYS K 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 569 through 570 removed outlier: 8.317A pdb=" N LEU K 598 " --> pdb=" O VAL K 543 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE K 545 " --> pdb=" O LEU K 598 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 284 hydrogen bonds 568 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 181 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1829 1.31 - 1.44: 4870 1.44 - 1.56: 7386 1.56 - 1.69: 442 1.69 - 1.81: 55 Bond restraints: 14582 Sorted by residual: bond pdb=" C THR A 80 " pdb=" O THR A 80 " ideal model delta sigma weight residual 1.234 1.185 0.049 1.16e-02 7.43e+03 1.76e+01 bond pdb=" CA LYS K 233 " pdb=" C LYS K 233 " ideal model delta sigma weight residual 1.520 1.464 0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" CA TYR K 511 " pdb=" C TYR K 511 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.28e-02 6.10e+03 1.49e+01 bond pdb=" CA THR A 80 " pdb=" C THR A 80 " ideal model delta sigma weight residual 1.528 1.481 0.048 1.28e-02 6.10e+03 1.40e+01 bond pdb=" CA ARG B 95 " pdb=" C ARG B 95 " ideal model delta sigma weight residual 1.521 1.478 0.044 1.17e-02 7.31e+03 1.39e+01 ... (remaining 14577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 20510 4.43 - 8.87: 98 8.87 - 13.30: 7 13.30 - 17.73: 1 17.73 - 22.17: 1 Bond angle restraints: 20617 Sorted by residual: angle pdb=" N GLY K 509 " pdb=" CA GLY K 509 " pdb=" C GLY K 509 " ideal model delta sigma weight residual 114.95 92.78 22.17 1.41e+00 5.03e-01 2.47e+02 angle pdb=" N GLN K 504 " pdb=" CA GLN K 504 " pdb=" C GLN K 504 " ideal model delta sigma weight residual 111.03 98.83 12.20 1.11e+00 8.12e-01 1.21e+02 angle pdb=" N LEU K 231 " pdb=" CA LEU K 231 " pdb=" C LEU K 231 " ideal model delta sigma weight residual 111.07 101.86 9.21 1.07e+00 8.73e-01 7.41e+01 angle pdb=" N TYR K 511 " pdb=" CA TYR K 511 " pdb=" C TYR K 511 " ideal model delta sigma weight residual 111.02 101.59 9.43 1.22e+00 6.72e-01 5.98e+01 angle pdb=" N THR A 80 " pdb=" CA THR A 80 " pdb=" C THR A 80 " ideal model delta sigma weight residual 109.86 121.17 -11.31 1.55e+00 4.16e-01 5.33e+01 ... (remaining 20612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.99: 6741 26.99 - 53.98: 1202 53.98 - 80.97: 260 80.97 - 107.96: 7 107.96 - 134.95: 1 Dihedral angle restraints: 8211 sinusoidal: 4840 harmonic: 3371 Sorted by residual: dihedral pdb=" CA THR K 453 " pdb=" C THR K 453 " pdb=" N ASP K 454 " pdb=" CA ASP K 454 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LYS K 344 " pdb=" C LYS K 344 " pdb=" N LEU K 345 " pdb=" CA LEU K 345 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA TYR K 325 " pdb=" C TYR K 325 " pdb=" N PRO K 326 " pdb=" CA PRO K 326 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 8208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2070 0.080 - 0.160: 252 0.160 - 0.240: 12 0.240 - 0.321: 2 0.321 - 0.401: 2 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CA GLN K 228 " pdb=" N GLN K 228 " pdb=" C GLN K 228 " pdb=" CB GLN K 228 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA THR A 80 " pdb=" N THR A 80 " pdb=" C THR A 80 " pdb=" CB THR A 80 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ASP K 227 " pdb=" N ASP K 227 " pdb=" C ASP K 227 " pdb=" CB ASP K 227 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 2335 not shown) Planarity restraints: 1836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 230 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C GLY K 230 " 0.054 2.00e-02 2.50e+03 pdb=" O GLY K 230 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU K 231 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 373 " -0.023 2.00e-02 2.50e+03 1.75e-02 7.69e+00 pdb=" CG TRP K 373 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP K 373 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP K 373 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 373 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP K 373 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 373 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 373 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 373 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP K 373 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 42 " -0.015 2.00e-02 2.50e+03 1.95e-02 6.63e+00 pdb=" CG PHE G 42 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE G 42 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE G 42 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE G 42 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 42 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE G 42 " 0.000 2.00e-02 2.50e+03 ... (remaining 1833 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 12 2.21 - 2.88: 4832 2.88 - 3.55: 22771 3.55 - 4.23: 36049 4.23 - 4.90: 54027 Nonbonded interactions: 117691 Sorted by model distance: nonbonded pdb=" CE1 HIS K 282 " pdb=" CB SER K 310 " model vdw 1.534 3.660 nonbonded pdb=" O LEU B 90 " pdb=" O ARG B 95 " model vdw 1.843 3.040 nonbonded pdb=" CA GLY K 505 " pdb=" OD2 ASP K 508 " model vdw 1.903 3.440 nonbonded pdb=" NZ LYS K 233 " pdb=" O THR K 361 " model vdw 1.931 3.120 nonbonded pdb=" O ARG G 51 " pdb=" OG1 THR H 113 " model vdw 2.101 3.040 ... (remaining 117686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 61 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 32 through 113) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.340 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 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 : 0.006 0.060 14582 Z= 0.479 Angle : 0.923 22.166 20617 Z= 0.676 Chirality : 0.052 0.401 2338 Planarity : 0.006 0.066 1836 Dihedral : 24.019 134.951 6031 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.30 % Allowed : 1.00 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.25), residues: 1142 helix: 0.43 (0.18), residues: 765 sheet: -1.33 (0.60), residues: 64 loop : -0.92 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 580 TYR 0.021 0.002 TYR K 663 PHE 0.045 0.002 PHE G 42 TRP 0.047 0.003 TRP K 373 HIS 0.011 0.001 HIS K 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.48 (14582) covalent geometry : angle 0.92318 / 0.68 (20617) hydrogen bonds : bond 0.10711 / 7.65 ( 861) hydrogen bonds : angle 5.17276 / 3.58 ( 2278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 491 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.7989 (pt) cc_final: 0.7644 (mt) REVERT: A 64 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7909 (mttp) REVERT: A 80 THR cc_start: 0.8557 (p) cc_final: 0.8238 (p) REVERT: A 86 SER cc_start: 0.8211 (m) cc_final: 0.7551 (t) REVERT: A 89 VAL cc_start: 0.7749 (t) cc_final: 0.7466 (m) REVERT: A 109 LEU cc_start: 0.8865 (tp) cc_final: 0.8600 (tp) REVERT: A 118 THR cc_start: 0.8376 (m) cc_final: 0.8045 (m) REVERT: A 133 GLU cc_start: 0.6612 (pm20) cc_final: 0.6385 (pt0) REVERT: B 27 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7110 (tt0) REVERT: B 31 LYS cc_start: 0.8720 (tttt) cc_final: 0.8476 (mmtm) REVERT: B 45 ARG cc_start: 0.6727 (tpt170) cc_final: 0.6522 (mmm160) REVERT: B 49 LEU cc_start: 0.9000 (mp) cc_final: 0.8727 (tt) REVERT: B 84 MET cc_start: 0.7223 (tpt) cc_final: 0.6515 (mmm) REVERT: B 88 TYR cc_start: 0.6724 (m-80) cc_final: 0.6190 (m-80) REVERT: B 91 LYS cc_start: 0.7818 (tmmt) cc_final: 0.7447 (tttt) REVERT: C 28 MET cc_start: 0.5940 (mtm) cc_final: 0.5198 (ttp) REVERT: C 42 PHE cc_start: 0.7579 (m-10) cc_final: 0.7284 (m-80) REVERT: C 98 ASN cc_start: 0.7733 (m-40) cc_final: 0.7531 (t0) REVERT: D 62 TYR cc_start: 0.7562 (m-10) cc_final: 0.7098 (m-10) REVERT: D 63 LYS cc_start: 0.7570 (mptt) cc_final: 0.7163 (mmmm) REVERT: D 91 ILE cc_start: 0.8204 (mm) cc_final: 0.7911 (mm) REVERT: D 112 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7831 (Cg_endo) REVERT: D 130 GLU cc_start: 0.7793 (mp0) cc_final: 0.7257 (mt-10) REVERT: E 73 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7942 (tm-30) REVERT: E 79 LYS cc_start: 0.7158 (tmtt) cc_final: 0.6418 (mmtp) REVERT: E 94 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7874 (mt-10) REVERT: F 22 LEU cc_start: 0.7228 (tt) cc_final: 0.6985 (pp) REVERT: F 30 THR cc_start: 0.7357 (p) cc_final: 0.7080 (t) REVERT: G 34 PHE cc_start: 0.5253 (m-10) cc_final: 0.4813 (m-80) REVERT: G 42 PHE cc_start: 0.7250 (m-80) cc_final: 0.6938 (m-80) REVERT: H 110 LYS cc_start: 0.6715 (tptt) cc_final: 0.6180 (ttmt) REVERT: H 125 LEU cc_start: 0.9147 (tt) cc_final: 0.8288 (tt) REVERT: H 127 LEU cc_start: 0.7947 (mm) cc_final: 0.7621 (mp) REVERT: K 241 LEU cc_start: 0.8096 (mm) cc_final: 0.7836 (mm) REVERT: K 249 LEU cc_start: 0.8247 (mt) cc_final: 0.7784 (tp) REVERT: K 253 TYR cc_start: 0.6356 (m-80) cc_final: 0.5353 (m-10) REVERT: K 254 LEU cc_start: 0.7308 (tp) cc_final: 0.6870 (tp) REVERT: K 324 HIS cc_start: 0.6129 (m90) cc_final: 0.5764 (t-170) REVERT: K 329 TYR cc_start: 0.7325 (m-80) cc_final: 0.6659 (t80) REVERT: K 352 LEU cc_start: 0.7898 (mt) cc_final: 0.7511 (tp) REVERT: K 373 TRP cc_start: 0.6791 (t-100) cc_final: 0.6201 (t-100) REVERT: K 382 ASP cc_start: 0.6786 (m-30) cc_final: 0.6384 (m-30) REVERT: K 384 PHE cc_start: 0.8174 (m-80) cc_final: 0.7613 (m-80) REVERT: K 459 PHE cc_start: 0.7264 (m-10) cc_final: 0.7042 (m-80) REVERT: K 468 LEU cc_start: 0.8389 (tp) cc_final: 0.7951 (tp) REVERT: K 557 ASP cc_start: 0.8072 (t0) cc_final: 0.7637 (t70) REVERT: K 569 ARG cc_start: 0.6738 (ttt90) cc_final: 0.6049 (ttm-80) REVERT: K 618 TYR cc_start: 0.7568 (t80) cc_final: 0.6966 (t80) REVERT: K 621 ASP cc_start: 0.7324 (t0) cc_final: 0.6952 (m-30) REVERT: K 623 ASN cc_start: 0.8221 (t0) cc_final: 0.7983 (t0) REVERT: K 631 MET cc_start: 0.6804 (ppp) cc_final: 0.6599 (tpt) REVERT: K 636 ARG cc_start: 0.5498 (ttt90) cc_final: 0.5272 (tmt170) REVERT: K 748 TRP cc_start: 0.5448 (p-90) cc_final: 0.5222 (p-90) REVERT: K 755 SER cc_start: 0.7446 (p) cc_final: 0.7226 (t) outliers start: 3 outliers final: 0 residues processed: 493 average time/residue: 0.1511 time to fit residues: 99.7302 Evaluate side-chains 268 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN C 33 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN G 98 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.068852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050682 restraints weight = 80804.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052056 restraints weight = 46630.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.052949 restraints weight = 32684.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053471 restraints weight = 26197.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.053695 restraints weight = 23124.595| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14582 Z= 0.250 Angle : 0.853 11.697 20617 Z= 0.467 Chirality : 0.052 0.244 2338 Planarity : 0.007 0.067 1836 Dihedral : 28.644 136.603 3682 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.90 % Allowed : 9.18 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.47 (0.23), residues: 1142 helix: 0.18 (0.17), residues: 770 sheet: -0.83 (0.61), residues: 60 loop : -1.19 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG K 579 TYR 0.020 0.003 TYR K 281 PHE 0.026 0.003 PHE A 78 TRP 0.028 0.002 TRP K 373 HIS 0.021 0.002 HIS K 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 (14582) covalent geometry : angle 0.85271 / 0.47 (20617) hydrogen bonds : bond 0.06184 / 4.21 ( 861) hydrogen bonds : angle 4.62401 / 3.24 ( 2278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 299 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7694 (t80) cc_final: 0.7401 (t80) REVERT: A 86 SER cc_start: 0.8498 (m) cc_final: 0.8180 (t) REVERT: A 118 THR cc_start: 0.8883 (m) cc_final: 0.8266 (p) REVERT: A 133 GLU cc_start: 0.6525 (pm20) cc_final: 0.5839 (pt0) REVERT: B 27 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6686 (tt0) REVERT: B 84 MET cc_start: 0.7237 (tpt) cc_final: 0.6832 (mmm) REVERT: B 88 TYR cc_start: 0.6872 (m-80) cc_final: 0.6260 (m-80) REVERT: B 91 LYS cc_start: 0.7803 (tmmt) cc_final: 0.7314 (tttt) REVERT: B 98 TYR cc_start: 0.6757 (m-10) cc_final: 0.6496 (m-10) REVERT: C 28 MET cc_start: 0.5286 (mtm) cc_final: 0.4428 (ttp) REVERT: C 42 PHE cc_start: 0.7306 (m-10) cc_final: 0.7059 (m-80) REVERT: C 70 GLU cc_start: 0.7234 (tt0) cc_final: 0.6799 (tt0) REVERT: C 98 ASN cc_start: 0.7762 (m-40) cc_final: 0.7269 (t0) REVERT: D 63 LYS cc_start: 0.7187 (mptt) cc_final: 0.6649 (mmmt) REVERT: D 64 ILE cc_start: 0.7931 (pt) cc_final: 0.7681 (pt) REVERT: D 110 LYS cc_start: 0.6787 (mmtt) cc_final: 0.6232 (mtpp) REVERT: D 125 LEU cc_start: 0.7696 (pp) cc_final: 0.7493 (pp) REVERT: D 130 GLU cc_start: 0.7878 (mp0) cc_final: 0.7159 (mt-10) REVERT: E 70 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8754 (tt) REVERT: E 79 LYS cc_start: 0.7047 (tmtt) cc_final: 0.6648 (mmtt) REVERT: E 94 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6585 (mm-30) REVERT: F 21 VAL cc_start: 0.6321 (t) cc_final: 0.5086 (m) REVERT: G 83 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7007 (ptpp) REVERT: H 105 LEU cc_start: 0.7420 (pp) cc_final: 0.7101 (pp) REVERT: H 110 LYS cc_start: 0.6695 (tptt) cc_final: 0.6129 (ttmt) REVERT: K 229 MET cc_start: 0.5058 (ptt) cc_final: 0.4608 (ptt) REVERT: K 249 LEU cc_start: 0.8255 (mt) cc_final: 0.7576 (tp) REVERT: K 281 TYR cc_start: 0.7406 (t80) cc_final: 0.6249 (t80) REVERT: K 282 HIS cc_start: 0.5248 (m90) cc_final: 0.4932 (m-70) REVERT: K 321 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6557 (mp) REVERT: K 373 TRP cc_start: 0.6891 (t-100) cc_final: 0.6550 (t-100) REVERT: K 382 ASP cc_start: 0.6803 (m-30) cc_final: 0.6411 (m-30) REVERT: K 384 PHE cc_start: 0.8313 (m-80) cc_final: 0.7624 (m-80) REVERT: K 553 LEU cc_start: 0.7407 (mp) cc_final: 0.7088 (mt) REVERT: K 570 ILE cc_start: 0.6750 (mm) cc_final: 0.6256 (mp) REVERT: K 621 ASP cc_start: 0.7429 (t0) cc_final: 0.6820 (m-30) REVERT: K 623 ASN cc_start: 0.8198 (t0) cc_final: 0.7877 (t0) outliers start: 9 outliers final: 1 residues processed: 304 average time/residue: 0.1259 time to fit residues: 54.2113 Evaluate side-chains 218 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 75 optimal weight: 50.0000 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.068895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051833 restraints weight = 80735.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053527 restraints weight = 41427.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054586 restraints weight = 26726.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.055271 restraints weight = 20275.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055620 restraints weight = 17098.530| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14582 Z= 0.159 Angle : 0.715 8.408 20617 Z= 0.401 Chirality : 0.046 0.191 2338 Planarity : 0.006 0.048 1836 Dihedral : 28.608 135.876 3682 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % 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: -0.17 (0.24), residues: 1142 helix: 0.52 (0.18), residues: 775 sheet: -0.50 (0.72), residues: 49 loop : -1.44 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 23 TYR 0.027 0.002 TYR D 108 PHE 0.030 0.002 PHE K 596 TRP 0.022 0.002 TRP K 748 HIS 0.011 0.002 HIS K 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (14582) covalent geometry : angle 0.71544 / 0.40 (20617) hydrogen bonds : bond 0.05036 / 3.43 ( 861) hydrogen bonds : angle 4.28554 / 3.03 ( 2278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7708 (t80) cc_final: 0.7263 (t80) REVERT: A 86 SER cc_start: 0.8355 (m) cc_final: 0.7607 (t) REVERT: A 89 VAL cc_start: 0.7594 (t) cc_final: 0.7376 (m) REVERT: A 109 LEU cc_start: 0.8996 (tp) cc_final: 0.8727 (tp) REVERT: A 118 THR cc_start: 0.8492 (m) cc_final: 0.8270 (m) REVERT: A 133 GLU cc_start: 0.6568 (pm20) cc_final: 0.6036 (pt0) REVERT: B 60 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8859 (tp) REVERT: B 78 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8241 (mtm180) REVERT: B 84 MET cc_start: 0.7350 (tpt) cc_final: 0.7146 (mmm) REVERT: B 91 LYS cc_start: 0.7707 (tmmt) cc_final: 0.7164 (tttt) REVERT: B 98 TYR cc_start: 0.6684 (m-10) cc_final: 0.6478 (m-10) REVERT: C 28 MET cc_start: 0.5044 (mtm) cc_final: 0.4110 (ttp) REVERT: C 42 PHE cc_start: 0.7425 (m-10) cc_final: 0.7044 (m-80) REVERT: C 80 ARG cc_start: 0.6107 (mpt90) cc_final: 0.5851 (mtm-85) REVERT: C 98 ASN cc_start: 0.7817 (m-40) cc_final: 0.7402 (t0) REVERT: D 63 LYS cc_start: 0.7644 (mptt) cc_final: 0.7001 (mmmt) REVERT: D 110 LYS cc_start: 0.6830 (mmtt) cc_final: 0.6280 (mtpp) REVERT: D 125 LEU cc_start: 0.7693 (pp) cc_final: 0.7405 (pp) REVERT: D 130 GLU cc_start: 0.7781 (mp0) cc_final: 0.6985 (mt-10) REVERT: E 79 LYS cc_start: 0.6879 (tmtt) cc_final: 0.6475 (mmtt) REVERT: F 63 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7820 (mm-30) REVERT: G 42 PHE cc_start: 0.7253 (m-80) cc_final: 0.6423 (m-80) REVERT: G 83 LYS cc_start: 0.8256 (mmmm) cc_final: 0.7119 (ptpp) REVERT: H 60 GLU cc_start: 0.5610 (mp0) cc_final: 0.5248 (tt0) REVERT: H 95 PHE cc_start: 0.7989 (t80) cc_final: 0.7745 (t80) REVERT: K 214 ILE cc_start: 0.8266 (mt) cc_final: 0.8003 (mt) REVERT: K 237 THR cc_start: 0.7760 (p) cc_final: 0.7554 (p) REVERT: K 249 LEU cc_start: 0.8278 (mt) cc_final: 0.7825 (tp) REVERT: K 281 TYR cc_start: 0.6368 (t80) cc_final: 0.5852 (t80) REVERT: K 289 ASP cc_start: 0.8432 (m-30) cc_final: 0.8229 (m-30) REVERT: K 315 MET cc_start: 0.7474 (tpp) cc_final: 0.7261 (tpp) REVERT: K 373 TRP cc_start: 0.6630 (t-100) cc_final: 0.6284 (t-100) REVERT: K 382 ASP cc_start: 0.6765 (m-30) cc_final: 0.6435 (m-30) REVERT: K 384 PHE cc_start: 0.8332 (m-80) cc_final: 0.7382 (m-80) REVERT: K 552 LEU cc_start: 0.7923 (tt) cc_final: 0.7655 (tp) REVERT: K 557 ASP cc_start: 0.8020 (t0) cc_final: 0.7759 (t70) REVERT: K 560 PHE cc_start: 0.7803 (m-80) cc_final: 0.7523 (m-10) REVERT: K 570 ILE cc_start: 0.6394 (mm) cc_final: 0.6167 (mp) REVERT: K 621 ASP cc_start: 0.7401 (t0) cc_final: 0.6956 (m-30) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.1278 time to fit residues: 56.5399 Evaluate side-chains 223 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 3 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 40.0000 chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 93 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.051126 restraints weight = 82362.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052697 restraints weight = 43191.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053723 restraints weight = 28338.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054359 restraints weight = 21724.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054768 restraints weight = 18497.773| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14582 Z= 0.169 Angle : 0.706 8.366 20617 Z= 0.395 Chirality : 0.045 0.244 2338 Planarity : 0.006 0.070 1836 Dihedral : 28.699 136.199 3682 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % Rotamer: Outliers : 0.30 % Allowed : 5.09 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.02 (0.24), residues: 1142 helix: 0.69 (0.18), residues: 771 sheet: -0.56 (0.74), residues: 49 loop : -1.39 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 117 TYR 0.031 0.002 TYR B 88 PHE 0.032 0.002 PHE D 67 TRP 0.012 0.002 TRP K 373 HIS 0.009 0.002 HIS K 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (14582) covalent geometry : angle 0.70600 / 0.39 (20617) hydrogen bonds : bond 0.04945 / 3.35 ( 861) hydrogen bonds : angle 4.21395 / 2.97 ( 2278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7705 (t80) cc_final: 0.7304 (t80) REVERT: A 86 SER cc_start: 0.8375 (m) cc_final: 0.7632 (t) REVERT: A 89 VAL cc_start: 0.7581 (t) cc_final: 0.7353 (m) REVERT: A 94 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 133 GLU cc_start: 0.6628 (pm20) cc_final: 0.6077 (pt0) REVERT: B 84 MET cc_start: 0.7414 (tpt) cc_final: 0.7132 (mmm) REVERT: B 91 LYS cc_start: 0.7670 (tmmt) cc_final: 0.7298 (tttt) REVERT: B 97 LEU cc_start: 0.7602 (tp) cc_final: 0.7334 (tp) REVERT: B 98 TYR cc_start: 0.6770 (m-10) cc_final: 0.6392 (m-10) REVERT: C 28 MET cc_start: 0.5137 (mtm) cc_final: 0.4139 (ttp) REVERT: C 42 PHE cc_start: 0.7424 (m-10) cc_final: 0.7071 (m-80) REVERT: C 80 ARG cc_start: 0.6210 (mpt90) cc_final: 0.5909 (mtm-85) REVERT: C 98 ASN cc_start: 0.7828 (m-40) cc_final: 0.7415 (t0) REVERT: D 62 TYR cc_start: 0.6988 (m-80) cc_final: 0.6668 (m-10) REVERT: D 63 LYS cc_start: 0.7703 (mptt) cc_final: 0.7218 (mmmm) REVERT: D 84 MET cc_start: 0.6686 (ttp) cc_final: 0.6209 (ttm) REVERT: D 110 LYS cc_start: 0.5943 (mmtp) cc_final: 0.5375 (mtpp) REVERT: D 130 GLU cc_start: 0.7745 (mp0) cc_final: 0.7003 (mt-10) REVERT: E 79 LYS cc_start: 0.7125 (tmtt) cc_final: 0.6602 (mmtt) REVERT: F 63 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7884 (mm-30) REVERT: G 77 ASN cc_start: 0.8175 (t0) cc_final: 0.7941 (t0) REVERT: G 83 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7136 (ptpp) REVERT: K 249 LEU cc_start: 0.8371 (mt) cc_final: 0.7929 (tp) REVERT: K 281 TYR cc_start: 0.6256 (t80) cc_final: 0.6002 (t80) REVERT: K 315 MET cc_start: 0.7701 (tpp) cc_final: 0.7498 (tpp) REVERT: K 329 TYR cc_start: 0.7005 (m-80) cc_final: 0.6443 (t80) REVERT: K 354 MET cc_start: 0.6227 (ppp) cc_final: 0.6002 (ppp) REVERT: K 373 TRP cc_start: 0.6653 (t-100) cc_final: 0.6350 (t-100) REVERT: K 382 ASP cc_start: 0.6869 (m-30) cc_final: 0.6479 (m-30) REVERT: K 384 PHE cc_start: 0.8375 (m-80) cc_final: 0.7396 (m-10) REVERT: K 527 ARG cc_start: 0.8536 (ppt170) cc_final: 0.8258 (ptt90) REVERT: K 553 LEU cc_start: 0.7184 (mt) cc_final: 0.6806 (mt) REVERT: K 570 ILE cc_start: 0.6460 (mm) cc_final: 0.6182 (mp) REVERT: K 581 ARG cc_start: 0.7025 (ptt180) cc_final: 0.6679 (tmm-80) REVERT: K 621 ASP cc_start: 0.7487 (t0) cc_final: 0.6723 (m-30) REVERT: K 622 TRP cc_start: 0.6813 (m100) cc_final: 0.6502 (m-10) outliers start: 3 outliers final: 1 residues processed: 287 average time/residue: 0.1118 time to fit residues: 46.9641 Evaluate side-chains 221 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 70 optimal weight: 30.0000 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 112 optimal weight: 0.0050 chunk 72 optimal weight: 40.0000 chunk 82 optimal weight: 30.0000 chunk 131 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.068870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051747 restraints weight = 83047.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053342 restraints weight = 44404.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054331 restraints weight = 29219.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.054956 restraints weight = 22615.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055278 restraints weight = 19381.986| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14582 Z= 0.152 Angle : 0.698 9.739 20617 Z= 0.389 Chirality : 0.045 0.315 2338 Planarity : 0.005 0.083 1836 Dihedral : 28.712 136.020 3682 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.31 % 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: 0.07 (0.24), residues: 1142 helix: 0.73 (0.18), residues: 773 sheet: -0.45 (0.75), residues: 49 loop : -1.44 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 117 TYR 0.034 0.002 TYR B 88 PHE 0.020 0.002 PHE H 95 TRP 0.034 0.003 TRP K 622 HIS 0.015 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (14582) covalent geometry : angle 0.69797 / 0.39 (20617) hydrogen bonds : bond 0.04657 / 3.17 ( 861) hydrogen bonds : angle 4.09168 / 2.89 ( 2278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7651 (t80) cc_final: 0.7286 (t80) REVERT: A 86 SER cc_start: 0.8339 (m) cc_final: 0.7612 (t) REVERT: A 89 VAL cc_start: 0.7530 (t) cc_final: 0.7225 (m) REVERT: A 133 GLU cc_start: 0.6549 (pm20) cc_final: 0.5989 (pt0) REVERT: B 84 MET cc_start: 0.7390 (tpt) cc_final: 0.7124 (mmm) REVERT: B 91 LYS cc_start: 0.7680 (tmmt) cc_final: 0.7313 (tttt) REVERT: B 97 LEU cc_start: 0.7764 (tp) cc_final: 0.7472 (tp) REVERT: B 98 TYR cc_start: 0.6617 (m-10) cc_final: 0.6335 (m-10) REVERT: C 28 MET cc_start: 0.5124 (mtm) cc_final: 0.4078 (ttp) REVERT: C 42 PHE cc_start: 0.7403 (m-10) cc_final: 0.7151 (m-80) REVERT: C 80 ARG cc_start: 0.6264 (mpt90) cc_final: 0.5955 (mtm-85) REVERT: C 98 ASN cc_start: 0.7830 (m-40) cc_final: 0.7402 (t0) REVERT: D 62 TYR cc_start: 0.7140 (m-80) cc_final: 0.6829 (m-10) REVERT: D 63 LYS cc_start: 0.7575 (mptt) cc_final: 0.7024 (mmmt) REVERT: D 84 MET cc_start: 0.6587 (ttp) cc_final: 0.6280 (ttm) REVERT: D 101 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7372 (mm-30) REVERT: D 110 LYS cc_start: 0.5768 (mmtp) cc_final: 0.5308 (mtpp) REVERT: D 130 GLU cc_start: 0.7588 (mp0) cc_final: 0.6936 (mt-10) REVERT: E 79 LYS cc_start: 0.6977 (tmtt) cc_final: 0.6640 (mmtt) REVERT: F 63 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7952 (mm-30) REVERT: G 77 ASN cc_start: 0.8100 (t0) cc_final: 0.7876 (t0) REVERT: G 83 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7038 (ptpp) REVERT: K 214 ILE cc_start: 0.7907 (mm) cc_final: 0.7473 (mm) REVERT: K 237 THR cc_start: 0.7908 (p) cc_final: 0.7653 (p) REVERT: K 243 HIS cc_start: 0.5935 (t-170) cc_final: 0.5551 (t-170) REVERT: K 249 LEU cc_start: 0.8361 (mt) cc_final: 0.7974 (tp) REVERT: K 253 TYR cc_start: 0.5890 (m-80) cc_final: 0.4923 (m-10) REVERT: K 281 TYR cc_start: 0.6280 (t80) cc_final: 0.5933 (t80) REVERT: K 315 MET cc_start: 0.7654 (tpp) cc_final: 0.7415 (tpp) REVERT: K 329 TYR cc_start: 0.6951 (m-80) cc_final: 0.6649 (t80) REVERT: K 373 TRP cc_start: 0.6638 (t-100) cc_final: 0.6311 (t-100) REVERT: K 382 ASP cc_start: 0.7026 (m-30) cc_final: 0.6635 (m-30) REVERT: K 384 PHE cc_start: 0.8327 (m-80) cc_final: 0.7307 (m-10) REVERT: K 527 ARG cc_start: 0.8502 (ppt170) cc_final: 0.8251 (ptt90) REVERT: K 570 ILE cc_start: 0.6561 (mm) cc_final: 0.6310 (mp) REVERT: K 623 ASN cc_start: 0.7960 (t0) cc_final: 0.7670 (t0) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.1106 time to fit residues: 46.6944 Evaluate side-chains 214 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 65 optimal weight: 40.0000 chunk 119 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 30.0000 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.069640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.052236 restraints weight = 81586.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.053891 restraints weight = 43430.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054945 restraints weight = 28571.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055514 restraints weight = 21890.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055958 restraints weight = 18900.881| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14582 Z= 0.150 Angle : 0.684 12.782 20617 Z= 0.383 Chirality : 0.044 0.237 2338 Planarity : 0.006 0.103 1836 Dihedral : 28.683 135.524 3682 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % Rotamer: Outliers : 0.20 % Allowed : 4.69 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.22 (0.24), residues: 1142 helix: 0.89 (0.18), residues: 767 sheet: -0.38 (0.76), residues: 49 loop : -1.45 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 661 TYR 0.034 0.002 TYR B 88 PHE 0.037 0.002 PHE D 67 TRP 0.025 0.002 TRP K 622 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (14582) covalent geometry : angle 0.68417 / 0.38 (20617) hydrogen bonds : bond 0.04537 / 3.10 ( 861) hydrogen bonds : angle 4.03733 / 2.86 ( 2278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7644 (t80) cc_final: 0.7283 (t80) REVERT: A 86 SER cc_start: 0.8285 (m) cc_final: 0.7504 (t) REVERT: A 89 VAL cc_start: 0.7487 (t) cc_final: 0.7223 (m) REVERT: A 109 LEU cc_start: 0.9049 (tp) cc_final: 0.8789 (tp) REVERT: A 133 GLU cc_start: 0.6560 (pm20) cc_final: 0.6092 (pt0) REVERT: B 91 LYS cc_start: 0.7702 (tmmt) cc_final: 0.7319 (tttt) REVERT: B 97 LEU cc_start: 0.7618 (tp) cc_final: 0.7366 (tp) REVERT: B 98 TYR cc_start: 0.6841 (m-10) cc_final: 0.6500 (m-10) REVERT: C 28 MET cc_start: 0.4988 (mtm) cc_final: 0.4356 (tpt) REVERT: C 39 ILE cc_start: 0.7808 (pt) cc_final: 0.7579 (pt) REVERT: C 42 PHE cc_start: 0.7403 (m-10) cc_final: 0.7167 (m-80) REVERT: C 72 LEU cc_start: 0.8031 (mp) cc_final: 0.7632 (tp) REVERT: C 98 ASN cc_start: 0.7980 (m-40) cc_final: 0.7498 (t0) REVERT: D 62 TYR cc_start: 0.7138 (m-80) cc_final: 0.6859 (m-10) REVERT: D 63 LYS cc_start: 0.7423 (mptt) cc_final: 0.7124 (mmtp) REVERT: D 67 PHE cc_start: 0.6272 (m-80) cc_final: 0.6029 (m-80) REVERT: D 84 MET cc_start: 0.6703 (ttp) cc_final: 0.6315 (ttm) REVERT: D 110 LYS cc_start: 0.5716 (mmtp) cc_final: 0.5281 (mtpp) REVERT: D 130 GLU cc_start: 0.7555 (mp0) cc_final: 0.6743 (mt-10) REVERT: E 79 LYS cc_start: 0.6960 (tmtt) cc_final: 0.6549 (mmtt) REVERT: E 120 MET cc_start: 0.6779 (mmm) cc_final: 0.6571 (mmt) REVERT: F 30 THR cc_start: 0.7739 (p) cc_final: 0.7219 (t) REVERT: F 63 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7897 (mm-30) REVERT: F 100 PHE cc_start: 0.6772 (m-10) cc_final: 0.6369 (m-10) REVERT: G 77 ASN cc_start: 0.8137 (t0) cc_final: 0.7896 (t0) REVERT: G 83 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7047 (ptpp) REVERT: K 243 HIS cc_start: 0.6312 (t-170) cc_final: 0.6060 (t-170) REVERT: K 249 LEU cc_start: 0.8381 (mt) cc_final: 0.7997 (tp) REVERT: K 253 TYR cc_start: 0.5638 (m-80) cc_final: 0.5043 (m-80) REVERT: K 329 TYR cc_start: 0.6955 (m-80) cc_final: 0.6585 (t80) REVERT: K 373 TRP cc_start: 0.6619 (t-100) cc_final: 0.6313 (t-100) REVERT: K 380 LEU cc_start: 0.7467 (mp) cc_final: 0.7203 (mp) REVERT: K 382 ASP cc_start: 0.7025 (m-30) cc_final: 0.6693 (m-30) REVERT: K 384 PHE cc_start: 0.8407 (m-80) cc_final: 0.7357 (m-10) REVERT: K 527 ARG cc_start: 0.8401 (ppt170) cc_final: 0.8134 (ptt90) REVERT: K 623 ASN cc_start: 0.7966 (t0) cc_final: 0.7620 (t0) outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.1081 time to fit residues: 46.9917 Evaluate side-chains 218 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 chunk 113 optimal weight: 8.9990 chunk 65 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.068593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051390 restraints weight = 84027.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052976 restraints weight = 44043.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.053986 restraints weight = 29028.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054639 restraints weight = 22408.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.054972 restraints weight = 19137.967| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14582 Z= 0.177 Angle : 0.737 10.741 20617 Z= 0.409 Chirality : 0.046 0.238 2338 Planarity : 0.005 0.091 1836 Dihedral : 28.784 136.414 3682 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.01 (0.24), residues: 1142 helix: 0.70 (0.18), residues: 767 sheet: -0.26 (0.78), residues: 49 loop : -1.52 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 661 TYR 0.035 0.002 TYR B 88 PHE 0.038 0.003 PHE D 67 TRP 0.031 0.003 TRP K 622 HIS 0.009 0.001 HIS K 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (14582) covalent geometry : angle 0.73655 / 0.41 (20617) hydrogen bonds : bond 0.04936 / 3.38 ( 861) hydrogen bonds : angle 4.13394 / 2.94 ( 2278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7728 (t80) cc_final: 0.7325 (t80) REVERT: A 86 SER cc_start: 0.8372 (m) cc_final: 0.7589 (t) REVERT: A 105 GLU cc_start: 0.7870 (tp30) cc_final: 0.7666 (tp30) REVERT: A 118 THR cc_start: 0.8458 (m) cc_final: 0.8109 (m) REVERT: A 133 GLU cc_start: 0.6556 (pm20) cc_final: 0.6055 (pt0) REVERT: B 45 ARG cc_start: 0.6411 (tpt90) cc_final: 0.6141 (mmm160) REVERT: B 91 LYS cc_start: 0.7581 (tmmt) cc_final: 0.7194 (tttt) REVERT: B 97 LEU cc_start: 0.7680 (tp) cc_final: 0.7297 (tp) REVERT: B 98 TYR cc_start: 0.6578 (m-10) cc_final: 0.6270 (m-10) REVERT: C 28 MET cc_start: 0.4928 (mtm) cc_final: 0.4196 (tpt) REVERT: C 39 ILE cc_start: 0.7785 (pt) cc_final: 0.7548 (pt) REVERT: C 42 PHE cc_start: 0.7260 (m-10) cc_final: 0.6995 (m-80) REVERT: C 98 ASN cc_start: 0.7950 (m-40) cc_final: 0.7408 (t0) REVERT: D 63 LYS cc_start: 0.7307 (mptt) cc_final: 0.7063 (mmmt) REVERT: D 84 MET cc_start: 0.6615 (ttp) cc_final: 0.6342 (ttp) REVERT: D 110 LYS cc_start: 0.5791 (mmtp) cc_final: 0.5367 (mtpp) REVERT: D 120 GLN cc_start: 0.7821 (pp30) cc_final: 0.7560 (pp30) REVERT: D 130 GLU cc_start: 0.7488 (mp0) cc_final: 0.6651 (mt-10) REVERT: E 79 LYS cc_start: 0.6949 (tmtt) cc_final: 0.6688 (tttt) REVERT: G 38 ARG cc_start: 0.6647 (ttt180) cc_final: 0.6252 (tpp80) REVERT: G 77 ASN cc_start: 0.8129 (t0) cc_final: 0.7917 (t0) REVERT: G 83 LYS cc_start: 0.8230 (mmmm) cc_final: 0.6998 (ptpp) REVERT: H 125 LEU cc_start: 0.9042 (mt) cc_final: 0.8555 (mp) REVERT: H 137 SER cc_start: 0.7385 (p) cc_final: 0.7180 (p) REVERT: H 138 GLU cc_start: 0.6573 (tm-30) cc_final: 0.6329 (mt-10) REVERT: K 249 LEU cc_start: 0.8390 (mt) cc_final: 0.8018 (tp) REVERT: K 253 TYR cc_start: 0.5575 (m-80) cc_final: 0.5058 (m-80) REVERT: K 315 MET cc_start: 0.7320 (tpp) cc_final: 0.7086 (tpp) REVERT: K 329 TYR cc_start: 0.6991 (m-80) cc_final: 0.6596 (t80) REVERT: K 354 MET cc_start: 0.6392 (ppp) cc_final: 0.6143 (ppp) REVERT: K 373 TRP cc_start: 0.6622 (t-100) cc_final: 0.6333 (t-100) REVERT: K 382 ASP cc_start: 0.7089 (m-30) cc_final: 0.6786 (m-30) REVERT: K 384 PHE cc_start: 0.8433 (m-80) cc_final: 0.7370 (m-10) REVERT: K 652 GLN cc_start: 0.5321 (tm130) cc_final: 0.4806 (tm-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1062 time to fit residues: 44.0187 Evaluate side-chains 215 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 111 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 50.0000 chunk 87 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 30.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.069067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.052182 restraints weight = 81557.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053791 restraints weight = 42425.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.054809 restraints weight = 27497.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055385 restraints weight = 20939.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055816 restraints weight = 17963.432| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14582 Z= 0.151 Angle : 0.702 9.308 20617 Z= 0.393 Chirality : 0.045 0.206 2338 Planarity : 0.005 0.055 1836 Dihedral : 28.688 135.534 3682 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.11 (0.24), residues: 1142 helix: 0.81 (0.18), residues: 767 sheet: -0.28 (0.77), residues: 49 loop : -1.56 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 661 TYR 0.025 0.002 TYR H 65 PHE 0.040 0.002 PHE D 67 TRP 0.015 0.002 TRP K 622 HIS 0.009 0.001 HIS K 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (14582) covalent geometry : angle 0.70199 / 0.39 (20617) hydrogen bonds : bond 0.04555 / 3.12 ( 861) hydrogen bonds : angle 3.99863 / 2.85 ( 2278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7761 (t80) cc_final: 0.7345 (t80) REVERT: A 86 SER cc_start: 0.7934 (m) cc_final: 0.7568 (t) REVERT: A 97 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6929 (mp0) REVERT: A 118 THR cc_start: 0.8350 (m) cc_final: 0.7975 (m) REVERT: A 133 GLU cc_start: 0.6529 (pm20) cc_final: 0.6126 (pt0) REVERT: B 45 ARG cc_start: 0.6279 (tpt90) cc_final: 0.5880 (mmm160) REVERT: B 84 MET cc_start: 0.7304 (tpt) cc_final: 0.6098 (tpp) REVERT: B 91 LYS cc_start: 0.7762 (tmmt) cc_final: 0.7283 (tttt) REVERT: B 97 LEU cc_start: 0.7611 (tp) cc_final: 0.7364 (tp) REVERT: B 98 TYR cc_start: 0.6724 (m-10) cc_final: 0.6358 (m-10) REVERT: C 28 MET cc_start: 0.4804 (mtm) cc_final: 0.4092 (tpt) REVERT: C 39 ILE cc_start: 0.7775 (pt) cc_final: 0.7459 (pt) REVERT: C 42 PHE cc_start: 0.7270 (m-10) cc_final: 0.7029 (m-80) REVERT: C 65 GLU cc_start: 0.8427 (tt0) cc_final: 0.7391 (tp30) REVERT: C 72 LEU cc_start: 0.7883 (mp) cc_final: 0.7487 (tp) REVERT: C 80 ARG cc_start: 0.5558 (mmt-90) cc_final: 0.5344 (mmt-90) REVERT: C 98 ASN cc_start: 0.8124 (m-40) cc_final: 0.7589 (t0) REVERT: D 84 MET cc_start: 0.6582 (ttp) cc_final: 0.6381 (ttp) REVERT: D 111 LYS cc_start: 0.7737 (tptt) cc_final: 0.7498 (tptt) REVERT: D 130 GLU cc_start: 0.7343 (mp0) cc_final: 0.6582 (mt-10) REVERT: E 79 LYS cc_start: 0.6919 (tmtt) cc_final: 0.6497 (mmtt) REVERT: F 63 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7918 (mm-30) REVERT: G 38 ARG cc_start: 0.6646 (ttt180) cc_final: 0.6059 (tpp80) REVERT: G 77 ASN cc_start: 0.8127 (t0) cc_final: 0.7915 (t0) REVERT: G 83 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7037 (ptpp) REVERT: K 249 LEU cc_start: 0.8348 (mt) cc_final: 0.7966 (tp) REVERT: K 253 TYR cc_start: 0.5260 (m-80) cc_final: 0.4960 (m-80) REVERT: K 315 MET cc_start: 0.7378 (tpp) cc_final: 0.7142 (tpp) REVERT: K 329 TYR cc_start: 0.6922 (m-80) cc_final: 0.6561 (t80) REVERT: K 373 TRP cc_start: 0.6650 (t-100) cc_final: 0.6343 (t-100) REVERT: K 380 LEU cc_start: 0.7413 (mp) cc_final: 0.7174 (mp) REVERT: K 382 ASP cc_start: 0.7074 (m-30) cc_final: 0.6772 (m-30) REVERT: K 384 PHE cc_start: 0.8400 (m-80) cc_final: 0.7284 (m-10) REVERT: K 537 PHE cc_start: 0.8243 (t80) cc_final: 0.8026 (t80) REVERT: K 623 ASN cc_start: 0.7900 (t0) cc_final: 0.7594 (t0) REVERT: K 658 VAL cc_start: 0.8474 (t) cc_final: 0.8245 (t) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1072 time to fit residues: 45.6750 Evaluate side-chains 213 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 58 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 38 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 65 optimal weight: 40.0000 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 40.0000 chunk 111 optimal weight: 10.0000 chunk 63 optimal weight: 50.0000 chunk 42 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 HIS ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 ASN ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.068362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051108 restraints weight = 83383.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.052670 restraints weight = 44186.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053661 restraints weight = 29096.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054275 restraints weight = 22419.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054591 restraints weight = 19256.053| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14582 Z= 0.185 Angle : 0.760 11.413 20617 Z= 0.416 Chirality : 0.047 0.224 2338 Planarity : 0.006 0.099 1836 Dihedral : 28.778 136.323 3682 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 0.10 % Allowed : 1.60 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.08 (0.24), residues: 1142 helix: 0.75 (0.18), residues: 757 sheet: -0.77 (0.75), residues: 52 loop : -1.72 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 661 TYR 0.028 0.003 TYR H 65 PHE 0.049 0.003 PHE D 67 TRP 0.020 0.003 TRP K 327 HIS 0.009 0.002 HIS K 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (14582) covalent geometry : angle 0.75991 / 0.42 (20617) hydrogen bonds : bond 0.05136 / 3.51 ( 861) hydrogen bonds : angle 4.15220 / 2.95 ( 2278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7764 (t80) cc_final: 0.7324 (t80) REVERT: A 86 SER cc_start: 0.7984 (m) cc_final: 0.7658 (t) REVERT: A 97 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6888 (mt-10) REVERT: A 118 THR cc_start: 0.8443 (m) cc_final: 0.8006 (m) REVERT: A 133 GLU cc_start: 0.6441 (pm20) cc_final: 0.5979 (pt0) REVERT: B 45 ARG cc_start: 0.6302 (tpt90) cc_final: 0.5877 (mmm160) REVERT: B 91 LYS cc_start: 0.7813 (tmmt) cc_final: 0.7331 (tttt) REVERT: B 97 LEU cc_start: 0.7725 (tp) cc_final: 0.7355 (tp) REVERT: B 98 TYR cc_start: 0.6935 (m-10) cc_final: 0.6522 (m-10) REVERT: C 28 MET cc_start: 0.4734 (mtm) cc_final: 0.3840 (tpt) REVERT: C 42 PHE cc_start: 0.7200 (m-10) cc_final: 0.6935 (m-80) REVERT: C 65 GLU cc_start: 0.8624 (tt0) cc_final: 0.7529 (tp30) REVERT: C 98 ASN cc_start: 0.8035 (m-40) cc_final: 0.7453 (t0) REVERT: D 63 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6636 (mmmt) REVERT: D 84 MET cc_start: 0.6545 (ttp) cc_final: 0.6107 (ttp) REVERT: D 130 GLU cc_start: 0.7383 (mp0) cc_final: 0.6641 (mt-10) REVERT: E 79 LYS cc_start: 0.6968 (tmtt) cc_final: 0.6694 (tttt) REVERT: F 63 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7918 (mm-30) REVERT: G 38 ARG cc_start: 0.6572 (ttt180) cc_final: 0.6135 (tpp80) REVERT: G 60 MET cc_start: 0.8242 (ptm) cc_final: 0.8037 (ptm) REVERT: G 73 GLU cc_start: 0.7111 (pt0) cc_final: 0.6774 (pt0) REVERT: G 77 ASN cc_start: 0.8111 (t0) cc_final: 0.7893 (t0) REVERT: G 83 LYS cc_start: 0.8195 (mmmm) cc_final: 0.6981 (ptpp) REVERT: K 229 MET cc_start: 0.4229 (tmm) cc_final: 0.3941 (tmm) REVERT: K 233 LYS cc_start: 0.7361 (tttt) cc_final: 0.7130 (tttt) REVERT: K 249 LEU cc_start: 0.8336 (mt) cc_final: 0.7847 (tp) REVERT: K 315 MET cc_start: 0.7519 (tpp) cc_final: 0.7211 (tpp) REVERT: K 333 ASP cc_start: 0.7181 (t0) cc_final: 0.6960 (t0) REVERT: K 373 TRP cc_start: 0.6610 (t-100) cc_final: 0.6316 (t-100) REVERT: K 380 LEU cc_start: 0.7405 (mp) cc_final: 0.7164 (mp) REVERT: K 382 ASP cc_start: 0.7289 (m-30) cc_final: 0.7082 (m-30) REVERT: K 384 PHE cc_start: 0.8436 (m-80) cc_final: 0.7298 (m-10) REVERT: K 623 ASN cc_start: 0.7813 (t0) cc_final: 0.7541 (t0) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.0987 time to fit residues: 40.0996 Evaluate side-chains 198 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 9 optimal weight: 0.0270 chunk 105 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 82 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.051981 restraints weight = 82277.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.053541 restraints weight = 43542.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054529 restraints weight = 28705.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055152 restraints weight = 22230.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055446 restraints weight = 19103.463| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14582 Z= 0.150 Angle : 0.734 9.826 20617 Z= 0.405 Chirality : 0.045 0.272 2338 Planarity : 0.005 0.096 1836 Dihedral : 28.724 135.268 3682 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.97 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.02 (0.24), residues: 1142 helix: 0.83 (0.18), residues: 759 sheet: -0.61 (0.75), residues: 50 loop : -1.71 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 531 TYR 0.025 0.002 TYR F 72 PHE 0.022 0.002 PHE C 34 TRP 0.017 0.002 TRP K 217 HIS 0.010 0.001 HIS K 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (14582) covalent geometry : angle 0.73384 / 0.40 (20617) hydrogen bonds : bond 0.04527 / 3.07 ( 861) hydrogen bonds : angle 4.07614 / 2.89 ( 2278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8709 (t80) cc_final: 0.8430 (t80) REVERT: A 78 PHE cc_start: 0.7730 (t80) cc_final: 0.7371 (t80) REVERT: A 86 SER cc_start: 0.8032 (m) cc_final: 0.7615 (t) REVERT: A 92 LEU cc_start: 0.8554 (mt) cc_final: 0.8256 (mp) REVERT: A 97 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 118 THR cc_start: 0.8316 (m) cc_final: 0.7884 (m) REVERT: A 133 GLU cc_start: 0.6322 (pm20) cc_final: 0.5912 (pt0) REVERT: B 45 ARG cc_start: 0.6277 (tpt90) cc_final: 0.5876 (mmm160) REVERT: B 84 MET cc_start: 0.7202 (tpt) cc_final: 0.6082 (tpp) REVERT: B 91 LYS cc_start: 0.7789 (tmmt) cc_final: 0.7252 (tttt) REVERT: C 28 MET cc_start: 0.4491 (mtm) cc_final: 0.3684 (tpt) REVERT: C 42 PHE cc_start: 0.7153 (m-10) cc_final: 0.6852 (m-80) REVERT: C 65 GLU cc_start: 0.8514 (tt0) cc_final: 0.7723 (tp30) REVERT: C 66 TYR cc_start: 0.6092 (t80) cc_final: 0.5842 (t80) REVERT: C 70 GLU cc_start: 0.7395 (tt0) cc_final: 0.6960 (tt0) REVERT: C 98 ASN cc_start: 0.8032 (m-40) cc_final: 0.7411 (t0) REVERT: D 63 LYS cc_start: 0.7233 (mmtp) cc_final: 0.6662 (mmmt) REVERT: D 84 MET cc_start: 0.6326 (ttp) cc_final: 0.6018 (ttp) REVERT: D 87 MET cc_start: 0.8182 (mmm) cc_final: 0.7921 (mmm) REVERT: D 130 GLU cc_start: 0.7063 (mp0) cc_final: 0.6412 (mt-10) REVERT: E 79 LYS cc_start: 0.6871 (tmtt) cc_final: 0.6536 (mmtt) REVERT: F 63 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7755 (mm-30) REVERT: F 66 ILE cc_start: 0.8758 (mm) cc_final: 0.8493 (mm) REVERT: G 38 ARG cc_start: 0.6608 (ttt180) cc_final: 0.6110 (tpp80) REVERT: G 73 GLU cc_start: 0.7043 (pt0) cc_final: 0.6682 (pt0) REVERT: G 83 LYS cc_start: 0.8160 (mmmm) cc_final: 0.6819 (ptpp) REVERT: H 108 TYR cc_start: 0.4549 (m-10) cc_final: 0.4261 (m-10) REVERT: H 118 GLU cc_start: 0.8225 (mp0) cc_final: 0.7345 (mp0) REVERT: H 125 LEU cc_start: 0.9153 (mm) cc_final: 0.8860 (mp) REVERT: H 127 LEU cc_start: 0.7921 (mm) cc_final: 0.7521 (mp) REVERT: K 233 LYS cc_start: 0.7400 (tttt) cc_final: 0.7093 (tttt) REVERT: K 249 LEU cc_start: 0.8278 (mt) cc_final: 0.7701 (tp) REVERT: K 253 TYR cc_start: 0.7160 (m-10) cc_final: 0.6546 (m-80) REVERT: K 315 MET cc_start: 0.7419 (tpp) cc_final: 0.7009 (tpp) REVERT: K 373 TRP cc_start: 0.6618 (t-100) cc_final: 0.6301 (t-100) REVERT: K 384 PHE cc_start: 0.8297 (m-80) cc_final: 0.7195 (m-10) REVERT: K 623 ASN cc_start: 0.7779 (t0) cc_final: 0.7534 (t0) REVERT: K 652 GLN cc_start: 0.5703 (OUTLIER) cc_final: 0.5192 (tm-30) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.1115 time to fit residues: 44.9917 Evaluate side-chains 214 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 chunk 82 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 68 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.068431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051123 restraints weight = 82828.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.052690 restraints weight = 43408.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053680 restraints weight = 28467.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054322 restraints weight = 21922.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.054657 restraints weight = 18693.281| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14582 Z= 0.172 Angle : 0.731 9.442 20617 Z= 0.403 Chirality : 0.046 0.252 2338 Planarity : 0.005 0.097 1836 Dihedral : 28.794 136.048 3682 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1142 helix: 0.80 (0.18), residues: 761 sheet: -0.83 (0.75), residues: 50 loop : -1.82 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 531 TYR 0.013 0.002 TYR C 59 PHE 0.033 0.002 PHE C 34 TRP 0.020 0.003 TRP K 327 HIS 0.009 0.002 HIS K 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (14582) covalent geometry : angle 0.73064 / 0.40 (20617) hydrogen bonds : bond 0.04981 / 3.37 ( 861) hydrogen bonds : angle 4.10734 / 2.91 ( 2278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.93 seconds wall clock time: 36 minutes 56.64 seconds (2216.64 seconds total)