Starting phenix.real_space_refine on Sun Nov 17 11:38:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j90_36083/11_2024/8j90_36083.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j90_36083/11_2024/8j90_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j90_36083/11_2024/8j90_36083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j90_36083/11_2024/8j90_36083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j90_36083/11_2024/8j90_36083.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j90_36083/11_2024/8j90_36083.cif" } resolution = 4.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 7.92, per 1000 atoms: 0.57 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: 3.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.01 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: 7.33 Time building geometry restraints manager: 4.20 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 38.460 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- 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= 0.258 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.047 0.003 TRP K 373 HIS 0.011 0.001 HIS K 455 PHE 0.045 0.002 PHE G 42 TYR 0.021 0.002 TYR K 663 ARG 0.014 0.001 ARG K 580 *********************** 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 : 1.235 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: 0.3556 time to fit residues: 231.7180 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 : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ** 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 377 ASN K 421 HIS ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 ASN ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 675 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3607 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= 0.225 Angle : 0.696 8.598 20617 Z= 0.385 Chirality : 0.042 0.233 2338 Planarity : 0.005 0.048 1836 Dihedral : 28.308 137.830 3682 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.00 % Allowed : 7.88 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1142 helix: 0.70 (0.18), residues: 774 sheet: -0.27 (0.76), residues: 49 loop : -1.08 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 373 HIS 0.014 0.002 HIS B 75 PHE 0.032 0.002 PHE K 596 TYR 0.019 0.002 TYR C 48 ARG 0.011 0.001 ARG F 77 *********************** 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 326 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 316 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7732 (t80) cc_final: 0.7265 (t80) REVERT: A 86 SER cc_start: 0.8292 (m) cc_final: 0.7949 (t) REVERT: A 133 GLU cc_start: 0.6887 (pm20) cc_final: 0.6448 (pt0) REVERT: B 78 ARG cc_start: 0.8447 (ptp90) cc_final: 0.8246 (mtm180) REVERT: B 84 MET cc_start: 0.7207 (tpt) cc_final: 0.6979 (mmm) REVERT: B 88 TYR cc_start: 0.7112 (m-80) cc_final: 0.6163 (m-80) REVERT: B 91 LYS cc_start: 0.7837 (tmmt) cc_final: 0.7300 (tttt) REVERT: B 98 TYR cc_start: 0.6997 (m-10) cc_final: 0.6358 (m-10) REVERT: C 28 MET cc_start: 0.5129 (mtm) cc_final: 0.4144 (ttp) REVERT: C 42 PHE cc_start: 0.7491 (m-10) cc_final: 0.7148 (m-80) REVERT: C 98 ASN cc_start: 0.7836 (m-40) cc_final: 0.7455 (t0) REVERT: D 63 LYS cc_start: 0.7330 (mptt) cc_final: 0.6700 (mmmt) REVERT: D 110 LYS cc_start: 0.6812 (mmtt) cc_final: 0.6297 (mtpp) REVERT: D 111 LYS cc_start: 0.8033 (tptt) cc_final: 0.7376 (tptt) REVERT: D 112 PRO cc_start: 0.7841 (Cg_exo) cc_final: 0.7611 (Cg_endo) REVERT: D 130 GLU cc_start: 0.7900 (mp0) cc_final: 0.7204 (mt-10) REVERT: E 79 LYS cc_start: 0.6795 (tmtt) cc_final: 0.6432 (mmtt) REVERT: F 21 VAL cc_start: 0.6171 (t) cc_final: 0.4518 (m) REVERT: G 47 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7610 (mmm-85) REVERT: G 83 LYS cc_start: 0.8039 (mmmm) cc_final: 0.7030 (ptpp) REVERT: H 125 LEU cc_start: 0.8619 (tt) cc_final: 0.8414 (tt) REVERT: K 224 ILE cc_start: 0.8507 (mp) cc_final: 0.8083 (mm) REVERT: K 229 MET cc_start: 0.5091 (ptt) cc_final: 0.4722 (ptt) REVERT: K 249 LEU cc_start: 0.8254 (mt) cc_final: 0.7797 (tp) REVERT: K 281 TYR cc_start: 0.7330 (t80) cc_final: 0.6214 (t80) REVERT: K 282 HIS cc_start: 0.5120 (m90) cc_final: 0.4756 (m-70) REVERT: K 321 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6743 (mm) REVERT: K 373 TRP cc_start: 0.6596 (t-100) cc_final: 0.6090 (t-100) REVERT: K 382 ASP cc_start: 0.6695 (m-30) cc_final: 0.6374 (m-30) REVERT: K 384 PHE cc_start: 0.8396 (m-80) cc_final: 0.7974 (m-80) REVERT: K 468 LEU cc_start: 0.8292 (tp) cc_final: 0.7927 (tt) REVERT: K 553 LEU cc_start: 0.7377 (mp) cc_final: 0.6956 (mp) REVERT: K 557 ASP cc_start: 0.7913 (t0) cc_final: 0.7468 (t70) REVERT: K 570 ILE cc_start: 0.6588 (mm) cc_final: 0.6363 (mp) REVERT: K 621 ASP cc_start: 0.7538 (t0) cc_final: 0.7122 (m-30) REVERT: K 623 ASN cc_start: 0.7867 (t0) cc_final: 0.7474 (t0) REVERT: K 748 TRP cc_start: 0.5607 (p-90) cc_final: 0.5403 (p-90) REVERT: K 755 SER cc_start: 0.7240 (p) cc_final: 0.7004 (t) outliers start: 10 outliers final: 1 residues processed: 322 average time/residue: 0.3024 time to fit residues: 137.2389 Evaluate side-chains 220 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 41 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN 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 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14582 Z= 0.277 Angle : 0.710 11.499 20617 Z= 0.391 Chirality : 0.042 0.202 2338 Planarity : 0.006 0.079 1836 Dihedral : 28.573 140.392 3682 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1142 helix: 0.74 (0.18), residues: 772 sheet: -0.46 (0.71), residues: 53 loop : -1.37 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 622 HIS 0.009 0.002 HIS B 75 PHE 0.035 0.003 PHE K 390 TYR 0.021 0.003 TYR C 48 ARG 0.011 0.001 ARG K 661 *********************** 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 293 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 1.248 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: 0.7732 (t80) cc_final: 0.7148 (t80) REVERT: A 86 SER cc_start: 0.8343 (m) cc_final: 0.7989 (t) REVERT: A 133 GLU cc_start: 0.6650 (pm20) cc_final: 0.6383 (pt0) REVERT: B 27 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7955 (mm-40) REVERT: B 84 MET cc_start: 0.7331 (tpt) cc_final: 0.7129 (mmm) REVERT: B 88 TYR cc_start: 0.7096 (m-80) cc_final: 0.6290 (m-80) REVERT: B 91 LYS cc_start: 0.7664 (tmmt) cc_final: 0.7256 (tttt) REVERT: B 98 TYR cc_start: 0.6832 (m-10) cc_final: 0.6452 (m-10) REVERT: C 28 MET cc_start: 0.4667 (mtm) cc_final: 0.3723 (tpt) REVERT: C 39 ILE cc_start: 0.7687 (pt) cc_final: 0.7364 (pt) REVERT: C 42 PHE cc_start: 0.7288 (m-10) cc_final: 0.7075 (m-80) REVERT: C 98 ASN cc_start: 0.7884 (m-40) cc_final: 0.7387 (t0) REVERT: D 110 LYS cc_start: 0.6970 (mmtt) cc_final: 0.6647 (mtpp) REVERT: D 130 GLU cc_start: 0.7777 (mp0) cc_final: 0.7194 (mt-10) REVERT: F 21 VAL cc_start: 0.5877 (t) cc_final: 0.4662 (m) REVERT: F 63 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8273 (mm-30) REVERT: G 38 ARG cc_start: 0.6572 (ttt180) cc_final: 0.6010 (tpp80) REVERT: G 73 GLU cc_start: 0.7284 (pt0) cc_final: 0.7046 (pt0) REVERT: G 77 ASN cc_start: 0.8290 (t0) cc_final: 0.8049 (t0) REVERT: G 83 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7099 (ptpp) REVERT: G 90 ARG cc_start: 0.7431 (tpm170) cc_final: 0.7170 (tpm170) REVERT: G 99 ASP cc_start: 0.6957 (t0) cc_final: 0.6746 (t0) REVERT: K 241 LEU cc_start: 0.8190 (mm) cc_final: 0.7934 (mt) REVERT: K 249 LEU cc_start: 0.8287 (mt) cc_final: 0.7782 (tp) REVERT: K 315 MET cc_start: 0.7319 (tpp) cc_final: 0.6905 (tpp) REVERT: K 329 TYR cc_start: 0.6968 (m-80) cc_final: 0.6385 (t80) REVERT: K 373 TRP cc_start: 0.6524 (t-100) cc_final: 0.6173 (t-100) REVERT: K 384 PHE cc_start: 0.8492 (m-80) cc_final: 0.7387 (m-10) REVERT: K 468 LEU cc_start: 0.8450 (tp) cc_final: 0.8199 (tp) REVERT: K 570 ILE cc_start: 0.7065 (mm) cc_final: 0.6701 (mp) REVERT: K 652 GLN cc_start: 0.5017 (tm-30) cc_final: 0.4771 (tm-30) REVERT: K 755 SER cc_start: 0.6807 (p) cc_final: 0.6595 (t) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.2745 time to fit residues: 115.5346 Evaluate side-chains 202 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN D 109 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.5272 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= 0.176 Angle : 0.634 7.937 20617 Z= 0.355 Chirality : 0.039 0.232 2338 Planarity : 0.005 0.047 1836 Dihedral : 28.325 136.317 3682 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 0.20 % Allowed : 3.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1142 helix: 1.12 (0.18), residues: 771 sheet: -0.16 (0.76), residues: 49 loop : -1.35 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 748 HIS 0.006 0.001 HIS B 75 PHE 0.027 0.002 PHE D 67 TYR 0.018 0.002 TYR K 646 ARG 0.006 0.001 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 1.268 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 73 GLU cc_start: 0.8448 (tp30) cc_final: 0.8005 (tm-30) REVERT: A 78 PHE cc_start: 0.7760 (t80) cc_final: 0.7282 (t80) REVERT: A 86 SER cc_start: 0.8316 (m) cc_final: 0.7469 (t) REVERT: B 24 ASP cc_start: 0.6309 (t0) cc_final: 0.5958 (t0) REVERT: B 27 GLN cc_start: 0.8107 (tp-100) cc_final: 0.7891 (mm-40) REVERT: B 88 TYR cc_start: 0.7131 (m-80) cc_final: 0.6464 (m-80) REVERT: B 91 LYS cc_start: 0.8030 (tmmt) cc_final: 0.7692 (tttt) REVERT: B 98 TYR cc_start: 0.6772 (m-10) cc_final: 0.6066 (m-10) REVERT: C 28 MET cc_start: 0.4692 (mtm) cc_final: 0.3676 (tpt) REVERT: C 39 ILE cc_start: 0.7601 (pt) cc_final: 0.7266 (pt) REVERT: C 42 PHE cc_start: 0.7284 (m-10) cc_final: 0.6921 (m-80) REVERT: C 72 LEU cc_start: 0.8046 (mp) cc_final: 0.7693 (tp) REVERT: C 98 ASN cc_start: 0.7956 (m-40) cc_final: 0.7371 (t0) REVERT: D 130 GLU cc_start: 0.7342 (mp0) cc_final: 0.6488 (mt-10) REVERT: E 74 ILE cc_start: 0.8964 (tp) cc_final: 0.8743 (tt) REVERT: F 63 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8191 (mm-30) REVERT: G 38 ARG cc_start: 0.6240 (ttt180) cc_final: 0.5667 (tpp80) REVERT: G 60 MET cc_start: 0.8266 (ttt) cc_final: 0.7916 (ptm) REVERT: G 73 GLU cc_start: 0.7271 (pt0) cc_final: 0.6998 (pt0) REVERT: G 77 ASN cc_start: 0.8271 (t0) cc_final: 0.8049 (t0) REVERT: G 83 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7070 (ptpp) REVERT: G 90 ARG cc_start: 0.7566 (tpm170) cc_final: 0.7280 (tpm170) REVERT: H 94 ILE cc_start: 0.8414 (mm) cc_final: 0.8162 (mm) REVERT: H 118 GLU cc_start: 0.8255 (mp0) cc_final: 0.7359 (mp0) REVERT: K 205 TYR cc_start: 0.6971 (m-10) cc_final: 0.6571 (m-10) REVERT: K 224 ILE cc_start: 0.8368 (mp) cc_final: 0.8146 (mm) REVERT: K 249 LEU cc_start: 0.8241 (mt) cc_final: 0.7738 (tp) REVERT: K 281 TYR cc_start: 0.6671 (t80) cc_final: 0.6106 (t80) REVERT: K 296 MET cc_start: 0.3379 (ptm) cc_final: 0.2267 (ppp) REVERT: K 315 MET cc_start: 0.7241 (tpp) cc_final: 0.6766 (tpp) REVERT: K 373 TRP cc_start: 0.6541 (t-100) cc_final: 0.6281 (t-100) REVERT: K 384 PHE cc_start: 0.8375 (m-80) cc_final: 0.7206 (m-10) REVERT: K 537 PHE cc_start: 0.8558 (t80) cc_final: 0.8260 (t80) REVERT: K 556 MET cc_start: 0.8055 (ttm) cc_final: 0.7831 (ttm) REVERT: K 570 ILE cc_start: 0.6926 (mm) cc_final: 0.6663 (mp) REVERT: K 623 ASN cc_start: 0.7663 (t0) cc_final: 0.7233 (t0) REVERT: K 755 SER cc_start: 0.7166 (p) cc_final: 0.6930 (t) outliers start: 2 outliers final: 1 residues processed: 293 average time/residue: 0.2819 time to fit residues: 117.8465 Evaluate side-chains 215 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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** B 93 GLN C 113 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 ASN ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 HIS K 471 HIS ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14582 Z= 0.295 Angle : 0.714 8.197 20617 Z= 0.395 Chirality : 0.042 0.247 2338 Planarity : 0.006 0.067 1836 Dihedral : 28.689 139.396 3682 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1142 helix: 0.88 (0.18), residues: 773 sheet: -0.76 (0.71), residues: 54 loop : -1.68 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP K 622 HIS 0.011 0.002 HIS K 455 PHE 0.036 0.003 PHE A 67 TYR 0.018 0.002 TYR H 65 ARG 0.006 0.001 ARG E 128 *********************** 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 259 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7907 (t80) cc_final: 0.7451 (t80) REVERT: A 86 SER cc_start: 0.7970 (m) cc_final: 0.7701 (t) REVERT: B 75 HIS cc_start: 0.8800 (t70) cc_final: 0.8136 (t70) REVERT: B 84 MET cc_start: 0.7210 (tpt) cc_final: 0.6920 (mmm) REVERT: B 91 LYS cc_start: 0.7614 (tmmt) cc_final: 0.7209 (tttt) REVERT: B 98 TYR cc_start: 0.6758 (m-10) cc_final: 0.6344 (m-10) REVERT: C 98 ASN cc_start: 0.8055 (m-40) cc_final: 0.7638 (t0) REVERT: C 107 SER cc_start: 0.6914 (t) cc_final: 0.6651 (p) REVERT: D 130 GLU cc_start: 0.7390 (mp0) cc_final: 0.6752 (mt-10) REVERT: F 63 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8294 (mm-30) REVERT: G 38 ARG cc_start: 0.6738 (ttt180) cc_final: 0.6149 (tpp80) REVERT: G 60 MET cc_start: 0.8372 (ttt) cc_final: 0.7877 (ptm) REVERT: G 73 GLU cc_start: 0.7476 (pt0) cc_final: 0.7139 (pt0) REVERT: G 77 ASN cc_start: 0.8224 (t0) cc_final: 0.8018 (t0) REVERT: G 83 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7090 (ptpp) REVERT: G 90 ARG cc_start: 0.7574 (tpm170) cc_final: 0.7270 (tpm170) REVERT: G 99 ASP cc_start: 0.6836 (t0) cc_final: 0.6217 (t0) REVERT: H 87 MET cc_start: 0.8463 (tpp) cc_final: 0.7922 (tmm) REVERT: H 118 GLU cc_start: 0.8275 (mp0) cc_final: 0.7419 (mp0) REVERT: H 138 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6147 (mt-10) REVERT: K 205 TYR cc_start: 0.7040 (m-10) cc_final: 0.6632 (m-10) REVERT: K 249 LEU cc_start: 0.8376 (mt) cc_final: 0.7790 (tp) REVERT: K 296 MET cc_start: 0.3449 (ptm) cc_final: 0.2621 (ppp) REVERT: K 315 MET cc_start: 0.7307 (tpp) cc_final: 0.6794 (tpp) REVERT: K 373 TRP cc_start: 0.6561 (t-100) cc_final: 0.6314 (t-100) REVERT: K 384 PHE cc_start: 0.8353 (m-80) cc_final: 0.6954 (m-80) REVERT: K 409 GLU cc_start: 0.4114 (mm-30) cc_final: 0.3662 (pm20) REVERT: K 570 ILE cc_start: 0.7051 (mm) cc_final: 0.6814 (mp) REVERT: K 623 ASN cc_start: 0.7612 (t0) cc_final: 0.7357 (t0) REVERT: K 755 SER cc_start: 0.7307 (p) cc_final: 0.7087 (t) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2643 time to fit residues: 99.1235 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 : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS D 88 ASN F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 243 HIS ** 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 541 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 675 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14582 Z= 0.189 Angle : 0.647 9.510 20617 Z= 0.361 Chirality : 0.039 0.179 2338 Planarity : 0.005 0.091 1836 Dihedral : 28.453 136.595 3682 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1142 helix: 1.11 (0.18), residues: 767 sheet: -0.91 (0.69), residues: 55 loop : -1.64 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 748 HIS 0.009 0.001 HIS K 455 PHE 0.022 0.001 PHE D 67 TYR 0.020 0.002 TYR B 88 ARG 0.006 0.001 ARG K 633 *********************** 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 270 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8307 (tp30) cc_final: 0.7959 (tm-30) REVERT: A 78 PHE cc_start: 0.7814 (t80) cc_final: 0.7348 (t80) REVERT: A 86 SER cc_start: 0.7906 (m) cc_final: 0.7597 (t) REVERT: A 97 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7092 (mt-10) REVERT: B 84 MET cc_start: 0.7333 (tpt) cc_final: 0.6158 (tpt) REVERT: B 91 LYS cc_start: 0.7721 (tmmt) cc_final: 0.7223 (tttt) REVERT: B 98 TYR cc_start: 0.6680 (m-10) cc_final: 0.6274 (m-10) REVERT: C 39 ILE cc_start: 0.7605 (pt) cc_final: 0.7269 (pt) REVERT: C 42 PHE cc_start: 0.7209 (m-10) cc_final: 0.6994 (m-80) REVERT: C 72 LEU cc_start: 0.7981 (mp) cc_final: 0.7609 (tt) REVERT: C 98 ASN cc_start: 0.8023 (m-40) cc_final: 0.7547 (t0) REVERT: C 107 SER cc_start: 0.6858 (t) cc_final: 0.6613 (p) REVERT: D 63 LYS cc_start: 0.7080 (mmtp) cc_final: 0.6331 (mmmt) REVERT: D 125 LEU cc_start: 0.7414 (tt) cc_final: 0.7100 (tt) REVERT: D 130 GLU cc_start: 0.7076 (mp0) cc_final: 0.6355 (mt-10) REVERT: E 79 LYS cc_start: 0.6892 (tttt) cc_final: 0.6603 (tptm) REVERT: E 94 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7913 (tt0) REVERT: E 128 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7442 (mmm-85) REVERT: F 22 LEU cc_start: 0.7294 (tp) cc_final: 0.7066 (tp) REVERT: G 38 ARG cc_start: 0.6629 (ttt180) cc_final: 0.6123 (tpp80) REVERT: G 60 MET cc_start: 0.8387 (ttt) cc_final: 0.8024 (ptm) REVERT: G 73 GLU cc_start: 0.7459 (pt0) cc_final: 0.7046 (pt0) REVERT: G 77 ASN cc_start: 0.8196 (t0) cc_final: 0.7994 (t0) REVERT: G 83 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7003 (ptpp) REVERT: G 90 ARG cc_start: 0.7590 (tpm170) cc_final: 0.7303 (tpm170) REVERT: G 99 ASP cc_start: 0.6815 (t0) cc_final: 0.6412 (t0) REVERT: H 87 MET cc_start: 0.8488 (tpp) cc_final: 0.7985 (tmm) REVERT: H 118 GLU cc_start: 0.8296 (mp0) cc_final: 0.7426 (mp0) REVERT: H 137 SER cc_start: 0.7554 (p) cc_final: 0.7242 (p) REVERT: K 205 TYR cc_start: 0.7004 (m-10) cc_final: 0.6563 (m-10) REVERT: K 249 LEU cc_start: 0.8310 (mt) cc_final: 0.7659 (tp) REVERT: K 281 TYR cc_start: 0.6451 (t80) cc_final: 0.6062 (t80) REVERT: K 315 MET cc_start: 0.7674 (tpp) cc_final: 0.7103 (tpp) REVERT: K 373 TRP cc_start: 0.6592 (t-100) cc_final: 0.6358 (t-100) REVERT: K 384 PHE cc_start: 0.8322 (m-80) cc_final: 0.6923 (m-80) REVERT: K 570 ILE cc_start: 0.7028 (mm) cc_final: 0.6778 (mp) REVERT: K 623 ASN cc_start: 0.7449 (t0) cc_final: 0.7066 (t0) REVERT: K 659 LEU cc_start: 0.9430 (tt) cc_final: 0.9179 (pp) REVERT: K 755 SER cc_start: 0.7312 (p) cc_final: 0.7100 (t) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2692 time to fit residues: 104.1494 Evaluate side-chains 201 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS D 88 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 HIS ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 541 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 670 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.6677 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= 0.278 Angle : 0.708 7.991 20617 Z= 0.391 Chirality : 0.042 0.174 2338 Planarity : 0.005 0.047 1836 Dihedral : 28.685 138.988 3682 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1142 helix: 0.88 (0.18), residues: 769 sheet: -1.07 (0.64), residues: 55 loop : -1.74 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP K 748 HIS 0.012 0.002 HIS K 455 PHE 0.040 0.003 PHE A 67 TYR 0.024 0.002 TYR B 88 ARG 0.007 0.001 ARG D 117 *********************** 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 261 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7840 (t80) cc_final: 0.7401 (t80) REVERT: A 86 SER cc_start: 0.7917 (m) cc_final: 0.7622 (t) REVERT: B 84 MET cc_start: 0.7406 (tpt) cc_final: 0.6600 (tpt) REVERT: B 91 LYS cc_start: 0.7627 (tmmt) cc_final: 0.7099 (tttt) REVERT: B 98 TYR cc_start: 0.6811 (m-10) cc_final: 0.6348 (m-10) REVERT: C 98 ASN cc_start: 0.8116 (m-40) cc_final: 0.7591 (t0) REVERT: C 107 SER cc_start: 0.7007 (t) cc_final: 0.6738 (p) REVERT: D 130 GLU cc_start: 0.7183 (mp0) cc_final: 0.6567 (mt-10) REVERT: E 83 ARG cc_start: 0.7135 (tpp-160) cc_final: 0.6820 (tpp-160) REVERT: G 38 ARG cc_start: 0.6304 (ttt180) cc_final: 0.5964 (tpp80) REVERT: G 60 MET cc_start: 0.8405 (ttt) cc_final: 0.8003 (ptm) REVERT: G 83 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7055 (ptpp) REVERT: G 99 ASP cc_start: 0.6669 (t0) cc_final: 0.6299 (t0) REVERT: H 87 MET cc_start: 0.8450 (tpp) cc_final: 0.8009 (tmm) REVERT: H 94 ILE cc_start: 0.8376 (mm) cc_final: 0.8165 (mm) REVERT: H 118 GLU cc_start: 0.8310 (mp0) cc_final: 0.7452 (mp0) REVERT: K 205 TYR cc_start: 0.7183 (m-10) cc_final: 0.6784 (m-10) REVERT: K 249 LEU cc_start: 0.8453 (mt) cc_final: 0.7796 (tp) REVERT: K 373 TRP cc_start: 0.6562 (t-100) cc_final: 0.6304 (t-100) REVERT: K 384 PHE cc_start: 0.8341 (m-80) cc_final: 0.6890 (m-10) REVERT: K 409 GLU cc_start: 0.4147 (mm-30) cc_final: 0.3660 (pm20) REVERT: K 552 LEU cc_start: 0.7986 (tt) cc_final: 0.7725 (tt) REVERT: K 570 ILE cc_start: 0.7153 (mm) cc_final: 0.6813 (mp) REVERT: K 599 SER cc_start: 0.8575 (m) cc_final: 0.8120 (p) REVERT: K 623 ASN cc_start: 0.7528 (t0) cc_final: 0.7205 (t0) REVERT: K 670 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.8427 (t70) REVERT: K 755 SER cc_start: 0.7333 (p) cc_final: 0.7100 (t) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.2592 time to fit residues: 97.7419 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 : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 12 optimal weight: 0.0470 chunk 102 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 overall best weight: 3.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 113 HIS ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 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 471 HIS K 541 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14582 Z= 0.264 Angle : 0.710 10.124 20617 Z= 0.392 Chirality : 0.042 0.276 2338 Planarity : 0.005 0.044 1836 Dihedral : 28.714 137.867 3682 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1142 helix: 0.82 (0.18), residues: 768 sheet: -1.10 (0.67), residues: 58 loop : -1.79 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP K 748 HIS 0.013 0.002 HIS B 75 PHE 0.019 0.002 PHE K 526 TYR 0.023 0.002 TYR B 72 ARG 0.007 0.001 ARG D 117 *********************** 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 256 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7783 (t80) cc_final: 0.7386 (t80) REVERT: A 86 SER cc_start: 0.7887 (m) cc_final: 0.7623 (t) REVERT: B 84 MET cc_start: 0.7468 (tpt) cc_final: 0.7244 (tpt) REVERT: B 88 TYR cc_start: 0.7340 (m-80) cc_final: 0.7101 (m-80) REVERT: B 91 LYS cc_start: 0.7656 (tmmt) cc_final: 0.7171 (tttt) REVERT: B 98 TYR cc_start: 0.6762 (m-10) cc_final: 0.6276 (m-10) REVERT: C 72 LEU cc_start: 0.8050 (mp) cc_final: 0.7666 (tp) REVERT: C 98 ASN cc_start: 0.8089 (m-40) cc_final: 0.7883 (m-40) REVERT: D 130 GLU cc_start: 0.7192 (mp0) cc_final: 0.6587 (mt-10) REVERT: E 83 ARG cc_start: 0.7111 (tpp-160) cc_final: 0.6787 (tpp-160) REVERT: G 38 ARG cc_start: 0.6297 (ttt180) cc_final: 0.5895 (tpp80) REVERT: G 60 MET cc_start: 0.8386 (ttt) cc_final: 0.8068 (ptm) REVERT: G 83 LYS cc_start: 0.7996 (mmmm) cc_final: 0.6981 (ptpp) REVERT: G 90 ARG cc_start: 0.7169 (tpm170) cc_final: 0.6922 (tpm170) REVERT: G 99 ASP cc_start: 0.6459 (t0) cc_final: 0.5961 (t0) REVERT: H 87 MET cc_start: 0.8443 (tpp) cc_final: 0.8085 (tmm) REVERT: H 94 ILE cc_start: 0.8323 (mm) cc_final: 0.8068 (mm) REVERT: H 118 GLU cc_start: 0.8327 (mp0) cc_final: 0.7490 (mp0) REVERT: H 127 LEU cc_start: 0.7774 (mm) cc_final: 0.7370 (mp) REVERT: H 138 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6273 (mt-10) REVERT: K 205 TYR cc_start: 0.7036 (m-10) cc_final: 0.6667 (m-10) REVERT: K 281 TYR cc_start: 0.6752 (t80) cc_final: 0.5785 (t80) REVERT: K 296 MET cc_start: 0.4902 (ptm) cc_final: 0.4531 (ptm) REVERT: K 315 MET cc_start: 0.7365 (tpp) cc_final: 0.6969 (tpp) REVERT: K 373 TRP cc_start: 0.6550 (t-100) cc_final: 0.6257 (t-100) REVERT: K 384 PHE cc_start: 0.8362 (m-80) cc_final: 0.6834 (m-10) REVERT: K 409 GLU cc_start: 0.4067 (mm-30) cc_final: 0.3568 (pm20) REVERT: K 468 LEU cc_start: 0.8374 (mt) cc_final: 0.7631 (tp) REVERT: K 570 ILE cc_start: 0.7207 (mm) cc_final: 0.6835 (mp) REVERT: K 623 ASN cc_start: 0.7439 (t0) cc_final: 0.7217 (t0) REVERT: K 626 MET cc_start: 0.7949 (ttt) cc_final: 0.7478 (ttm) REVERT: K 755 SER cc_start: 0.7182 (p) cc_final: 0.6951 (t) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2537 time to fit residues: 96.0772 Evaluate side-chains 188 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 0.0670 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 243 HIS K 324 HIS ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14582 Z= 0.202 Angle : 0.676 10.177 20617 Z= 0.374 Chirality : 0.040 0.217 2338 Planarity : 0.005 0.101 1836 Dihedral : 28.503 136.887 3682 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1142 helix: 1.01 (0.18), residues: 761 sheet: -1.12 (0.68), residues: 53 loop : -1.79 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 393 HIS 0.011 0.001 HIS B 75 PHE 0.038 0.002 PHE D 67 TYR 0.021 0.002 TYR B 88 ARG 0.007 0.001 ARG D 117 *********************** 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 262 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7739 (t80) cc_final: 0.7381 (t80) REVERT: A 86 SER cc_start: 0.7837 (m) cc_final: 0.7525 (t) REVERT: B 91 LYS cc_start: 0.7759 (tmmt) cc_final: 0.7345 (tttt) REVERT: B 98 TYR cc_start: 0.6913 (m-10) cc_final: 0.6691 (m-10) REVERT: C 107 SER cc_start: 0.6894 (t) cc_final: 0.6643 (p) REVERT: D 120 GLN cc_start: 0.7227 (pp30) cc_final: 0.6996 (pp30) REVERT: D 124 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6419 (ttm-80) REVERT: D 130 GLU cc_start: 0.6938 (mp0) cc_final: 0.6397 (mt-10) REVERT: E 83 ARG cc_start: 0.7061 (tpp-160) cc_final: 0.6604 (tpp-160) REVERT: F 98 TYR cc_start: 0.4975 (m-80) cc_final: 0.4198 (m-80) REVERT: G 38 ARG cc_start: 0.6232 (ttt180) cc_final: 0.5820 (tpp80) REVERT: G 60 MET cc_start: 0.8386 (ttt) cc_final: 0.8173 (ptm) REVERT: G 83 LYS cc_start: 0.7873 (mmmm) cc_final: 0.6852 (ptpp) REVERT: G 90 ARG cc_start: 0.7223 (tpm170) cc_final: 0.6898 (tpm170) REVERT: G 99 ASP cc_start: 0.6468 (t0) cc_final: 0.6012 (t0) REVERT: H 87 MET cc_start: 0.8432 (tpp) cc_final: 0.8036 (tmm) REVERT: H 94 ILE cc_start: 0.8418 (mm) cc_final: 0.8217 (mm) REVERT: H 118 GLU cc_start: 0.8299 (mp0) cc_final: 0.7430 (mp0) REVERT: H 127 LEU cc_start: 0.7876 (mm) cc_final: 0.7515 (mp) REVERT: H 137 SER cc_start: 0.7603 (p) cc_final: 0.7290 (p) REVERT: H 138 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6225 (mt-10) REVERT: K 205 TYR cc_start: 0.6875 (m-10) cc_final: 0.6473 (m-10) REVERT: K 249 LEU cc_start: 0.8078 (mt) cc_final: 0.7709 (tp) REVERT: K 315 MET cc_start: 0.7494 (tpp) cc_final: 0.6655 (tpp) REVERT: K 373 TRP cc_start: 0.6462 (t-100) cc_final: 0.6256 (t-100) REVERT: K 384 PHE cc_start: 0.8309 (m-80) cc_final: 0.6874 (m-80) REVERT: K 409 GLU cc_start: 0.4080 (mm-30) cc_final: 0.3583 (pm20) REVERT: K 468 LEU cc_start: 0.8233 (mt) cc_final: 0.7471 (tp) REVERT: K 570 ILE cc_start: 0.7255 (mm) cc_final: 0.6928 (mp) REVERT: K 599 SER cc_start: 0.8197 (m) cc_final: 0.7721 (p) REVERT: K 623 ASN cc_start: 0.7357 (t0) cc_final: 0.7066 (t0) REVERT: K 626 MET cc_start: 0.7930 (ttt) cc_final: 0.7725 (ttm) REVERT: K 652 GLN cc_start: 0.4868 (tm-30) cc_final: 0.4661 (tm-30) REVERT: K 669 GLU cc_start: 0.9296 (tp30) cc_final: 0.9067 (tp30) REVERT: K 755 SER cc_start: 0.7222 (p) cc_final: 0.7000 (t) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2544 time to fit residues: 96.5586 Evaluate side-chains 200 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 HIS ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.7285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14582 Z= 0.236 Angle : 0.702 11.957 20617 Z= 0.387 Chirality : 0.041 0.231 2338 Planarity : 0.005 0.097 1836 Dihedral : 28.505 137.916 3682 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1142 helix: 1.01 (0.19), residues: 757 sheet: -0.98 (0.66), residues: 51 loop : -1.85 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 393 HIS 0.011 0.002 HIS B 75 PHE 0.036 0.002 PHE D 67 TYR 0.038 0.002 TYR H 65 ARG 0.005 0.001 ARG K 633 ********************** 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 257 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.278 Fit side-chains REVERT: A 67 PHE cc_start: 0.8409 (t80) cc_final: 0.8205 (t80) REVERT: A 78 PHE cc_start: 0.7780 (t80) cc_final: 0.7390 (t80) REVERT: A 86 SER cc_start: 0.7853 (m) cc_final: 0.7569 (t) REVERT: B 84 MET cc_start: 0.7353 (tpt) cc_final: 0.6775 (tpp) REVERT: B 91 LYS cc_start: 0.7693 (tmmt) cc_final: 0.7176 (tttt) REVERT: B 98 TYR cc_start: 0.7149 (m-10) cc_final: 0.6655 (m-10) REVERT: C 107 SER cc_start: 0.6999 (t) cc_final: 0.6740 (p) REVERT: D 84 MET cc_start: 0.6793 (ttp) cc_final: 0.6084 (mtt) REVERT: D 120 GLN cc_start: 0.7217 (pp30) cc_final: 0.6970 (pp30) REVERT: D 124 ARG cc_start: 0.7171 (mtp180) cc_final: 0.6432 (ttm-80) REVERT: D 130 GLU cc_start: 0.7009 (mp0) cc_final: 0.6462 (mt-10) REVERT: E 83 ARG cc_start: 0.7064 (tpp-160) cc_final: 0.6695 (tpp-160) REVERT: F 98 TYR cc_start: 0.4925 (m-80) cc_final: 0.4222 (m-80) REVERT: G 38 ARG cc_start: 0.6303 (ttt180) cc_final: 0.5923 (tpp80) REVERT: G 60 MET cc_start: 0.8413 (ttt) cc_final: 0.8128 (ptm) REVERT: G 83 LYS cc_start: 0.7906 (mmmm) cc_final: 0.6859 (ptpp) REVERT: G 90 ARG cc_start: 0.7208 (tpm170) cc_final: 0.6840 (tpm170) REVERT: G 99 ASP cc_start: 0.6539 (t0) cc_final: 0.6074 (t0) REVERT: H 87 MET cc_start: 0.8449 (tpp) cc_final: 0.8025 (tmm) REVERT: H 94 ILE cc_start: 0.8351 (mm) cc_final: 0.8115 (mm) REVERT: H 118 GLU cc_start: 0.8355 (mp0) cc_final: 0.7533 (mp0) REVERT: H 127 LEU cc_start: 0.7516 (mm) cc_final: 0.7080 (mp) REVERT: H 137 SER cc_start: 0.7637 (p) cc_final: 0.7296 (p) REVERT: H 138 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6297 (mt-10) REVERT: K 205 TYR cc_start: 0.6914 (m-10) cc_final: 0.6532 (m-10) REVERT: K 249 LEU cc_start: 0.8118 (mt) cc_final: 0.7716 (tp) REVERT: K 315 MET cc_start: 0.7459 (tpp) cc_final: 0.7089 (tpp) REVERT: K 373 TRP cc_start: 0.6488 (t-100) cc_final: 0.6252 (t-100) REVERT: K 384 PHE cc_start: 0.8319 (m-80) cc_final: 0.6962 (m-80) REVERT: K 409 GLU cc_start: 0.4025 (mm-30) cc_final: 0.3540 (pm20) REVERT: K 468 LEU cc_start: 0.8325 (mt) cc_final: 0.7581 (tp) REVERT: K 557 ASP cc_start: 0.6939 (m-30) cc_final: 0.6679 (p0) REVERT: K 570 ILE cc_start: 0.7310 (mm) cc_final: 0.6958 (mp) REVERT: K 623 ASN cc_start: 0.7297 (t0) cc_final: 0.7024 (t0) REVERT: K 755 SER cc_start: 0.7186 (p) cc_final: 0.6976 (t) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2580 time to fit residues: 96.6397 Evaluate side-chains 190 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 GLN K 499 HIS K 625 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.069421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.052680 restraints weight = 83482.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054249 restraints weight = 45070.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055252 restraints weight = 29959.023| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.7453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14582 Z= 0.189 Angle : 0.675 11.020 20617 Z= 0.371 Chirality : 0.039 0.172 2338 Planarity : 0.005 0.092 1836 Dihedral : 28.273 136.252 3682 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1142 helix: 1.15 (0.19), residues: 760 sheet: -0.96 (0.65), residues: 54 loop : -1.76 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 217 HIS 0.007 0.001 HIS K 387 PHE 0.011 0.001 PHE A 67 TYR 0.036 0.002 TYR B 88 ARG 0.015 0.001 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.66 seconds wall clock time: 51 minutes 22.79 seconds (3082.79 seconds total)