Starting phenix.real_space_refine on Sat Aug 23 17:25:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j90_36083/08_2025/8j90_36083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j90_36083/08_2025/8j90_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_2025/8j90_36083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j90_36083/08_2025/8j90_36083.map" model { file = "/net/cci-nas-00/data/ceres_data/8j90_36083/08_2025/8j90_36083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j90_36083/08_2025/8j90_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-2.0-5787/lib/python3.9/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: 2.69, per 1000 atoms: 0.19 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: 0.92 Conformation dependent library (CDL) restraints added in 528.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.95 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: 2.75 Time building geometry restraints manager: 1.31 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: 20511 4.43 - 8.87: 97 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: 2166 0.080 - 0.160: 157 0.160 - 0.240: 11 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: 0.660 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 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 : 0.005 0.060 14582 Z= 0.244 Angle : 0.842 22.166 20617 Z= 0.491 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00451 (14582) covalent geometry : angle 0.84201 (20617) hydrogen bonds : bond 0.10711 ( 861) hydrogen bonds : angle 5.17276 ( 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 : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.7989 (pt) cc_final: 0.7644 (mt) REVERT: A 64 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7909 (mttp) REVERT: A 80 THR cc_start: 0.8557 (p) cc_final: 0.8238 (p) REVERT: A 86 SER cc_start: 0.8211 (m) cc_final: 0.7551 (t) REVERT: A 89 VAL cc_start: 0.7749 (t) cc_final: 0.7466 (m) REVERT: A 109 LEU cc_start: 0.8866 (tp) cc_final: 0.8600 (tp) REVERT: A 118 THR cc_start: 0.8376 (m) cc_final: 0.8045 (m) REVERT: A 133 GLU cc_start: 0.6612 (pm20) cc_final: 0.6385 (pt0) REVERT: B 27 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7110 (tt0) REVERT: B 31 LYS cc_start: 0.8720 (tttt) cc_final: 0.8476 (mmtm) REVERT: B 45 ARG cc_start: 0.6727 (tpt170) cc_final: 0.6522 (mmm160) REVERT: B 49 LEU cc_start: 0.9000 (mp) cc_final: 0.8727 (tt) REVERT: B 84 MET cc_start: 0.7224 (tpt) cc_final: 0.6515 (mmm) REVERT: B 88 TYR cc_start: 0.6724 (m-80) cc_final: 0.6190 (m-80) REVERT: B 91 LYS cc_start: 0.7818 (tmmt) cc_final: 0.7447 (tttt) REVERT: C 28 MET cc_start: 0.5940 (mtm) cc_final: 0.5198 (ttp) REVERT: C 42 PHE cc_start: 0.7579 (m-10) cc_final: 0.7284 (m-80) REVERT: C 98 ASN cc_start: 0.7733 (m-40) cc_final: 0.7531 (t0) REVERT: D 62 TYR cc_start: 0.7562 (m-10) cc_final: 0.7098 (m-10) REVERT: D 63 LYS cc_start: 0.7569 (mptt) cc_final: 0.7163 (mmmm) REVERT: D 91 ILE cc_start: 0.8204 (mm) cc_final: 0.7911 (mm) REVERT: D 112 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7831 (Cg_endo) REVERT: D 130 GLU cc_start: 0.7793 (mp0) cc_final: 0.7256 (mt-10) REVERT: E 73 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7942 (tm-30) REVERT: E 79 LYS cc_start: 0.7157 (tmtt) cc_final: 0.6418 (mmtp) REVERT: E 94 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7874 (mt-10) REVERT: F 22 LEU cc_start: 0.7228 (tt) cc_final: 0.6985 (pp) REVERT: F 30 THR cc_start: 0.7357 (p) cc_final: 0.7080 (t) REVERT: G 34 PHE cc_start: 0.5253 (m-10) cc_final: 0.4813 (m-80) REVERT: G 42 PHE cc_start: 0.7250 (m-80) cc_final: 0.6938 (m-80) REVERT: H 110 LYS cc_start: 0.6715 (tptt) cc_final: 0.6180 (ttmt) REVERT: H 125 LEU cc_start: 0.9147 (tt) cc_final: 0.8288 (tt) REVERT: H 127 LEU cc_start: 0.7947 (mm) cc_final: 0.7621 (mp) REVERT: K 241 LEU cc_start: 0.8096 (mm) cc_final: 0.7835 (mm) REVERT: K 249 LEU cc_start: 0.8247 (mt) cc_final: 0.7784 (tp) REVERT: K 253 TYR cc_start: 0.6356 (m-80) cc_final: 0.5353 (m-10) REVERT: K 254 LEU cc_start: 0.7308 (tp) cc_final: 0.6870 (tp) REVERT: K 324 HIS cc_start: 0.6129 (m90) cc_final: 0.5764 (t-170) REVERT: K 329 TYR cc_start: 0.7325 (m-80) cc_final: 0.6659 (t80) REVERT: K 352 LEU cc_start: 0.7898 (mt) cc_final: 0.7511 (tp) REVERT: K 373 TRP cc_start: 0.6790 (t-100) cc_final: 0.6201 (t-100) REVERT: K 382 ASP cc_start: 0.6786 (m-30) cc_final: 0.6384 (m-30) REVERT: K 384 PHE cc_start: 0.8174 (m-80) cc_final: 0.7613 (m-80) REVERT: K 459 PHE cc_start: 0.7264 (m-10) cc_final: 0.7042 (m-80) REVERT: K 468 LEU cc_start: 0.8389 (tp) cc_final: 0.7951 (tp) REVERT: K 557 ASP cc_start: 0.8072 (t0) cc_final: 0.7637 (t70) REVERT: K 569 ARG cc_start: 0.6738 (ttt90) cc_final: 0.6049 (ttm-80) REVERT: K 618 TYR cc_start: 0.7568 (t80) cc_final: 0.6966 (t80) REVERT: K 621 ASP cc_start: 0.7324 (t0) cc_final: 0.6952 (m-30) REVERT: K 623 ASN cc_start: 0.8221 (t0) cc_final: 0.7983 (t0) REVERT: K 631 MET cc_start: 0.6804 (ppp) cc_final: 0.6599 (tpt) REVERT: K 636 ARG cc_start: 0.5498 (ttt90) cc_final: 0.5272 (tmt170) REVERT: K 748 TRP cc_start: 0.5448 (p-90) cc_final: 0.5222 (p-90) REVERT: K 755 SER cc_start: 0.7445 (p) cc_final: 0.7226 (t) outliers start: 3 outliers final: 0 residues processed: 493 average time/residue: 0.1346 time to fit residues: 88.1169 Evaluate side-chains 268 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 33 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 ASN ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.068318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050108 restraints weight = 81921.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.051525 restraints weight = 46558.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052430 restraints weight = 32374.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.052988 restraints weight = 25873.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.053201 restraints weight = 22695.358| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14582 Z= 0.234 Angle : 0.778 9.366 20617 Z= 0.426 Chirality : 0.045 0.261 2338 Planarity : 0.006 0.049 1836 Dihedral : 28.634 140.117 3682 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.90 % Allowed : 9.28 % Favored : 89.82 % 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 aren not related in a simple way. whole: -0.25 (0.24), residues: 1142 helix: 0.39 (0.17), residues: 771 sheet: -0.26 (0.76), residues: 49 loop : -1.31 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 77 TYR 0.021 0.003 TYR C 48 PHE 0.027 0.003 PHE K 390 TRP 0.025 0.003 TRP K 373 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00527 (14582) covalent geometry : angle 0.77784 (20617) hydrogen bonds : bond 0.05369 ( 861) hydrogen bonds : angle 4.40123 ( 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 314 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 305 time to evaluate : 0.357 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: 0.7746 (t80) cc_final: 0.7467 (t80) REVERT: A 86 SER cc_start: 0.8531 (m) cc_final: 0.8173 (t) REVERT: A 106 ASP cc_start: 0.8703 (m-30) cc_final: 0.8474 (m-30) REVERT: A 118 THR cc_start: 0.8917 (m) cc_final: 0.8088 (m) REVERT: A 133 GLU cc_start: 0.6491 (pm20) cc_final: 0.5788 (pt0) REVERT: B 64 ASN cc_start: 0.7497 (t0) cc_final: 0.7193 (t0) REVERT: B 75 HIS cc_start: 0.8612 (t70) cc_final: 0.8401 (t70) REVERT: B 84 MET cc_start: 0.7338 (tpt) cc_final: 0.6895 (mmm) REVERT: B 88 TYR cc_start: 0.6915 (m-80) cc_final: 0.6307 (m-80) REVERT: B 91 LYS cc_start: 0.7842 (tmmt) cc_final: 0.7363 (tttt) REVERT: B 98 TYR cc_start: 0.7085 (m-10) cc_final: 0.6291 (m-10) REVERT: C 28 MET cc_start: 0.4473 (mtm) cc_final: 0.3766 (tpt) REVERT: C 96 ILE cc_start: 0.7315 (mm) cc_final: 0.7101 (mm) REVERT: C 98 ASN cc_start: 0.7803 (m-40) cc_final: 0.7277 (t0) REVERT: D 62 TYR cc_start: 0.7470 (m-10) cc_final: 0.7235 (m-10) REVERT: D 63 LYS cc_start: 0.7359 (mptt) cc_final: 0.6621 (mmmt) REVERT: D 110 LYS cc_start: 0.6969 (mmtt) cc_final: 0.6505 (mtpp) REVERT: D 111 LYS cc_start: 0.7880 (tptt) cc_final: 0.7630 (tptt) REVERT: D 130 GLU cc_start: 0.7749 (mp0) cc_final: 0.7087 (mt-10) REVERT: E 79 LYS cc_start: 0.7099 (tmtt) cc_final: 0.6739 (mmtt) REVERT: E 85 GLN cc_start: 0.8061 (pm20) cc_final: 0.7840 (pm20) REVERT: F 21 VAL cc_start: 0.6508 (t) cc_final: 0.5623 (m) REVERT: G 38 ARG cc_start: 0.6350 (ptm160) cc_final: 0.5777 (ttm170) REVERT: G 83 LYS cc_start: 0.7975 (mmmm) cc_final: 0.6910 (ptpp) REVERT: H 94 ILE cc_start: 0.8555 (mm) cc_final: 0.8263 (mm) REVERT: H 110 LYS cc_start: 0.6680 (tptt) cc_final: 0.6150 (tttt) REVERT: H 125 LEU cc_start: 0.8721 (tt) cc_final: 0.8483 (tt) REVERT: K 229 MET cc_start: 0.4967 (ptt) cc_final: 0.4559 (ptt) REVERT: K 249 LEU cc_start: 0.8338 (mt) cc_final: 0.7622 (tp) REVERT: K 281 TYR cc_start: 0.7370 (t80) cc_final: 0.6179 (t80) REVERT: K 282 HIS cc_start: 0.5007 (m90) cc_final: 0.4530 (m-70) REVERT: K 315 MET cc_start: 0.7076 (tpp) cc_final: 0.6850 (tpp) REVERT: K 321 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6754 (mm) REVERT: K 373 TRP cc_start: 0.6660 (t-100) cc_final: 0.6366 (t-100) REVERT: K 380 LEU cc_start: 0.7392 (mt) cc_final: 0.7060 (mp) REVERT: K 382 ASP cc_start: 0.6781 (m-30) cc_final: 0.6427 (m-30) REVERT: K 384 PHE cc_start: 0.8510 (m-80) cc_final: 0.7466 (m-10) REVERT: K 468 LEU cc_start: 0.8315 (tp) cc_final: 0.7869 (tt) REVERT: K 553 LEU cc_start: 0.7341 (mp) cc_final: 0.7129 (mp) REVERT: K 557 ASP cc_start: 0.7909 (t0) cc_final: 0.7005 (t70) REVERT: K 570 ILE cc_start: 0.6731 (mm) cc_final: 0.6205 (mp) REVERT: K 622 TRP cc_start: 0.6687 (m100) cc_final: 0.6374 (m100) REVERT: K 623 ASN cc_start: 0.7740 (t0) cc_final: 0.7316 (t0) outliers start: 9 outliers final: 2 residues processed: 312 average time/residue: 0.1044 time to fit residues: 46.6420 Evaluate side-chains 218 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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: 2.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 77 ASN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN K 219 ASN ** K 236 GLN ** 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** K 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.067838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050754 restraints weight = 83613.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052328 restraints weight = 44222.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.053332 restraints weight = 29015.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.053962 restraints weight = 22394.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054304 restraints weight = 19177.835| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14582 Z= 0.179 Angle : 0.674 10.530 20617 Z= 0.373 Chirality : 0.041 0.231 2338 Planarity : 0.005 0.044 1836 Dihedral : 28.590 138.593 3682 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.61 % 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 aren not related in a simple way. whole: 0.24 (0.24), residues: 1142 helix: 0.85 (0.18), residues: 772 sheet: -0.20 (0.74), residues: 49 loop : -1.38 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 45 TYR 0.020 0.002 TYR C 48 PHE 0.029 0.002 PHE K 390 TRP 0.023 0.003 TRP K 748 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00402 (14582) covalent geometry : angle 0.67382 (20617) hydrogen bonds : bond 0.04521 ( 861) hydrogen bonds : angle 4.02989 ( 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 297 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8351 (pt) cc_final: 0.8044 (pt) REVERT: A 78 PHE cc_start: 0.7751 (t80) cc_final: 0.7267 (t80) REVERT: A 86 SER cc_start: 0.8459 (m) cc_final: 0.7653 (t) REVERT: A 89 VAL cc_start: 0.7388 (t) cc_final: 0.7165 (m) REVERT: A 94 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6875 (mt-10) REVERT: A 109 LEU cc_start: 0.8364 (mt) cc_final: 0.8085 (mt) REVERT: A 133 GLU cc_start: 0.6287 (pm20) cc_final: 0.5931 (pt0) REVERT: B 84 MET cc_start: 0.7482 (tpt) cc_final: 0.7238 (mmm) REVERT: B 88 TYR cc_start: 0.7171 (m-80) cc_final: 0.6386 (m-80) REVERT: B 91 LYS cc_start: 0.8003 (tmmt) cc_final: 0.7714 (tttt) REVERT: B 98 TYR cc_start: 0.6697 (m-10) cc_final: 0.6207 (m-10) REVERT: C 28 MET cc_start: 0.4670 (mtm) cc_final: 0.3699 (tpt) REVERT: C 98 ASN cc_start: 0.7947 (m-40) cc_final: 0.7382 (t0) REVERT: D 110 LYS cc_start: 0.6988 (mmtt) cc_final: 0.6660 (mtpp) REVERT: D 111 LYS cc_start: 0.7791 (tptt) cc_final: 0.7329 (tptt) REVERT: D 130 GLU cc_start: 0.7523 (mp0) cc_final: 0.6822 (mt-10) REVERT: E 79 LYS cc_start: 0.6888 (tmtt) cc_final: 0.6516 (mmtt) REVERT: F 21 VAL cc_start: 0.6254 (t) cc_final: 0.5155 (m) REVERT: F 63 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8148 (mm-30) REVERT: G 38 ARG cc_start: 0.6636 (ttt180) cc_final: 0.5976 (tpp80) REVERT: G 73 GLU cc_start: 0.7386 (pt0) cc_final: 0.7130 (pt0) REVERT: G 77 ASN cc_start: 0.8113 (t0) cc_final: 0.7898 (t0) REVERT: G 83 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7060 (ptpp) REVERT: H 65 TYR cc_start: 0.4840 (m-80) cc_final: 0.4639 (m-80) REVERT: H 118 GLU cc_start: 0.8244 (mp0) cc_final: 0.7403 (mp0) REVERT: K 205 TYR cc_start: 0.7123 (m-10) cc_final: 0.6774 (m-10) REVERT: K 249 LEU cc_start: 0.8378 (mt) cc_final: 0.7892 (tp) REVERT: K 281 TYR cc_start: 0.6405 (t80) cc_final: 0.6062 (t80) REVERT: K 315 MET cc_start: 0.7200 (tpp) cc_final: 0.6725 (tpp) REVERT: K 333 ASP cc_start: 0.7776 (t0) cc_final: 0.7076 (t0) REVERT: K 373 TRP cc_start: 0.6570 (t-100) cc_final: 0.6246 (t-100) REVERT: K 380 LEU cc_start: 0.7550 (mt) cc_final: 0.7303 (mp) REVERT: K 382 ASP cc_start: 0.6770 (m-30) cc_final: 0.6560 (m-30) REVERT: K 384 PHE cc_start: 0.8464 (m-80) cc_final: 0.7429 (m-10) REVERT: K 468 LEU cc_start: 0.8259 (tp) cc_final: 0.8042 (tp) REVERT: K 553 LEU cc_start: 0.7238 (mp) cc_final: 0.6813 (mp) REVERT: K 554 ASP cc_start: 0.7540 (m-30) cc_final: 0.7326 (m-30) REVERT: K 570 ILE cc_start: 0.6868 (mm) cc_final: 0.6571 (mp) REVERT: K 623 ASN cc_start: 0.7864 (t0) cc_final: 0.7609 (t0) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.1146 time to fit residues: 47.3727 Evaluate side-chains 215 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 0.9980 chunk 130 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 HIS ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052473 restraints weight = 82370.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054017 restraints weight = 44568.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054998 restraints weight = 29413.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055564 restraints weight = 22673.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055992 restraints weight = 19576.723| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14582 Z= 0.146 Angle : 0.635 8.910 20617 Z= 0.356 Chirality : 0.039 0.286 2338 Planarity : 0.004 0.047 1836 Dihedral : 28.377 136.729 3682 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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 aren not related in a simple way. whole: 0.41 (0.24), residues: 1142 helix: 1.01 (0.18), residues: 774 sheet: -0.15 (0.73), residues: 49 loop : -1.42 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 55 TYR 0.017 0.002 TYR C 48 PHE 0.027 0.002 PHE D 67 TRP 0.027 0.002 TRP K 748 HIS 0.012 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00315 (14582) covalent geometry : angle 0.63497 (20617) hydrogen bonds : bond 0.04027 ( 861) hydrogen bonds : angle 3.82153 ( 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 292 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7666 (t80) cc_final: 0.7265 (t80) REVERT: A 86 SER cc_start: 0.8446 (m) cc_final: 0.7572 (t) REVERT: A 133 GLU cc_start: 0.6324 (pm20) cc_final: 0.5866 (pt0) REVERT: B 88 TYR cc_start: 0.7089 (m-80) cc_final: 0.6290 (m-80) REVERT: B 91 LYS cc_start: 0.7929 (tmmt) cc_final: 0.7552 (tttt) REVERT: B 98 TYR cc_start: 0.6750 (m-10) cc_final: 0.6359 (m-10) REVERT: C 28 MET cc_start: 0.4703 (mtm) cc_final: 0.3339 (ttp) REVERT: C 72 LEU cc_start: 0.7895 (mp) cc_final: 0.7509 (tt) REVERT: C 98 ASN cc_start: 0.7915 (m-40) cc_final: 0.7242 (t0) REVERT: D 110 LYS cc_start: 0.7016 (mmtt) cc_final: 0.6689 (mtpp) REVERT: D 114 ILE cc_start: 0.8000 (pt) cc_final: 0.7507 (pt) REVERT: D 130 GLU cc_start: 0.7142 (mp0) cc_final: 0.6396 (mt-10) REVERT: E 74 ILE cc_start: 0.9092 (tp) cc_final: 0.8840 (tt) REVERT: E 79 LYS cc_start: 0.6907 (tmtt) cc_final: 0.6577 (tttt) REVERT: F 21 VAL cc_start: 0.5881 (t) cc_final: 0.4849 (m) REVERT: F 22 LEU cc_start: 0.6688 (tp) cc_final: 0.6362 (pp) REVERT: G 38 ARG cc_start: 0.6493 (ttt180) cc_final: 0.5819 (tpp80) REVERT: G 77 ASN cc_start: 0.7993 (t0) cc_final: 0.7789 (t0) REVERT: G 83 LYS cc_start: 0.7903 (mmmm) cc_final: 0.6725 (ptpp) REVERT: H 118 GLU cc_start: 0.8197 (mp0) cc_final: 0.7820 (mp0) REVERT: K 205 TYR cc_start: 0.7128 (m-10) cc_final: 0.6691 (m-10) REVERT: K 249 LEU cc_start: 0.8198 (mt) cc_final: 0.7797 (tp) REVERT: K 315 MET cc_start: 0.7264 (tpp) cc_final: 0.6654 (tpp) REVERT: K 329 TYR cc_start: 0.6758 (m-80) cc_final: 0.6097 (t80) REVERT: K 373 TRP cc_start: 0.6602 (t-100) cc_final: 0.6283 (t-100) REVERT: K 380 LEU cc_start: 0.7608 (mt) cc_final: 0.7354 (mp) REVERT: K 384 PHE cc_start: 0.8277 (m-80) cc_final: 0.7278 (m-10) REVERT: K 511 TYR cc_start: 0.6600 (m-10) cc_final: 0.6143 (m-10) REVERT: K 527 ARG cc_start: 0.8521 (ppt170) cc_final: 0.7955 (ppt90) REVERT: K 556 MET cc_start: 0.7965 (ttm) cc_final: 0.7573 (ttm) REVERT: K 623 ASN cc_start: 0.7672 (t0) cc_final: 0.7451 (t0) REVERT: K 646 TYR cc_start: 0.5971 (m-80) cc_final: 0.5682 (m-10) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1100 time to fit residues: 45.6433 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 : 0.419 ------------------------------------------------------------------------------- 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: 8.9990 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 112 optimal weight: 0.0970 chunk 72 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 92 optimal weight: 0.0050 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 64 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS D 88 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 541 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.069781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052151 restraints weight = 80067.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053611 restraints weight = 45155.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054529 restraints weight = 30713.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055174 restraints weight = 24221.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055507 restraints weight = 20865.845| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14582 Z= 0.151 Angle : 0.626 7.062 20617 Z= 0.350 Chirality : 0.039 0.252 2338 Planarity : 0.005 0.063 1836 Dihedral : 28.336 137.256 3682 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 aren not related in a simple way. whole: 0.61 (0.24), residues: 1142 helix: 1.20 (0.18), residues: 767 sheet: -0.24 (0.72), residues: 49 loop : -1.37 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 633 TYR 0.015 0.002 TYR C 48 PHE 0.030 0.002 PHE D 67 TRP 0.032 0.003 TRP K 622 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00333 (14582) covalent geometry : angle 0.62554 (20617) hydrogen bonds : bond 0.04054 ( 861) hydrogen bonds : angle 3.72281 ( 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 286 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7771 (t80) cc_final: 0.7364 (t80) REVERT: A 86 SER cc_start: 0.8118 (m) cc_final: 0.7791 (t) REVERT: A 133 GLU cc_start: 0.6208 (pm20) cc_final: 0.5849 (pt0) REVERT: B 88 TYR cc_start: 0.7185 (m-80) cc_final: 0.6069 (m-80) REVERT: B 91 LYS cc_start: 0.8027 (tmmt) cc_final: 0.7646 (tttt) REVERT: B 98 TYR cc_start: 0.6746 (m-10) cc_final: 0.6168 (m-10) REVERT: C 28 MET cc_start: 0.4817 (mtm) cc_final: 0.4388 (mmp) REVERT: C 98 ASN cc_start: 0.7964 (m-40) cc_final: 0.7298 (t0) REVERT: D 63 LYS cc_start: 0.6847 (mmtp) cc_final: 0.6496 (mmmt) REVERT: D 110 LYS cc_start: 0.6239 (mmtp) cc_final: 0.5928 (mtpp) REVERT: D 130 GLU cc_start: 0.7106 (mp0) cc_final: 0.6446 (mt-10) REVERT: E 79 LYS cc_start: 0.6893 (tmtt) cc_final: 0.6518 (tttt) REVERT: G 38 ARG cc_start: 0.6592 (ttt180) cc_final: 0.6114 (tpp80) REVERT: G 83 LYS cc_start: 0.7815 (mmmm) cc_final: 0.6694 (ptpp) REVERT: G 90 ARG cc_start: 0.7632 (tpm170) cc_final: 0.7404 (tpm170) REVERT: H 87 MET cc_start: 0.8387 (tpp) cc_final: 0.7828 (tmm) REVERT: H 118 GLU cc_start: 0.8301 (mp0) cc_final: 0.7436 (mp0) REVERT: H 138 GLU cc_start: 0.6555 (tm-30) cc_final: 0.6318 (mt-10) REVERT: K 205 TYR cc_start: 0.7028 (m-10) cc_final: 0.6601 (m-10) REVERT: K 249 LEU cc_start: 0.8221 (mt) cc_final: 0.7697 (tp) REVERT: K 315 MET cc_start: 0.7302 (tpp) cc_final: 0.6668 (tpp) REVERT: K 373 TRP cc_start: 0.6597 (t-100) cc_final: 0.6292 (t-100) REVERT: K 380 LEU cc_start: 0.7707 (mt) cc_final: 0.7474 (mp) REVERT: K 384 PHE cc_start: 0.8363 (m-80) cc_final: 0.7295 (m-10) REVERT: K 526 PHE cc_start: 0.8687 (t80) cc_final: 0.8464 (t80) REVERT: K 527 ARG cc_start: 0.8491 (ppt170) cc_final: 0.7903 (ppt90) REVERT: K 623 ASN cc_start: 0.7662 (t0) cc_final: 0.7425 (t0) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1014 time to fit residues: 40.8704 Evaluate side-chains 215 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 10.0000 chunk 119 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 243 HIS ** K 366 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.071075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053289 restraints weight = 77621.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054771 restraints weight = 43877.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055702 restraints weight = 30032.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.056340 restraints weight = 23667.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056758 restraints weight = 20441.517| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14582 Z= 0.142 Angle : 0.621 8.574 20617 Z= 0.348 Chirality : 0.038 0.190 2338 Planarity : 0.004 0.049 1836 Dihedral : 28.179 136.145 3682 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.96 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 aren not related in a simple way. whole: 0.73 (0.25), residues: 1142 helix: 1.30 (0.18), residues: 767 sheet: -0.20 (0.73), residues: 49 loop : -1.34 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 116 TYR 0.014 0.002 TYR C 48 PHE 0.034 0.002 PHE D 67 TRP 0.027 0.002 TRP K 748 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00305 (14582) covalent geometry : angle 0.62052 (20617) hydrogen bonds : bond 0.03832 ( 861) hydrogen bonds : angle 3.62980 ( 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 283 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8704 (t80) cc_final: 0.8321 (t80) REVERT: A 78 PHE cc_start: 0.7736 (t80) cc_final: 0.7461 (t80) REVERT: A 86 SER cc_start: 0.8058 (m) cc_final: 0.7752 (t) REVERT: A 92 LEU cc_start: 0.8572 (mt) cc_final: 0.8306 (mp) REVERT: A 97 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6799 (mp0) REVERT: A 118 THR cc_start: 0.8457 (m) cc_final: 0.7966 (m) REVERT: A 133 GLU cc_start: 0.6162 (pm20) cc_final: 0.5900 (pt0) REVERT: B 35 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8020 (ttt90) REVERT: B 45 ARG cc_start: 0.6518 (tpt90) cc_final: 0.6124 (mmm160) REVERT: B 75 HIS cc_start: 0.8956 (t70) cc_final: 0.8649 (t-170) REVERT: B 84 MET cc_start: 0.7165 (tpt) cc_final: 0.6685 (mmm) REVERT: B 88 TYR cc_start: 0.7158 (m-80) cc_final: 0.5883 (m-80) REVERT: B 91 LYS cc_start: 0.8024 (tmmt) cc_final: 0.7488 (tttt) REVERT: B 98 TYR cc_start: 0.6699 (m-10) cc_final: 0.6341 (m-10) REVERT: C 28 MET cc_start: 0.4485 (mtm) cc_final: 0.4091 (mmp) REVERT: C 39 ILE cc_start: 0.7777 (pt) cc_final: 0.7508 (pt) REVERT: C 72 LEU cc_start: 0.7939 (mp) cc_final: 0.7494 (tp) REVERT: C 98 ASN cc_start: 0.8008 (m-40) cc_final: 0.7188 (t0) REVERT: D 67 PHE cc_start: 0.6181 (m-80) cc_final: 0.5642 (m-80) REVERT: D 111 LYS cc_start: 0.7676 (tptt) cc_final: 0.7317 (tptt) REVERT: D 120 GLN cc_start: 0.7612 (pp30) cc_final: 0.7369 (pp30) REVERT: D 124 ARG cc_start: 0.6553 (mtp180) cc_final: 0.6130 (ttm-80) REVERT: D 130 GLU cc_start: 0.6690 (mp0) cc_final: 0.6053 (mt-10) REVERT: E 79 LYS cc_start: 0.6887 (tmtt) cc_final: 0.6536 (tttt) REVERT: E 85 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: F 63 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8050 (mm-30) REVERT: F 66 ILE cc_start: 0.8723 (mm) cc_final: 0.8507 (mm) REVERT: F 71 THR cc_start: 0.8235 (m) cc_final: 0.7737 (p) REVERT: G 38 ARG cc_start: 0.6697 (ttt180) cc_final: 0.5847 (tpp80) REVERT: G 83 LYS cc_start: 0.7929 (mmmm) cc_final: 0.6764 (ptpp) REVERT: G 90 ARG cc_start: 0.7633 (tpm170) cc_final: 0.7330 (tpm170) REVERT: H 66 ILE cc_start: 0.8823 (pt) cc_final: 0.8382 (pt) REVERT: H 87 MET cc_start: 0.8446 (tpp) cc_final: 0.7873 (tmm) REVERT: H 91 ILE cc_start: 0.8379 (tp) cc_final: 0.8170 (tp) REVERT: H 118 GLU cc_start: 0.8254 (mp0) cc_final: 0.7425 (mp0) REVERT: K 205 TYR cc_start: 0.7061 (m-10) cc_final: 0.6586 (m-10) REVERT: K 249 LEU cc_start: 0.8130 (mt) cc_final: 0.7744 (tp) REVERT: K 253 TYR cc_start: 0.6828 (m-10) cc_final: 0.5740 (m-80) REVERT: K 281 TYR cc_start: 0.6401 (t80) cc_final: 0.6123 (t80) REVERT: K 315 MET cc_start: 0.7268 (tpp) cc_final: 0.6631 (tpp) REVERT: K 373 TRP cc_start: 0.6603 (t-100) cc_final: 0.6306 (t-100) REVERT: K 380 LEU cc_start: 0.7770 (mt) cc_final: 0.7566 (mp) REVERT: K 384 PHE cc_start: 0.8278 (m-80) cc_final: 0.7287 (m-10) REVERT: K 511 TYR cc_start: 0.5817 (m-80) cc_final: 0.5600 (m-10) REVERT: K 527 ARG cc_start: 0.8485 (ppt170) cc_final: 0.7886 (ppt90) REVERT: K 615 CYS cc_start: 0.6388 (t) cc_final: 0.5941 (m) REVERT: K 623 ASN cc_start: 0.7695 (t0) cc_final: 0.7332 (t0) REVERT: K 659 LEU cc_start: 0.9433 (tt) cc_final: 0.9187 (pp) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.0985 time to fit residues: 39.8846 Evaluate side-chains 217 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 GLN K 228 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 366 GLN ** 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 496 ASN ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053111 restraints weight = 80011.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054620 restraints weight = 45413.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055624 restraints weight = 31318.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056139 restraints weight = 24657.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056564 restraints weight = 21676.410| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.6210 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= 0.147 Angle : 0.628 7.470 20617 Z= 0.351 Chirality : 0.038 0.190 2338 Planarity : 0.005 0.092 1836 Dihedral : 28.184 136.614 3682 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.24), residues: 1142 helix: 1.27 (0.18), residues: 770 sheet: -0.57 (0.68), residues: 53 loop : -1.47 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 116 TYR 0.022 0.002 TYR K 311 PHE 0.029 0.002 PHE D 67 TRP 0.043 0.003 TRP K 748 HIS 0.011 0.001 HIS K 387 Details of bonding type rmsd covalent geometry : bond 0.00320 (14582) covalent geometry : angle 0.62844 (20617) hydrogen bonds : bond 0.03973 ( 861) hydrogen bonds : angle 3.66843 ( 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 274 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8842 (t80) cc_final: 0.8569 (t80) REVERT: A 78 PHE cc_start: 0.7816 (t80) cc_final: 0.7472 (t80) REVERT: A 86 SER cc_start: 0.7990 (m) cc_final: 0.7660 (t) REVERT: A 97 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6799 (mt-10) REVERT: A 133 GLU cc_start: 0.6295 (pm20) cc_final: 0.5926 (pt0) REVERT: B 88 TYR cc_start: 0.7184 (m-80) cc_final: 0.6888 (m-80) REVERT: B 91 LYS cc_start: 0.8041 (tmmt) cc_final: 0.7582 (tttt) REVERT: B 98 TYR cc_start: 0.7039 (m-10) cc_final: 0.6651 (m-10) REVERT: C 98 ASN cc_start: 0.8099 (m-40) cc_final: 0.7267 (t0) REVERT: D 67 PHE cc_start: 0.6196 (m-80) cc_final: 0.5925 (m-80) REVERT: D 108 TYR cc_start: 0.6566 (m-10) cc_final: 0.6272 (m-10) REVERT: D 111 LYS cc_start: 0.7590 (tptt) cc_final: 0.7218 (tptt) REVERT: D 120 GLN cc_start: 0.7668 (pp30) cc_final: 0.7249 (pp30) REVERT: D 124 ARG cc_start: 0.6682 (mtp180) cc_final: 0.6182 (ttm-80) REVERT: D 130 GLU cc_start: 0.6730 (mp0) cc_final: 0.6057 (mt-10) REVERT: E 120 MET cc_start: 0.6504 (mmm) cc_final: 0.6296 (mmt) REVERT: E 128 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7932 (mmm-85) REVERT: G 38 ARG cc_start: 0.6667 (ttt180) cc_final: 0.5945 (tpp80) REVERT: G 83 LYS cc_start: 0.7894 (mmmm) cc_final: 0.6690 (ptpp) REVERT: G 90 ARG cc_start: 0.7586 (tpm170) cc_final: 0.7326 (tpm170) REVERT: H 87 MET cc_start: 0.8473 (tpp) cc_final: 0.7891 (tmm) REVERT: H 118 GLU cc_start: 0.8344 (mp0) cc_final: 0.7426 (mp0) REVERT: K 205 TYR cc_start: 0.6729 (m-10) cc_final: 0.6239 (m-10) REVERT: K 233 LYS cc_start: 0.7473 (ttmt) cc_final: 0.7270 (tttt) REVERT: K 249 LEU cc_start: 0.8261 (mt) cc_final: 0.7811 (tp) REVERT: K 315 MET cc_start: 0.7393 (tpp) cc_final: 0.6807 (tpp) REVERT: K 328 LYS cc_start: 0.6213 (mmmt) cc_final: 0.5789 (mmtt) REVERT: K 373 TRP cc_start: 0.6633 (t-100) cc_final: 0.6353 (t-100) REVERT: K 384 PHE cc_start: 0.8300 (m-80) cc_final: 0.7278 (m-10) REVERT: K 527 ARG cc_start: 0.8450 (ppt170) cc_final: 0.7873 (ppt90) REVERT: K 615 CYS cc_start: 0.6551 (t) cc_final: 0.6058 (m) REVERT: K 623 ASN cc_start: 0.7634 (t0) cc_final: 0.7316 (t0) REVERT: K 626 MET cc_start: 0.7921 (ttt) cc_final: 0.7631 (ttm) REVERT: K 659 LEU cc_start: 0.9377 (tt) cc_final: 0.9092 (pp) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.0937 time to fit residues: 37.5405 Evaluate side-chains 212 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** 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** F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 243 HIS K 324 HIS K 351 HIS ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.070892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.053114 restraints weight = 80621.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054520 restraints weight = 47473.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055425 restraints weight = 33569.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.055931 restraints weight = 27133.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.056332 restraints weight = 24031.600| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14582 Z= 0.152 Angle : 0.650 9.676 20617 Z= 0.360 Chirality : 0.039 0.201 2338 Planarity : 0.005 0.086 1836 Dihedral : 28.142 136.175 3682 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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 aren not related in a simple way. whole: 0.67 (0.24), residues: 1142 helix: 1.30 (0.18), residues: 767 sheet: -0.58 (0.69), residues: 53 loop : -1.43 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.020 0.002 TYR B 88 PHE 0.030 0.002 PHE D 67 TRP 0.051 0.003 TRP K 748 HIS 0.010 0.001 HIS K 387 Details of bonding type rmsd covalent geometry : bond 0.00335 (14582) covalent geometry : angle 0.64971 (20617) hydrogen bonds : bond 0.04071 ( 861) hydrogen bonds : angle 3.68337 ( 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 263 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7995 (tp30) cc_final: 0.7766 (tm-30) REVERT: A 78 PHE cc_start: 0.7807 (t80) cc_final: 0.7511 (t80) REVERT: A 86 SER cc_start: 0.8009 (m) cc_final: 0.7675 (t) REVERT: A 92 LEU cc_start: 0.8641 (mt) cc_final: 0.8368 (mp) REVERT: A 97 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6860 (mt-10) REVERT: A 133 GLU cc_start: 0.6149 (pm20) cc_final: 0.5598 (pt0) REVERT: B 75 HIS cc_start: 0.8916 (t70) cc_final: 0.8482 (t-170) REVERT: B 88 TYR cc_start: 0.7225 (m-80) cc_final: 0.6929 (m-80) REVERT: B 91 LYS cc_start: 0.7922 (tmmt) cc_final: 0.7425 (tttt) REVERT: B 98 TYR cc_start: 0.7067 (m-10) cc_final: 0.6751 (m-10) REVERT: C 97 ARG cc_start: 0.5366 (mpt180) cc_final: 0.5104 (mpt180) REVERT: C 98 ASN cc_start: 0.8076 (m-40) cc_final: 0.7267 (t0) REVERT: D 108 TYR cc_start: 0.6604 (m-10) cc_final: 0.6365 (m-10) REVERT: D 111 LYS cc_start: 0.7631 (tptt) cc_final: 0.7299 (tptt) REVERT: D 120 GLN cc_start: 0.7523 (pp30) cc_final: 0.7184 (pp30) REVERT: D 124 ARG cc_start: 0.6635 (mtp180) cc_final: 0.6153 (ttm-80) REVERT: D 130 GLU cc_start: 0.6588 (mp0) cc_final: 0.6027 (mt-10) REVERT: E 61 LEU cc_start: 0.8269 (tp) cc_final: 0.8038 (tp) REVERT: E 128 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7858 (mmm-85) REVERT: G 38 ARG cc_start: 0.6493 (ttt180) cc_final: 0.5849 (tpp80) REVERT: G 83 LYS cc_start: 0.7797 (mmmm) cc_final: 0.6570 (ptpp) REVERT: G 90 ARG cc_start: 0.7347 (tpm170) cc_final: 0.7133 (tpm170) REVERT: H 66 ILE cc_start: 0.9017 (pt) cc_final: 0.8629 (pt) REVERT: H 87 MET cc_start: 0.8375 (tpp) cc_final: 0.7830 (tmm) REVERT: H 118 GLU cc_start: 0.8310 (mp0) cc_final: 0.7542 (mp0) REVERT: H 127 LEU cc_start: 0.7655 (mm) cc_final: 0.7304 (mp) REVERT: K 205 TYR cc_start: 0.6529 (m-10) cc_final: 0.6030 (m-10) REVERT: K 249 LEU cc_start: 0.8227 (mt) cc_final: 0.7725 (tp) REVERT: K 281 TYR cc_start: 0.6451 (t80) cc_final: 0.5908 (t80) REVERT: K 373 TRP cc_start: 0.6635 (t-100) cc_final: 0.6350 (t-100) REVERT: K 384 PHE cc_start: 0.8264 (m-80) cc_final: 0.7230 (m-10) REVERT: K 468 LEU cc_start: 0.7961 (tp) cc_final: 0.7543 (tp) REVERT: K 527 ARG cc_start: 0.8387 (ppt170) cc_final: 0.7755 (ppt90) REVERT: K 552 LEU cc_start: 0.7959 (tt) cc_final: 0.7591 (tt) REVERT: K 615 CYS cc_start: 0.6335 (t) cc_final: 0.5958 (m) REVERT: K 623 ASN cc_start: 0.7592 (t0) cc_final: 0.7281 (t0) REVERT: K 626 MET cc_start: 0.7842 (ttt) cc_final: 0.7544 (ttm) REVERT: K 659 LEU cc_start: 0.9396 (tt) cc_final: 0.9117 (pp) REVERT: K 744 LYS cc_start: 0.6478 (ptpp) cc_final: 0.6195 (mtpp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.0954 time to fit residues: 37.2247 Evaluate side-chains 208 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 4.9990 chunk 79 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS E 93 GLN F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 670 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.069686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.051664 restraints weight = 80933.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.053088 restraints weight = 46307.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054006 restraints weight = 32338.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.054592 restraints weight = 26019.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054912 restraints weight = 22844.282| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.6776 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= 0.197 Angle : 0.706 11.137 20617 Z= 0.386 Chirality : 0.041 0.164 2338 Planarity : 0.006 0.082 1836 Dihedral : 28.399 137.474 3682 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.97 % Rotamer: Outliers : 0.10 % Allowed : 1.30 % Favored : 98.60 % 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 aren not related in a simple way. whole: 0.32 (0.24), residues: 1142 helix: 1.02 (0.18), residues: 768 sheet: -0.83 (0.69), residues: 54 loop : -1.50 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 45 TYR 0.025 0.002 TYR H 65 PHE 0.039 0.003 PHE D 67 TRP 0.019 0.002 TRP K 327 HIS 0.011 0.002 HIS K 387 Details of bonding type rmsd covalent geometry : bond 0.00446 (14582) covalent geometry : angle 0.70552 (20617) hydrogen bonds : bond 0.04746 ( 861) hydrogen bonds : angle 3.92472 ( 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 257 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7838 (t80) cc_final: 0.7537 (t80) REVERT: A 86 SER cc_start: 0.8199 (m) cc_final: 0.7896 (t) REVERT: A 133 GLU cc_start: 0.5758 (pm20) cc_final: 0.5415 (pt0) REVERT: B 74 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 75 HIS cc_start: 0.8948 (t70) cc_final: 0.8728 (t70) REVERT: B 84 MET cc_start: 0.7146 (tpt) cc_final: 0.6871 (mmm) REVERT: B 88 TYR cc_start: 0.7164 (m-80) cc_final: 0.6179 (m-80) REVERT: B 91 LYS cc_start: 0.7889 (tmmt) cc_final: 0.7379 (tttt) REVERT: C 72 LEU cc_start: 0.7844 (mp) cc_final: 0.7402 (tp) REVERT: C 98 ASN cc_start: 0.7998 (m-40) cc_final: 0.7287 (t0) REVERT: D 67 PHE cc_start: 0.6738 (m-80) cc_final: 0.6182 (m-80) REVERT: D 120 GLN cc_start: 0.7676 (pp30) cc_final: 0.7217 (pp30) REVERT: D 130 GLU cc_start: 0.6772 (mp0) cc_final: 0.6304 (mt-10) REVERT: E 128 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7693 (mmm-85) REVERT: F 71 THR cc_start: 0.8466 (p) cc_final: 0.7538 (t) REVERT: G 38 ARG cc_start: 0.6427 (ttt180) cc_final: 0.5877 (tpp80) REVERT: G 77 ASN cc_start: 0.8072 (t0) cc_final: 0.7871 (t0) REVERT: G 83 LYS cc_start: 0.7695 (mmmm) cc_final: 0.6508 (ptpp) REVERT: G 90 ARG cc_start: 0.7378 (tpm170) cc_final: 0.7099 (tpm170) REVERT: H 87 MET cc_start: 0.8362 (tpp) cc_final: 0.7981 (tmm) REVERT: H 118 GLU cc_start: 0.8324 (mp0) cc_final: 0.7449 (mp0) REVERT: K 233 LYS cc_start: 0.7649 (tttt) cc_final: 0.7203 (tttt) REVERT: K 249 LEU cc_start: 0.8431 (mt) cc_final: 0.7844 (tp) REVERT: K 373 TRP cc_start: 0.6639 (t-100) cc_final: 0.6385 (t-100) REVERT: K 380 LEU cc_start: 0.7669 (mt) cc_final: 0.7447 (mt) REVERT: K 384 PHE cc_start: 0.8374 (m-80) cc_final: 0.7317 (m-10) REVERT: K 468 LEU cc_start: 0.8028 (tp) cc_final: 0.7578 (tp) REVERT: K 527 ARG cc_start: 0.8313 (ppt170) cc_final: 0.7757 (ppt90) REVERT: K 615 CYS cc_start: 0.6180 (t) cc_final: 0.5959 (m) REVERT: K 623 ASN cc_start: 0.7666 (t0) cc_final: 0.7399 (t0) REVERT: K 626 MET cc_start: 0.7912 (ttt) cc_final: 0.7538 (ttm) REVERT: K 659 LEU cc_start: 0.9468 (tt) cc_final: 0.9159 (pp) REVERT: K 670 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.8323 (t70) outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.0931 time to fit residues: 35.6682 Evaluate side-chains 186 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 121 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 455 HIS ** 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 = 0.3487 r_free = 0.3487 target = 0.070310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052672 restraints weight = 79269.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054006 restraints weight = 47598.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054867 restraints weight = 34085.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055367 restraints weight = 27751.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.055696 restraints weight = 24697.636| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14582 Z= 0.155 Angle : 0.661 10.773 20617 Z= 0.365 Chirality : 0.039 0.161 2338 Planarity : 0.005 0.083 1836 Dihedral : 28.216 135.655 3682 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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 aren not related in a simple way. whole: 0.50 (0.25), residues: 1142 helix: 1.15 (0.18), residues: 767 sheet: -0.58 (0.76), residues: 50 loop : -1.44 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.022 0.002 TYR C 66 PHE 0.035 0.002 PHE K 526 TRP 0.015 0.002 TRP K 217 HIS 0.016 0.002 HIS K 243 Details of bonding type rmsd covalent geometry : bond 0.00344 (14582) covalent geometry : angle 0.66141 (20617) hydrogen bonds : bond 0.04188 ( 861) hydrogen bonds : angle 3.77611 ( 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 251 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.411 Fit side-chains REVERT: A 73 GLU cc_start: 0.8010 (tp30) cc_final: 0.7688 (tm-30) REVERT: A 78 PHE cc_start: 0.7906 (t80) cc_final: 0.7580 (t80) REVERT: A 86 SER cc_start: 0.8082 (m) cc_final: 0.7787 (t) REVERT: A 92 LEU cc_start: 0.8550 (mt) cc_final: 0.8335 (mp) REVERT: A 97 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6966 (mt-10) REVERT: A 133 GLU cc_start: 0.5723 (pm20) cc_final: 0.5465 (pt0) REVERT: B 71 THR cc_start: 0.8245 (m) cc_final: 0.7563 (m) REVERT: B 75 HIS cc_start: 0.8824 (t70) cc_final: 0.8580 (t-170) REVERT: B 84 MET cc_start: 0.7259 (tpt) cc_final: 0.7016 (mmm) REVERT: B 88 TYR cc_start: 0.7225 (m-80) cc_final: 0.6261 (m-80) REVERT: B 91 LYS cc_start: 0.7921 (tmmt) cc_final: 0.7401 (tttt) REVERT: C 97 ARG cc_start: 0.5313 (mpt180) cc_final: 0.5054 (mpt180) REVERT: C 98 ASN cc_start: 0.8195 (m-40) cc_final: 0.7325 (t0) REVERT: D 67 PHE cc_start: 0.6807 (m-80) cc_final: 0.6385 (m-80) REVERT: D 111 LYS cc_start: 0.7751 (tptt) cc_final: 0.7449 (tptt) REVERT: D 130 GLU cc_start: 0.6550 (mp0) cc_final: 0.6047 (mt-10) REVERT: E 94 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7386 (mm-30) REVERT: E 97 GLU cc_start: 0.7451 (pt0) cc_final: 0.6933 (pt0) REVERT: E 128 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7638 (mmm-85) REVERT: F 71 THR cc_start: 0.8049 (p) cc_final: 0.7604 (t) REVERT: F 74 GLU cc_start: 0.7883 (pp20) cc_final: 0.7677 (pp20) REVERT: G 38 ARG cc_start: 0.6309 (ttt180) cc_final: 0.5751 (tpp80) REVERT: G 83 LYS cc_start: 0.7857 (mmmm) cc_final: 0.6559 (ptpp) REVERT: G 90 ARG cc_start: 0.7270 (tpm170) cc_final: 0.6939 (tpm170) REVERT: H 87 MET cc_start: 0.8443 (tpp) cc_final: 0.7994 (tmm) REVERT: H 108 TYR cc_start: 0.4526 (m-10) cc_final: 0.4158 (m-10) REVERT: H 118 GLU cc_start: 0.8333 (mp0) cc_final: 0.7419 (mp0) REVERT: H 127 LEU cc_start: 0.7860 (mm) cc_final: 0.7456 (mp) REVERT: K 214 ILE cc_start: 0.7579 (mm) cc_final: 0.7315 (mm) REVERT: K 233 LYS cc_start: 0.7535 (tttt) cc_final: 0.7079 (tttt) REVERT: K 249 LEU cc_start: 0.8307 (mt) cc_final: 0.7753 (tp) REVERT: K 286 ASN cc_start: 0.8658 (m110) cc_final: 0.8447 (m110) REVERT: K 315 MET cc_start: 0.7088 (mmm) cc_final: 0.6761 (tpp) REVERT: K 373 TRP cc_start: 0.6620 (t-100) cc_final: 0.6368 (t-100) REVERT: K 384 PHE cc_start: 0.8413 (m-80) cc_final: 0.7317 (m-10) REVERT: K 454 ASP cc_start: 0.7654 (t0) cc_final: 0.7418 (t70) REVERT: K 527 ARG cc_start: 0.8419 (ppt170) cc_final: 0.8038 (ptt180) REVERT: K 599 SER cc_start: 0.8418 (m) cc_final: 0.7757 (m) REVERT: K 623 ASN cc_start: 0.7468 (t0) cc_final: 0.7053 (t0) REVERT: K 626 MET cc_start: 0.7827 (ttt) cc_final: 0.7557 (ttm) REVERT: K 659 LEU cc_start: 0.9443 (tt) cc_final: 0.9177 (pp) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.0866 time to fit residues: 32.5669 Evaluate side-chains 194 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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: 0.8980 chunk 41 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS E 93 GLN F 25 ASN ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.071036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053706 restraints weight = 76612.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055180 restraints weight = 44179.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056157 restraints weight = 30530.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056688 restraints weight = 24120.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057147 restraints weight = 21114.211| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.7066 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= 0.148 Angle : 0.648 9.711 20617 Z= 0.360 Chirality : 0.039 0.170 2338 Planarity : 0.005 0.083 1836 Dihedral : 28.152 135.683 3682 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.50 % 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 aren not related in a simple way. whole: 0.45 (0.24), residues: 1142 helix: 1.15 (0.18), residues: 769 sheet: -0.99 (0.71), residues: 56 loop : -1.49 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.015 0.002 TYR B 88 PHE 0.037 0.002 PHE A 67 TRP 0.028 0.003 TRP K 393 HIS 0.011 0.001 HIS K 387 Details of bonding type rmsd covalent geometry : bond 0.00322 (14582) covalent geometry : angle 0.64779 (20617) hydrogen bonds : bond 0.04075 ( 861) hydrogen bonds : angle 3.70381 ( 2278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.84 seconds wall clock time: 33 minutes 28.53 seconds (2008.53 seconds total)