Starting phenix.real_space_refine on Thu Aug 6 04:54:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j90_36083/08_2026/8j90_36083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j90_36083/08_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_36083/08_2026/8j90_36083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j90_36083/08_2026/8j90_36083.map" model { file = "/net/cci-nas-00/data/ceres_data/8j90_36083/08_2026/8j90_36083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j90_36083/08_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-2.2rc3-6140/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: 2.51, per 1000 atoms: 0.18 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: 1.12 Conformation dependent library (CDL) restraints added in 453.9 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: 1.32 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: 2.63 Time building geometry restraints manager: 1.53 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- 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 : 0.926 22.166 20617 Z= 0.679 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 0.92630 / 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 : 0.290 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 62 ILE cc_start: 0.7989 (pt) cc_final: 0.7650 (mt) REVERT: A 64 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7910 (mttp) REVERT: A 80 THR cc_start: 0.8557 (p) cc_final: 0.8225 (p) REVERT: A 86 SER cc_start: 0.8211 (m) cc_final: 0.7542 (t) REVERT: A 89 VAL cc_start: 0.7749 (t) cc_final: 0.7465 (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: 0.8145 (m) REVERT: A 133 GLU cc_start: 0.6612 (pm20) cc_final: 0.6387 (pt0) REVERT: B 27 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7109 (tt0) REVERT: B 31 LYS cc_start: 0.8720 (tttt) cc_final: 0.8475 (mmtm) REVERT: B 49 LEU cc_start: 0.9000 (mp) cc_final: 0.8726 (tt) REVERT: B 84 MET cc_start: 0.7223 (tpt) cc_final: 0.6510 (mmm) REVERT: B 88 TYR cc_start: 0.6724 (m-80) cc_final: 0.6184 (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: 0.5200 (ttp) REVERT: C 42 PHE cc_start: 0.7579 (m-10) cc_final: 0.7297 (m-80) REVERT: C 98 ASN cc_start: 0.7733 (m-40) cc_final: 0.7532 (t0) REVERT: D 62 TYR cc_start: 0.7562 (m-10) cc_final: 0.7228 (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: 0.7914 (mm) REVERT: D 112 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7828 (Cg_endo) REVERT: D 130 GLU cc_start: 0.7793 (mp0) cc_final: 0.7256 (mt-10) REVERT: E 73 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7949 (tm-30) REVERT: E 79 LYS cc_start: 0.7158 (tmtt) cc_final: 0.6427 (mmtp) REVERT: E 94 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7878 (mt-10) REVERT: F 22 LEU cc_start: 0.7228 (tt) cc_final: 0.6993 (pp) REVERT: G 34 PHE cc_start: 0.5253 (m-10) cc_final: 0.4810 (m-80) REVERT: G 42 PHE cc_start: 0.7250 (m-80) cc_final: 0.6940 (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: 0.8291 (tt) REVERT: H 127 LEU cc_start: 0.7947 (mm) cc_final: 0.7618 (mp) REVERT: K 241 LEU cc_start: 0.8096 (mm) cc_final: 0.7835 (mm) REVERT: K 249 LEU cc_start: 0.8247 (mt) cc_final: 0.7782 (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: 0.6869 (tp) REVERT: K 324 HIS cc_start: 0.6129 (m90) cc_final: 0.5768 (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: 0.7512 (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: 0.6383 (m-30) REVERT: K 384 PHE cc_start: 0.8174 (m-80) cc_final: 0.7612 (m-80) REVERT: K 459 PHE cc_start: 0.7264 (m-10) cc_final: 0.7041 (m-80) REVERT: K 468 LEU cc_start: 0.8389 (tp) cc_final: 0.7953 (tp) REVERT: K 557 ASP cc_start: 0.8072 (t0) cc_final: 0.7651 (t70) REVERT: K 569 ARG cc_start: 0.6738 (ttt90) cc_final: 0.6035 (ttm-80) REVERT: K 618 TYR cc_start: 0.7568 (t80) cc_final: 0.6954 (t80) REVERT: K 621 ASP cc_start: 0.7324 (t0) cc_final: 0.6741 (m-30) REVERT: K 623 ASN cc_start: 0.8221 (t0) cc_final: 0.7978 (t0) REVERT: K 631 MET cc_start: 0.6804 (ppp) cc_final: 0.6600 (tpt) REVERT: K 636 ARG cc_start: 0.5498 (ttt90) cc_final: 0.5276 (tmt170) REVERT: K 748 TRP cc_start: 0.5448 (p-90) cc_final: 0.5217 (p-90) REVERT: K 755 SER cc_start: 0.7446 (p) cc_final: 0.7224 (t) outliers start: 3 outliers final: 0 residues processed: 493 average time/residue: 0.1320 time to fit residues: 87.6696 Evaluate side-chains 260 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 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 ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.068977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.050785 restraints weight = 81423.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052166 restraints weight = 46896.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.053041 restraints weight = 32808.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053524 restraints weight = 26439.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.053887 restraints weight = 23362.530| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3199 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= 0.247 Angle : 0.824 11.189 20617 Z= 0.454 Chirality : 0.051 0.278 2338 Planarity : 0.007 0.068 1836 Dihedral : 28.490 136.082 3682 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.40 % Allowed : 7.58 % Favored : 92.02 % 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: -0.33 (0.24), residues: 1142 helix: 0.31 (0.17), residues: 770 sheet: -0.45 (0.71), residues: 49 loop : -1.27 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 77 TYR 0.025 0.003 TYR K 281 PHE 0.025 0.003 PHE K 596 TRP 0.026 0.003 TRP K 373 HIS 0.021 0.002 HIS K 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.25 (14582) covalent geometry : angle 0.82395 / 0.45 (20617) hydrogen bonds : bond 0.06011 / 4.10 ( 861) hydrogen bonds : angle 4.63234 / 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 303 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 299 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7672 (t80) cc_final: 0.7368 (t80) REVERT: A 86 SER cc_start: 0.8470 (m) cc_final: 0.8182 (t) REVERT: A 133 GLU cc_start: 0.6543 (pm20) cc_final: 0.5767 (pt0) REVERT: B 27 GLN cc_start: 0.7324 (mm-40) cc_final: 0.6769 (tt0) REVERT: B 84 MET cc_start: 0.7223 (tpt) cc_final: 0.6653 (mmm) REVERT: B 88 TYR cc_start: 0.6829 (m-80) cc_final: 0.6300 (m-80) REVERT: B 91 LYS cc_start: 0.7880 (tmmt) cc_final: 0.7384 (tttt) REVERT: B 98 TYR cc_start: 0.6692 (m-10) cc_final: 0.6379 (m-10) REVERT: C 28 MET cc_start: 0.5250 (mtm) cc_final: 0.4454 (ttp) REVERT: C 42 PHE cc_start: 0.7375 (m-10) cc_final: 0.7156 (m-80) REVERT: C 98 ASN cc_start: 0.7775 (m-40) cc_final: 0.7289 (t0) REVERT: D 63 LYS cc_start: 0.7133 (mptt) cc_final: 0.6543 (mmmt) REVERT: D 64 ILE cc_start: 0.7965 (pt) cc_final: 0.7676 (pt) REVERT: D 110 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6298 (mtpp) REVERT: D 125 LEU cc_start: 0.7714 (pp) cc_final: 0.7495 (pp) REVERT: D 130 GLU cc_start: 0.7870 (mp0) cc_final: 0.7155 (mt-10) REVERT: E 70 LEU cc_start: 0.9047 (tt) cc_final: 0.8769 (tt) REVERT: E 79 LYS cc_start: 0.7023 (tmtt) cc_final: 0.6628 (mmtt) REVERT: E 94 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6481 (mm-30) REVERT: F 21 VAL cc_start: 0.6268 (t) cc_final: 0.5888 (m) REVERT: G 83 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7020 (ptpp) REVERT: H 105 LEU cc_start: 0.7386 (pp) cc_final: 0.7065 (pp) REVERT: H 110 LYS cc_start: 0.6730 (tptt) cc_final: 0.6162 (ttmt) REVERT: K 229 MET cc_start: 0.5193 (ptt) cc_final: 0.4757 (ptt) REVERT: K 249 LEU cc_start: 0.8261 (mt) cc_final: 0.7596 (tp) REVERT: K 281 TYR cc_start: 0.7454 (t80) cc_final: 0.6198 (t80) REVERT: K 282 HIS cc_start: 0.5146 (m90) cc_final: 0.4547 (m170) REVERT: K 315 MET cc_start: 0.7115 (tpp) cc_final: 0.6889 (tpp) REVERT: K 373 TRP cc_start: 0.6871 (t-100) cc_final: 0.6540 (t-100) REVERT: K 382 ASP cc_start: 0.6754 (m-30) cc_final: 0.6378 (m-30) REVERT: K 384 PHE cc_start: 0.8322 (m-80) cc_final: 0.7635 (m-80) REVERT: K 553 LEU cc_start: 0.7505 (mp) cc_final: 0.7168 (mt) REVERT: K 570 ILE cc_start: 0.6635 (mm) cc_final: 0.6134 (mp) REVERT: K 621 ASP cc_start: 0.7203 (t0) cc_final: 0.6693 (m-30) REVERT: K 623 ASN cc_start: 0.8073 (t0) cc_final: 0.7819 (t0) REVERT: K 646 TYR cc_start: 0.5204 (m-80) cc_final: 0.4988 (m-80) outliers start: 4 outliers final: 0 residues processed: 302 average time/residue: 0.0993 time to fit residues: 43.6346 Evaluate side-chains 216 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 75 optimal weight: 50.0000 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 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 = 0.3457 r_free = 0.3457 target = 0.068862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051554 restraints weight = 81862.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053133 restraints weight = 43575.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054143 restraints weight = 28855.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054775 restraints weight = 22277.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.055168 restraints weight = 19073.045| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14582 Z= 0.166 Angle : 0.726 11.081 20617 Z= 0.405 Chirality : 0.046 0.204 2338 Planarity : 0.005 0.049 1836 Dihedral : 28.520 135.761 3682 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % 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: -0.08 (0.24), residues: 1142 helix: 0.57 (0.18), residues: 774 sheet: -0.57 (0.71), residues: 49 loop : -1.33 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 531 TYR 0.015 0.002 TYR C 48 PHE 0.033 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 0.00317 / 0.17 (14582) covalent geometry : angle 0.72572 / 0.40 (20617) hydrogen bonds : bond 0.05076 / 3.45 ( 861) hydrogen bonds : angle 4.28684 / 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 308 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7659 (t80) cc_final: 0.7267 (t80) REVERT: A 86 SER cc_start: 0.8368 (m) cc_final: 0.7632 (t) REVERT: A 89 VAL cc_start: 0.7598 (t) cc_final: 0.7374 (m) REVERT: A 109 LEU cc_start: 0.8944 (tp) cc_final: 0.8572 (tp) REVERT: A 133 GLU cc_start: 0.6512 (pm20) cc_final: 0.6010 (pt0) REVERT: B 43 VAL cc_start: 0.6959 (t) cc_final: 0.6742 (t) REVERT: B 91 LYS cc_start: 0.7684 (tmmt) cc_final: 0.7283 (tttt) REVERT: C 28 MET cc_start: 0.5022 (mtm) cc_final: 0.4107 (ttp) REVERT: C 42 PHE cc_start: 0.7403 (m-10) cc_final: 0.7080 (m-80) REVERT: C 98 ASN cc_start: 0.7821 (m-40) cc_final: 0.7398 (t0) REVERT: D 63 LYS cc_start: 0.7368 (mptt) cc_final: 0.6894 (mmmm) REVERT: D 110 LYS cc_start: 0.6802 (mmtt) cc_final: 0.6265 (mtpp) REVERT: D 125 LEU cc_start: 0.7676 (pp) cc_final: 0.7450 (pp) REVERT: D 130 GLU cc_start: 0.7772 (mp0) cc_final: 0.6974 (mt-10) REVERT: E 79 LYS cc_start: 0.6892 (tmtt) cc_final: 0.6506 (mmtt) REVERT: G 83 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7074 (ptpp) REVERT: H 60 GLU cc_start: 0.5620 (mp0) cc_final: 0.5314 (tt0) REVERT: K 249 LEU cc_start: 0.8275 (mt) cc_final: 0.7818 (tp) REVERT: K 315 MET cc_start: 0.7073 (tpp) cc_final: 0.6602 (tpp) REVERT: K 373 TRP cc_start: 0.6632 (t-100) cc_final: 0.6314 (t-100) REVERT: K 382 ASP cc_start: 0.6765 (m-30) cc_final: 0.6456 (m-30) REVERT: K 384 PHE cc_start: 0.8366 (m-80) cc_final: 0.7420 (m-80) REVERT: K 552 LEU cc_start: 0.7946 (tt) cc_final: 0.7648 (tp) REVERT: K 557 ASP cc_start: 0.8044 (t0) cc_final: 0.7797 (t70) REVERT: K 560 PHE cc_start: 0.7782 (m-80) cc_final: 0.7499 (m-10) REVERT: K 570 ILE cc_start: 0.6384 (mm) cc_final: 0.6031 (mp) REVERT: K 621 ASP cc_start: 0.7300 (t0) cc_final: 0.6838 (m-30) REVERT: K 623 ASN cc_start: 0.8120 (t0) cc_final: 0.7891 (t0) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.0982 time to fit residues: 43.8109 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 : 0.406 ------------------------------------------------------------------------------- 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: 0.9990 chunk 130 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 50.0000 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** ** D 88 ASN ** 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 455 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.068271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051332 restraints weight = 80598.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052902 restraints weight = 42241.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.053879 restraints weight = 27673.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054537 restraints weight = 21293.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054923 restraints weight = 18175.573| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4055 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= 0.164 Angle : 0.706 9.491 20617 Z= 0.394 Chirality : 0.045 0.252 2338 Planarity : 0.005 0.058 1836 Dihedral : 28.575 136.037 3682 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 0.20 % Allowed : 4.59 % Favored : 95.21 % 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: 0.67 (0.18), residues: 771 sheet: -0.70 (0.71), residues: 49 loop : -1.31 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 117 TYR 0.033 0.002 TYR B 88 PHE 0.033 0.002 PHE D 67 TRP 0.032 0.002 TRP K 748 HIS 0.011 0.002 HIS K 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (14582) covalent geometry : angle 0.70620 / 0.39 (20617) hydrogen bonds : bond 0.04870 / 3.32 ( 861) hydrogen bonds : angle 4.20038 / 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 294 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.372 Fit side-chains 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: 0.7286 (t80) REVERT: A 86 SER cc_start: 0.8314 (m) cc_final: 0.7557 (t) REVERT: A 89 VAL cc_start: 0.7531 (t) cc_final: 0.7330 (m) REVERT: A 105 GLU cc_start: 0.7909 (tp30) cc_final: 0.7551 (tp30) REVERT: A 133 GLU cc_start: 0.6644 (pm20) cc_final: 0.6160 (pt0) REVERT: B 84 MET cc_start: 0.7264 (tpt) cc_final: 0.6800 (mmm) REVERT: B 88 TYR cc_start: 0.7166 (m-80) cc_final: 0.6648 (m-80) REVERT: B 91 LYS cc_start: 0.7641 (tmmt) cc_final: 0.7117 (tttt) REVERT: C 28 MET cc_start: 0.5073 (mtm) cc_final: 0.4124 (ttp) REVERT: C 42 PHE cc_start: 0.7418 (m-10) cc_final: 0.7076 (m-80) REVERT: C 98 ASN cc_start: 0.7834 (m-40) cc_final: 0.7405 (t0) REVERT: D 62 TYR cc_start: 0.6905 (m-10) cc_final: 0.6697 (m-10) REVERT: D 110 LYS cc_start: 0.6882 (mmtt) cc_final: 0.6318 (mtpp) REVERT: D 130 GLU cc_start: 0.7723 (mp0) cc_final: 0.6984 (mt-10) REVERT: E 79 LYS cc_start: 0.7130 (tmtt) cc_final: 0.6596 (mmtt) REVERT: F 63 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: G 77 ASN cc_start: 0.8178 (t0) cc_final: 0.7958 (t0) REVERT: G 83 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7142 (ptpp) REVERT: H 105 LEU cc_start: 0.7340 (pp) cc_final: 0.7023 (pp) REVERT: K 249 LEU cc_start: 0.8329 (mt) cc_final: 0.7892 (tp) REVERT: K 253 TYR cc_start: 0.5935 (m-80) cc_final: 0.4924 (m-10) REVERT: K 315 MET cc_start: 0.7161 (tpp) cc_final: 0.6655 (tpp) REVERT: K 329 TYR cc_start: 0.6945 (m-80) cc_final: 0.6613 (t80) REVERT: K 354 MET cc_start: 0.6301 (ppp) cc_final: 0.6075 (ppp) REVERT: K 373 TRP cc_start: 0.6674 (t-100) cc_final: 0.6356 (t-100) REVERT: K 380 LEU cc_start: 0.7325 (mp) cc_final: 0.6980 (mp) REVERT: K 382 ASP cc_start: 0.6847 (m-30) cc_final: 0.6462 (m-30) REVERT: K 384 PHE cc_start: 0.8246 (m-80) cc_final: 0.7247 (m-10) REVERT: K 468 LEU cc_start: 0.8113 (tp) cc_final: 0.7881 (tp) REVERT: K 527 ARG cc_start: 0.8453 (ppt170) cc_final: 0.8142 (ptt90) REVERT: K 552 LEU cc_start: 0.7913 (tt) cc_final: 0.7682 (tp) REVERT: K 557 ASP cc_start: 0.8070 (t0) cc_final: 0.7814 (t70) REVERT: K 560 PHE cc_start: 0.7851 (m-80) cc_final: 0.7559 (m-10) REVERT: K 621 ASP cc_start: 0.7496 (t0) cc_final: 0.7064 (m-30) REVERT: K 623 ASN cc_start: 0.7972 (t0) cc_final: 0.7688 (t0) REVERT: K 626 MET cc_start: 0.7841 (tpt) cc_final: 0.7464 (tpt) REVERT: K 652 GLN cc_start: 0.4907 (tm-30) cc_final: 0.4681 (tm-30) outliers start: 2 outliers final: 1 residues processed: 293 average time/residue: 0.0910 time to fit residues: 39.5044 Evaluate side-chains 222 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 20.0000 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 72 optimal weight: 50.0000 chunk 82 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN K 219 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.068274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051140 restraints weight = 81700.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052755 restraints weight = 42898.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053769 restraints weight = 28031.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.054410 restraints weight = 21487.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054762 restraints weight = 18337.799| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14582 Z= 0.164 Angle : 0.706 8.746 20617 Z= 0.394 Chirality : 0.045 0.203 2338 Planarity : 0.005 0.050 1836 Dihedral : 28.648 136.760 3682 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: -0.06 (0.24), residues: 1142 helix: 0.63 (0.18), residues: 770 sheet: -0.56 (0.75), residues: 49 loop : -1.44 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 288 TYR 0.020 0.002 TYR B 88 PHE 0.040 0.002 PHE D 67 TRP 0.040 0.003 TRP K 748 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (14582) covalent geometry : angle 0.70624 / 0.39 (20617) hydrogen bonds : bond 0.04819 / 3.28 ( 861) hydrogen bonds : angle 4.10415 / 2.90 ( 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 287 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7733 (t80) cc_final: 0.7341 (t80) REVERT: A 86 SER cc_start: 0.8390 (m) cc_final: 0.7651 (t) REVERT: A 89 VAL cc_start: 0.7555 (t) cc_final: 0.7217 (m) REVERT: A 105 GLU cc_start: 0.7861 (tp30) cc_final: 0.7532 (tp30) REVERT: A 109 LEU cc_start: 0.9036 (tp) cc_final: 0.8765 (tp) REVERT: A 133 GLU cc_start: 0.6623 (pm20) cc_final: 0.6119 (pt0) REVERT: B 43 VAL cc_start: 0.7012 (t) cc_final: 0.6788 (t) REVERT: B 46 ILE cc_start: 0.8171 (mt) cc_final: 0.7921 (mt) REVERT: B 75 HIS cc_start: 0.8882 (t70) cc_final: 0.8672 (t-170) REVERT: B 88 TYR cc_start: 0.7197 (m-80) cc_final: 0.6986 (m-80) REVERT: B 91 LYS cc_start: 0.7717 (tmmt) cc_final: 0.7246 (tttt) REVERT: B 97 LEU cc_start: 0.7740 (tp) cc_final: 0.7430 (tp) REVERT: C 28 MET cc_start: 0.5021 (mtm) cc_final: 0.3903 (ttp) REVERT: C 42 PHE cc_start: 0.7398 (m-10) cc_final: 0.7074 (m-80) REVERT: C 98 ASN cc_start: 0.7827 (m-40) cc_final: 0.7438 (t0) REVERT: D 110 LYS cc_start: 0.5817 (mmtp) cc_final: 0.5366 (mtpp) REVERT: D 130 GLU cc_start: 0.7727 (mp0) cc_final: 0.7004 (mt-10) REVERT: E 79 LYS cc_start: 0.7047 (tmtt) cc_final: 0.6687 (mmtt) REVERT: F 100 PHE cc_start: 0.6777 (m-10) cc_final: 0.6088 (m-10) REVERT: G 77 ASN cc_start: 0.8155 (t0) cc_final: 0.7926 (t0) REVERT: G 83 LYS cc_start: 0.8234 (mmmm) cc_final: 0.7056 (ptpp) REVERT: H 105 LEU cc_start: 0.7359 (pp) cc_final: 0.7105 (pp) REVERT: K 237 THR cc_start: 0.7869 (p) cc_final: 0.7652 (p) REVERT: K 249 LEU cc_start: 0.8344 (mt) cc_final: 0.7970 (tp) REVERT: K 253 TYR cc_start: 0.5752 (m-80) cc_final: 0.4736 (m-10) REVERT: K 315 MET cc_start: 0.7427 (tpp) cc_final: 0.6858 (tpp) REVERT: K 334 GLU cc_start: 0.7860 (pt0) cc_final: 0.7606 (mp0) REVERT: K 373 TRP cc_start: 0.6631 (t-100) cc_final: 0.6318 (t-100) REVERT: K 382 ASP cc_start: 0.6974 (m-30) cc_final: 0.6630 (m-30) REVERT: K 384 PHE cc_start: 0.8428 (m-80) cc_final: 0.7399 (m-10) REVERT: K 527 ARG cc_start: 0.8417 (ppt170) cc_final: 0.8199 (ptt90) REVERT: K 552 LEU cc_start: 0.7683 (tt) cc_final: 0.7464 (tp) REVERT: K 621 ASP cc_start: 0.7557 (t0) cc_final: 0.7297 (m-30) REVERT: K 623 ASN cc_start: 0.7870 (t0) cc_final: 0.7554 (t0) REVERT: K 652 GLN cc_start: 0.4919 (tm-30) cc_final: 0.4685 (tm-30) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.0984 time to fit residues: 41.8904 Evaluate side-chains 210 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 20.0000 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 85 optimal weight: 0.0020 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 40.0000 chunk 96 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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** ** H 120 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 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 455 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052079 restraints weight = 81830.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053608 restraints weight = 44285.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054574 restraints weight = 29669.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055121 restraints weight = 23206.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055546 restraints weight = 20169.593| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14582 Z= 0.143 Angle : 0.694 12.136 20617 Z= 0.386 Chirality : 0.045 0.304 2338 Planarity : 0.005 0.049 1836 Dihedral : 28.582 135.705 3682 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 0.10 % Allowed : 3.29 % Favored : 96.61 % 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: 0.27 (0.24), residues: 1142 helix: 0.87 (0.18), residues: 764 sheet: -0.77 (0.74), residues: 49 loop : -1.19 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 63 TYR 0.027 0.002 TYR B 88 PHE 0.027 0.002 PHE C 34 TRP 0.011 0.002 TRP K 217 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (14582) covalent geometry : angle 0.69450 / 0.39 (20617) hydrogen bonds : bond 0.04510 / 3.08 ( 861) hydrogen bonds : angle 4.00625 / 2.83 ( 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 289 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7649 (t80) cc_final: 0.7331 (t80) REVERT: A 86 SER cc_start: 0.8327 (m) cc_final: 0.7539 (t) REVERT: A 89 VAL cc_start: 0.7603 (t) cc_final: 0.7394 (m) REVERT: A 105 GLU cc_start: 0.7717 (tp30) cc_final: 0.7487 (tp30) REVERT: A 133 GLU cc_start: 0.6538 (pm20) cc_final: 0.6039 (pt0) REVERT: B 43 VAL cc_start: 0.7071 (t) cc_final: 0.6862 (t) REVERT: B 46 ILE cc_start: 0.8257 (mt) cc_final: 0.7985 (mt) REVERT: B 75 HIS cc_start: 0.8833 (t70) cc_final: 0.8568 (t-170) REVERT: B 91 LYS cc_start: 0.7807 (tmmt) cc_final: 0.7535 (tttt) REVERT: C 28 MET cc_start: 0.4905 (mtm) cc_final: 0.4301 (tpt) REVERT: C 98 ASN cc_start: 0.7923 (m-40) cc_final: 0.7335 (t0) REVERT: D 110 LYS cc_start: 0.5691 (mmtp) cc_final: 0.5249 (mtpp) REVERT: D 127 LEU cc_start: 0.8100 (mm) cc_final: 0.7751 (mm) REVERT: D 130 GLU cc_start: 0.7379 (mp0) cc_final: 0.6583 (mt-10) REVERT: E 79 LYS cc_start: 0.7051 (tmtt) cc_final: 0.6622 (mmtt) REVERT: G 83 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7042 (ptpp) REVERT: K 249 LEU cc_start: 0.8317 (mt) cc_final: 0.7860 (tp) REVERT: K 289 ASP cc_start: 0.8240 (m-30) cc_final: 0.8040 (m-30) REVERT: K 315 MET cc_start: 0.7234 (tpp) cc_final: 0.6630 (tpp) REVERT: K 373 TRP cc_start: 0.6684 (t-100) cc_final: 0.6311 (t-100) REVERT: K 380 LEU cc_start: 0.7539 (mp) cc_final: 0.7264 (mp) REVERT: K 382 ASP cc_start: 0.7102 (m-30) cc_final: 0.6776 (m-30) REVERT: K 384 PHE cc_start: 0.8241 (m-80) cc_final: 0.7230 (m-10) REVERT: K 537 PHE cc_start: 0.8264 (t80) cc_final: 0.8051 (t80) REVERT: K 557 ASP cc_start: 0.7855 (t0) cc_final: 0.7619 (t70) REVERT: K 621 ASP cc_start: 0.7375 (t0) cc_final: 0.7144 (m-30) REVERT: K 623 ASN cc_start: 0.7810 (t0) cc_final: 0.7548 (t0) REVERT: K 657 ARG cc_start: 0.8522 (ptm160) cc_final: 0.8020 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.1058 time to fit residues: 44.9178 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 : 0.450 ------------------------------------------------------------------------------- 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: 1.9990 chunk 127 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 75 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN ** 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** H 120 GLN K 219 ASN ** K 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051862 restraints weight = 82544.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.053359 restraints weight = 44748.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.054336 restraints weight = 30216.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054904 restraints weight = 23608.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.055200 restraints weight = 20540.360| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14582 Z= 0.159 Angle : 0.711 10.084 20617 Z= 0.394 Chirality : 0.045 0.259 2338 Planarity : 0.005 0.046 1836 Dihedral : 28.592 136.034 3682 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: 0.10 (0.24), residues: 1142 helix: 0.78 (0.18), residues: 765 sheet: -0.89 (0.73), residues: 49 loop : -1.37 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.040 0.003 TYR B 88 PHE 0.034 0.002 PHE C 34 TRP 0.011 0.002 TRP K 217 HIS 0.012 0.002 HIS K 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (14582) covalent geometry : angle 0.71121 / 0.39 (20617) hydrogen bonds : bond 0.04648 / 3.18 ( 861) hydrogen bonds : angle 4.03325 / 2.86 ( 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 276 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7790 (t80) cc_final: 0.7445 (t80) REVERT: A 86 SER cc_start: 0.8381 (m) cc_final: 0.7621 (t) REVERT: A 89 VAL cc_start: 0.7552 (t) cc_final: 0.7342 (m) REVERT: A 94 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6975 (mt-10) REVERT: A 105 GLU cc_start: 0.7772 (tp30) cc_final: 0.7526 (tp30) REVERT: A 133 GLU cc_start: 0.6545 (pm20) cc_final: 0.6022 (pt0) REVERT: B 46 ILE cc_start: 0.8223 (mt) cc_final: 0.7959 (mt) REVERT: B 75 HIS cc_start: 0.8910 (t70) cc_final: 0.8682 (t-170) REVERT: B 91 LYS cc_start: 0.7846 (tmmt) cc_final: 0.7486 (tttt) REVERT: C 28 MET cc_start: 0.5061 (mtm) cc_final: 0.4342 (tpt) REVERT: C 65 GLU cc_start: 0.8488 (tt0) cc_final: 0.8245 (tt0) REVERT: C 96 ILE cc_start: 0.7268 (mm) cc_final: 0.7043 (mm) REVERT: C 98 ASN cc_start: 0.7915 (m-40) cc_final: 0.7319 (t0) REVERT: D 120 GLN cc_start: 0.7851 (pp30) cc_final: 0.7551 (pp30) REVERT: D 130 GLU cc_start: 0.7340 (mp0) cc_final: 0.6566 (mt-10) REVERT: E 79 LYS cc_start: 0.7010 (tmtt) cc_final: 0.6582 (mmtt) REVERT: G 83 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7020 (ptpp) REVERT: H 101 GLU cc_start: 0.8032 (tp30) cc_final: 0.7830 (tp30) REVERT: K 214 ILE cc_start: 0.8064 (mm) cc_final: 0.7718 (mm) REVERT: K 237 THR cc_start: 0.7774 (p) cc_final: 0.7569 (p) REVERT: K 243 HIS cc_start: 0.5932 (t-170) cc_final: 0.5513 (t-170) REVERT: K 249 LEU cc_start: 0.8385 (mt) cc_final: 0.7941 (tp) REVERT: K 256 ILE cc_start: 0.8876 (mp) cc_final: 0.8660 (mp) REVERT: K 315 MET cc_start: 0.7093 (tpp) cc_final: 0.6499 (tpp) REVERT: K 354 MET cc_start: 0.6320 (ppp) cc_final: 0.6107 (ppp) REVERT: K 373 TRP cc_start: 0.6695 (t-100) cc_final: 0.6346 (t-100) REVERT: K 382 ASP cc_start: 0.7101 (m-30) cc_final: 0.6792 (m-30) REVERT: K 384 PHE cc_start: 0.8372 (m-80) cc_final: 0.7297 (m-10) REVERT: K 537 PHE cc_start: 0.8205 (t80) cc_final: 0.7969 (t80) REVERT: K 621 ASP cc_start: 0.7481 (t0) cc_final: 0.7236 (m-30) REVERT: K 623 ASN cc_start: 0.7872 (t0) cc_final: 0.7571 (t0) REVERT: K 652 GLN cc_start: 0.5458 (tm130) cc_final: 0.4981 (tm-30) REVERT: K 657 ARG cc_start: 0.8536 (ptm160) cc_final: 0.8030 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.0975 time to fit residues: 40.5426 Evaluate side-chains 210 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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: 7.9990 chunk 116 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 74 optimal weight: 50.0000 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 40.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** 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 282 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 = 0.3459 r_free = 0.3459 target = 0.069336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.051966 restraints weight = 82694.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053588 restraints weight = 43141.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054616 restraints weight = 28413.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055221 restraints weight = 21937.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055640 restraints weight = 18906.764| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14582 Z= 0.146 Angle : 0.711 9.672 20617 Z= 0.389 Chirality : 0.046 0.222 2338 Planarity : 0.005 0.053 1836 Dihedral : 28.573 135.664 3682 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % 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: 0.14 (0.24), residues: 1142 helix: 0.86 (0.18), residues: 760 sheet: -0.83 (0.74), residues: 49 loop : -1.44 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 531 TYR 0.036 0.002 TYR B 88 PHE 0.038 0.002 PHE K 596 TRP 0.013 0.002 TRP K 217 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (14582) covalent geometry : angle 0.71077 / 0.39 (20617) hydrogen bonds : bond 0.04447 / 3.05 ( 861) hydrogen bonds : angle 3.99623 / 2.84 ( 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 273 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7817 (t80) cc_final: 0.7446 (t80) REVERT: A 86 SER cc_start: 0.8336 (m) cc_final: 0.7580 (t) REVERT: A 105 GLU cc_start: 0.7885 (tp30) cc_final: 0.7615 (tp30) REVERT: A 133 GLU cc_start: 0.6644 (pm20) cc_final: 0.6213 (pt0) REVERT: B 46 ILE cc_start: 0.8139 (mt) cc_final: 0.7928 (mt) REVERT: B 91 LYS cc_start: 0.7863 (tmmt) cc_final: 0.7529 (tttt) REVERT: C 28 MET cc_start: 0.4711 (mtm) cc_final: 0.3976 (tpt) REVERT: C 65 GLU cc_start: 0.8095 (tt0) cc_final: 0.7778 (mt-10) REVERT: C 98 ASN cc_start: 0.8046 (m-40) cc_final: 0.7488 (t0) REVERT: D 120 GLN cc_start: 0.7850 (pp30) cc_final: 0.7578 (pp30) REVERT: D 130 GLU cc_start: 0.7266 (mp0) cc_final: 0.6489 (mt-10) REVERT: E 79 LYS cc_start: 0.6922 (tmtt) cc_final: 0.6487 (mmtt) REVERT: G 83 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7023 (ptpp) REVERT: H 101 GLU cc_start: 0.8010 (tp30) cc_final: 0.7778 (tp30) REVERT: H 125 LEU cc_start: 0.8726 (tt) cc_final: 0.8331 (tt) REVERT: K 214 ILE cc_start: 0.7923 (mm) cc_final: 0.7554 (mm) REVERT: K 243 HIS cc_start: 0.6188 (t-170) cc_final: 0.5696 (t-170) REVERT: K 249 LEU cc_start: 0.8459 (mt) cc_final: 0.8041 (tp) REVERT: K 288 ARG cc_start: 0.6215 (mpt-90) cc_final: 0.5960 (mpt-90) REVERT: K 315 MET cc_start: 0.7308 (tpp) cc_final: 0.6722 (tpp) REVERT: K 373 TRP cc_start: 0.6666 (t-100) cc_final: 0.6345 (t-100) REVERT: K 380 LEU cc_start: 0.7421 (mp) cc_final: 0.7165 (mp) REVERT: K 382 ASP cc_start: 0.7039 (m-30) cc_final: 0.6750 (m-30) REVERT: K 384 PHE cc_start: 0.8441 (m-80) cc_final: 0.7321 (m-10) REVERT: K 621 ASP cc_start: 0.7688 (t0) cc_final: 0.7469 (m-30) REVERT: K 623 ASN cc_start: 0.7860 (t0) cc_final: 0.7485 (t0) REVERT: K 657 ARG cc_start: 0.8556 (ptm160) cc_final: 0.8044 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.0985 time to fit residues: 40.0016 Evaluate side-chains 210 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 0.8980 chunk 79 optimal weight: 40.0000 chunk 38 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 65 optimal weight: 40.0000 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 chunk 63 optimal weight: 50.0000 chunk 42 optimal weight: 3.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN K 324 HIS ** K 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 ASN K 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.068231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.050974 restraints weight = 83444.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052458 restraints weight = 45304.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053395 restraints weight = 30589.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053915 restraints weight = 24139.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054317 restraints weight = 21129.562| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14582 Z= 0.183 Angle : 0.749 9.313 20617 Z= 0.409 Chirality : 0.047 0.321 2338 Planarity : 0.005 0.045 1836 Dihedral : 28.688 136.755 3682 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 0.10 % Allowed : 1.40 % Favored : 98.50 % 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: -0.04 (0.24), residues: 1142 helix: 0.73 (0.18), residues: 757 sheet: -0.93 (0.74), residues: 50 loop : -1.52 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 531 TYR 0.020 0.003 TYR H 65 PHE 0.038 0.002 PHE C 34 TRP 0.020 0.002 TRP K 327 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (14582) covalent geometry : angle 0.74930 / 0.41 (20617) hydrogen bonds : bond 0.05139 / 3.51 ( 861) hydrogen bonds : angle 4.13577 / 2.93 ( 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 271 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8389 (pt) cc_final: 0.8082 (pt) REVERT: A 78 PHE cc_start: 0.7804 (t80) cc_final: 0.7426 (t80) REVERT: A 86 SER cc_start: 0.8077 (m) cc_final: 0.7724 (t) REVERT: A 94 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 105 GLU cc_start: 0.7737 (tp30) cc_final: 0.7364 (tp30) REVERT: A 133 GLU cc_start: 0.6442 (pm20) cc_final: 0.5979 (pt0) REVERT: B 84 MET cc_start: 0.7341 (tpt) cc_final: 0.7041 (tpt) REVERT: B 91 LYS cc_start: 0.7829 (tmmt) cc_final: 0.7427 (tttt) REVERT: C 28 MET cc_start: 0.4538 (mtm) cc_final: 0.3669 (tpt) REVERT: C 65 GLU cc_start: 0.8445 (tt0) cc_final: 0.7542 (tp30) REVERT: C 98 ASN cc_start: 0.7965 (m-40) cc_final: 0.7321 (t0) REVERT: D 130 GLU cc_start: 0.7389 (mp0) cc_final: 0.6627 (mt-10) REVERT: E 79 LYS cc_start: 0.7027 (tmtt) cc_final: 0.6776 (tttt) REVERT: G 38 ARG cc_start: 0.6948 (ttt180) cc_final: 0.6281 (tpp80) REVERT: G 73 GLU cc_start: 0.7461 (pt0) cc_final: 0.7065 (pt0) REVERT: G 83 LYS cc_start: 0.8161 (mmmm) cc_final: 0.6941 (ptpp) REVERT: H 101 GLU cc_start: 0.7832 (tp30) cc_final: 0.7613 (tp30) REVERT: H 138 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6236 (mt-10) REVERT: K 214 ILE cc_start: 0.7911 (mm) cc_final: 0.7541 (mm) REVERT: K 243 HIS cc_start: 0.5822 (t-170) cc_final: 0.5444 (t-170) REVERT: K 249 LEU cc_start: 0.8371 (mt) cc_final: 0.7697 (tp) REVERT: K 256 ILE cc_start: 0.9257 (mt) cc_final: 0.9048 (mm) REVERT: K 288 ARG cc_start: 0.6269 (mpt-90) cc_final: 0.5925 (mpt-90) REVERT: K 315 MET cc_start: 0.7406 (tpp) cc_final: 0.6778 (tpp) REVERT: K 373 TRP cc_start: 0.6622 (t-100) cc_final: 0.6311 (t-100) REVERT: K 380 LEU cc_start: 0.7376 (mp) cc_final: 0.7167 (mp) REVERT: K 382 ASP cc_start: 0.7314 (m-30) cc_final: 0.7112 (m-30) REVERT: K 384 PHE cc_start: 0.8408 (m-80) cc_final: 0.7256 (m-10) REVERT: K 596 PHE cc_start: 0.7822 (t80) cc_final: 0.7619 (t80) REVERT: K 621 ASP cc_start: 0.7720 (t0) cc_final: 0.7432 (m-30) REVERT: K 623 ASN cc_start: 0.7805 (t0) cc_final: 0.7439 (t0) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.1049 time to fit residues: 42.2646 Evaluate side-chains 205 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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: 8.9990 chunk 131 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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** C 113 HIS ** 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** F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 HIS ** 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 = 0.3440 r_free = 0.3440 target = 0.068290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.051245 restraints weight = 82136.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052748 restraints weight = 44026.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053705 restraints weight = 29354.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054230 restraints weight = 22999.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054620 restraints weight = 20091.786| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14582 Z= 0.174 Angle : 0.741 9.511 20617 Z= 0.407 Chirality : 0.046 0.214 2338 Planarity : 0.005 0.049 1836 Dihedral : 28.735 136.396 3682 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % 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: -0.11 (0.24), residues: 1142 helix: 0.69 (0.18), residues: 760 sheet: -0.88 (0.74), residues: 49 loop : -1.63 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 531 TYR 0.035 0.002 TYR B 88 PHE 0.031 0.002 PHE A 67 TRP 0.020 0.003 TRP K 327 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (14582) covalent geometry : angle 0.74127 / 0.41 (20617) hydrogen bonds : bond 0.04912 / 3.33 ( 861) hydrogen bonds : angle 4.07944 / 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 264 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7778 (t80) cc_final: 0.7400 (t80) REVERT: A 86 SER cc_start: 0.8007 (m) cc_final: 0.7730 (t) REVERT: A 133 GLU cc_start: 0.6366 (pm20) cc_final: 0.5951 (pt0) REVERT: B 46 ILE cc_start: 0.8202 (mt) cc_final: 0.7980 (mt) REVERT: B 75 HIS cc_start: 0.8516 (t70) cc_final: 0.8038 (t-170) REVERT: B 84 MET cc_start: 0.7056 (tpt) cc_final: 0.6800 (tpp) REVERT: B 91 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7477 (tttt) REVERT: C 28 MET cc_start: 0.4599 (mtm) cc_final: 0.3602 (tpt) REVERT: C 98 ASN cc_start: 0.8028 (m-40) cc_final: 0.7394 (t0) REVERT: D 130 GLU cc_start: 0.7215 (mp0) cc_final: 0.6505 (mt-10) REVERT: E 79 LYS cc_start: 0.6912 (tmtt) cc_final: 0.6607 (tttt) REVERT: F 66 ILE cc_start: 0.8724 (mm) cc_final: 0.8505 (mm) REVERT: G 38 ARG cc_start: 0.6906 (ttt180) cc_final: 0.6187 (tpp80) REVERT: G 73 GLU cc_start: 0.7283 (pt0) cc_final: 0.6877 (pt0) REVERT: G 83 LYS cc_start: 0.8161 (mmmm) cc_final: 0.6915 (ptpp) REVERT: H 108 TYR cc_start: 0.4484 (m-10) cc_final: 0.4241 (m-10) REVERT: H 118 GLU cc_start: 0.8234 (mp0) cc_final: 0.7440 (mp0) REVERT: H 138 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6564 (mt-10) REVERT: K 243 HIS cc_start: 0.6102 (t-170) cc_final: 0.5856 (t-170) REVERT: K 249 LEU cc_start: 0.8252 (mt) cc_final: 0.7646 (tp) REVERT: K 288 ARG cc_start: 0.6247 (mpt-90) cc_final: 0.5999 (mpt-90) REVERT: K 315 MET cc_start: 0.7419 (tpp) cc_final: 0.6765 (tpp) REVERT: K 373 TRP cc_start: 0.6660 (t-100) cc_final: 0.6351 (t-100) REVERT: K 384 PHE cc_start: 0.8311 (m-80) cc_final: 0.7215 (m-10) REVERT: K 468 LEU cc_start: 0.8029 (mt) cc_final: 0.7223 (tp) REVERT: K 553 LEU cc_start: 0.7383 (mt) cc_final: 0.7177 (mt) REVERT: K 623 ASN cc_start: 0.7746 (t0) cc_final: 0.7405 (t0) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1050 time to fit residues: 41.2810 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 : 0.502 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 chunk 82 optimal weight: 30.0000 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 40.0000 chunk 79 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** C 113 HIS ** 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** F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.068637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051545 restraints weight = 82371.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.053001 restraints weight = 44883.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053948 restraints weight = 30264.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054531 restraints weight = 23760.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054774 restraints weight = 20658.949| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14582 Z= 0.153 Angle : 0.721 9.553 20617 Z= 0.398 Chirality : 0.046 0.277 2338 Planarity : 0.005 0.103 1836 Dihedral : 28.698 135.904 3682 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -0.04 (0.24), residues: 1142 helix: 0.81 (0.18), residues: 760 sheet: -0.93 (0.75), residues: 49 loop : -1.76 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 128 TYR 0.028 0.002 TYR K 281 PHE 0.024 0.002 PHE K 596 TRP 0.015 0.002 TRP K 327 HIS 0.013 0.002 HIS K 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (14582) covalent geometry : angle 0.72136 / 0.40 (20617) hydrogen bonds : bond 0.04710 / 3.20 ( 861) hydrogen bonds : angle 4.01917 / 2.86 ( 2278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.76 seconds wall clock time: 34 minutes 30.26 seconds (2070.26 seconds total)