Starting phenix.real_space_refine on Sun Mar 17 11:18:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2h_23128/03_2024/7l2h_23128_updated.pdb" } resolution = 2.63 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 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11514 2.51 5 N 2778 2.21 5 O 3155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17556 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4316 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 2 Chain: "D" Number of atoms: 4316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4316 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 2 Chain: "B" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4307 Classifications: {'peptide': 530} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 516} Chain breaks: 2 Chain: "C" Number of atoms: 4316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4316 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 517} Chain breaks: 2 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' NA': 1, 'XJ7': 1, 'XJD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'XJ7': 1, 'XJD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'XJ7': 1, 'XJD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'XJ7': 1, 'XJD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.10, per 1000 atoms: 0.52 Number of scatterers: 17556 At special positions: 0 Unit cell: (120.012, 119.19, 118.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 8 15.00 Na 1 11.00 O 3155 8.00 N 2778 7.00 C 11514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 6.96 Conformation dependent library (CDL) restraints added in 3.1 seconds 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 4 sheets defined 57.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.991A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.929A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.797A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 505 through 508 No H-bonds generated for 'chain 'D' and resid 505 through 508' Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.977A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 4.033A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.799A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 690 through 711 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.997A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.943A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.787A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 removed outlier: 3.609A pdb=" N LYS B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.007A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.919A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.772A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 741 through 747 removed outlier: 6.280A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP A 383 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 368 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 741 through 747 removed outlier: 6.363A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP D 383 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LYS D 368 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 741 through 747 removed outlier: 6.298A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP B 383 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS B 368 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 741 through 747 removed outlier: 6.316A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP C 383 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS C 368 " --> pdb=" O ASP C 383 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2699 1.31 - 1.43: 5090 1.43 - 1.56: 9994 1.56 - 1.69: 16 1.69 - 1.81: 164 Bond restraints: 17963 Sorted by residual: bond pdb=" C13 XJD C 902 " pdb=" O6 XJD C 902 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C13 XJD A 902 " pdb=" O6 XJD A 902 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C13 XJD B 902 " pdb=" O6 XJD B 902 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C7 XJD D 902 " pdb=" O1 XJD D 902 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C13 XJD D 902 " pdb=" O6 XJD D 902 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 17958 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.02: 215 105.02 - 112.28: 8805 112.28 - 119.55: 6133 119.55 - 126.81: 8947 126.81 - 134.07: 185 Bond angle restraints: 24285 Sorted by residual: angle pdb=" N TYR A 374 " pdb=" CA TYR A 374 " pdb=" C TYR A 374 " ideal model delta sigma weight residual 108.78 102.35 6.43 8.20e-01 1.49e+00 6.15e+01 angle pdb=" N TYR C 374 " pdb=" CA TYR C 374 " pdb=" C TYR C 374 " ideal model delta sigma weight residual 108.78 102.63 6.15 8.20e-01 1.49e+00 5.63e+01 angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 109.81 101.42 8.39 1.53e+00 4.27e-01 3.00e+01 angle pdb=" C SER D 711 " pdb=" N PHE D 712 " pdb=" CA PHE D 712 " ideal model delta sigma weight residual 121.54 130.74 -9.20 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 ... (remaining 24280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 10004 17.14 - 34.27: 415 34.27 - 51.41: 118 51.41 - 68.55: 64 68.55 - 85.68: 15 Dihedral angle restraints: 10616 sinusoidal: 4359 harmonic: 6257 Sorted by residual: dihedral pdb=" CA PHE B 712 " pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA PHE C 712 " pdb=" C PHE C 712 " pdb=" N LEU C 713 " pdb=" CA LEU C 713 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 10613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 2719 1.007 - 2.014: 0 2.014 - 3.021: 0 3.021 - 4.027: 0 4.027 - 5.034: 8 Chirality restraints: 2727 Sorted by residual: chirality pdb=" C3 XJ7 C 901 " pdb=" C2 XJ7 C 901 " pdb=" C24 XJ7 C 901 " pdb=" O3 XJ7 C 901 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.03 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" C3 XJ7 A 901 " pdb=" C2 XJ7 A 901 " pdb=" C24 XJ7 A 901 " pdb=" O3 XJ7 A 901 " both_signs ideal model delta sigma weight residual False -2.50 2.52 -5.03 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C3 XJ7 B 901 " pdb=" C2 XJ7 B 901 " pdb=" C24 XJ7 B 901 " pdb=" O3 XJ7 B 901 " both_signs ideal model delta sigma weight residual False -2.50 2.52 -5.02 2.00e-01 2.50e+01 6.30e+02 ... (remaining 2724 not shown) Planarity restraints: 2975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 373 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C ALA A 373 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 373 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 374 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 373 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C ALA B 373 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA B 373 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR B 374 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 373 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C ALA D 373 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA D 373 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR D 374 " 0.016 2.00e-02 2.50e+03 ... (remaining 2972 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 138 2.60 - 3.17: 15424 3.17 - 3.75: 27902 3.75 - 4.32: 39285 4.32 - 4.90: 64899 Nonbonded interactions: 147648 Sorted by model distance: nonbonded pdb=" OE2 GLU D 570 " pdb=" O11 XJ7 D 901 " model vdw 2.022 2.440 nonbonded pdb=" OE2 GLU A 570 " pdb=" O11 XJ7 A 901 " model vdw 2.038 2.440 nonbonded pdb=" OE2 GLU B 570 " pdb=" O11 XJ7 B 901 " model vdw 2.049 2.440 nonbonded pdb=" OE2 GLU C 570 " pdb=" O11 XJ7 C 901 " model vdw 2.080 2.440 nonbonded pdb=" O2 XJ7 D 901 " pdb=" O4 XJ7 D 901 " model vdw 2.145 2.440 ... (remaining 147643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 194 through 236 or resid 244 through 752 or resid 901 thro \ ugh 902)) selection = chain 'B' selection = (chain 'C' and (resid 194 through 236 or resid 244 through 752 or resid 901 thro \ ugh 902)) selection = (chain 'D' and (resid 194 through 236 or resid 244 through 752 or resid 901 thro \ ugh 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.060 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 45.970 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.100 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17963 Z= 0.280 Angle : 0.759 12.934 24285 Z= 0.393 Chirality : 0.273 5.034 2727 Planarity : 0.004 0.053 2975 Dihedral : 12.416 85.683 6591 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.85 % Allowed : 0.53 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.14 (0.18), residues: 2099 helix: 1.70 (0.14), residues: 1305 sheet: 0.35 (0.56), residues: 71 loop : -0.95 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 372 HIS 0.003 0.001 HIS D 410 PHE 0.015 0.002 PHE C 649 TYR 0.020 0.002 TYR C 374 ARG 0.002 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 514 time to evaluate : 2.012 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 339 LEU cc_start: 0.8785 (tp) cc_final: 0.8459 (tp) REVERT: A 343 SER cc_start: 0.8971 (m) cc_final: 0.8643 (p) REVERT: A 351 TYR cc_start: 0.8304 (t80) cc_final: 0.8070 (t80) REVERT: A 369 PHE cc_start: 0.4949 (t80) cc_final: 0.4637 (t80) REVERT: D 339 LEU cc_start: 0.8750 (tp) cc_final: 0.8344 (tt) REVERT: D 343 SER cc_start: 0.8989 (m) cc_final: 0.8673 (p) REVERT: B 339 LEU cc_start: 0.8776 (tp) cc_final: 0.8486 (tp) REVERT: B 343 SER cc_start: 0.8992 (m) cc_final: 0.8668 (p) REVERT: C 339 LEU cc_start: 0.8730 (tp) cc_final: 0.8462 (tm) REVERT: C 356 GLU cc_start: 0.7108 (tt0) cc_final: 0.6894 (tp30) REVERT: C 636 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8126 (tp30) REVERT: C 684 GLU cc_start: 0.7507 (tt0) cc_final: 0.7197 (tt0) outliers start: 16 outliers final: 7 residues processed: 524 average time/residue: 1.3065 time to fit residues: 760.9055 Evaluate side-chains 315 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 192 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 410 HIS D 354 GLN D 393 ASN D 410 HIS D 628 ASN B 393 ASN B 410 HIS C 320 HIS C 393 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17963 Z= 0.247 Angle : 0.585 11.734 24285 Z= 0.301 Chirality : 0.043 0.409 2727 Planarity : 0.004 0.044 2975 Dihedral : 10.295 65.921 2597 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.86 % Favored : 94.95 % Rotamer: Outliers : 2.71 % Allowed : 9.21 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.26 (0.18), residues: 2099 helix: 1.82 (0.14), residues: 1305 sheet: 1.49 (0.55), residues: 56 loop : -1.04 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 372 HIS 0.006 0.001 HIS C 320 PHE 0.016 0.002 PHE C 438 TYR 0.013 0.001 TYR C 309 ARG 0.007 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 339 time to evaluate : 1.977 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: D 293 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: D 308 MET cc_start: 0.8693 (tpp) cc_final: 0.8464 (tpp) REVERT: B 308 MET cc_start: 0.8645 (tpp) cc_final: 0.8112 (tpp) REVERT: B 363 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6252 (ttt90) REVERT: C 308 MET cc_start: 0.8663 (tpp) cc_final: 0.8404 (tpp) REVERT: C 356 GLU cc_start: 0.7129 (tt0) cc_final: 0.6883 (tp30) REVERT: C 639 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8531 (mttt) outliers start: 51 outliers final: 18 residues processed: 362 average time/residue: 1.1603 time to fit residues: 472.4416 Evaluate side-chains 306 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 285 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 0.0370 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 208 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 191 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS A 393 ASN D 393 ASN D 560 GLN B 354 GLN B 393 ASN C 206 HIS C 393 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17963 Z= 0.172 Angle : 0.517 12.287 24285 Z= 0.271 Chirality : 0.038 0.235 2727 Planarity : 0.004 0.041 2975 Dihedral : 9.599 62.411 2595 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.82 % Allowed : 12.19 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.39 (0.19), residues: 2099 helix: 1.95 (0.14), residues: 1308 sheet: 1.85 (0.54), residues: 56 loop : -1.09 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 372 HIS 0.005 0.001 HIS A 320 PHE 0.010 0.001 PHE C 438 TYR 0.012 0.001 TYR A 309 ARG 0.004 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 291 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7051 (t0) REVERT: D 293 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: B 214 MET cc_start: 0.6030 (ptp) cc_final: 0.5594 (tpt) REVERT: B 308 MET cc_start: 0.8637 (tpp) cc_final: 0.8269 (tpp) REVERT: B 363 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6251 (ttt90) REVERT: B 471 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7929 (t70) REVERT: C 304 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7774 (t80) REVERT: C 356 GLU cc_start: 0.7162 (tt0) cc_final: 0.6900 (tp30) REVERT: C 471 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7837 (t70) outliers start: 53 outliers final: 25 residues processed: 316 average time/residue: 1.1245 time to fit residues: 402.4728 Evaluate side-chains 312 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 281 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 726 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 0.0030 chunk 204 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 498 GLN D 393 ASN B 354 GLN B 393 ASN C 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17963 Z= 0.156 Angle : 0.510 14.255 24285 Z= 0.264 Chirality : 0.038 0.236 2727 Planarity : 0.004 0.043 2975 Dihedral : 9.096 61.634 2590 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.35 % Allowed : 12.77 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.42 (0.19), residues: 2099 helix: 2.03 (0.14), residues: 1304 sheet: 1.87 (0.51), residues: 56 loop : -1.19 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 697 HIS 0.004 0.001 HIS D 320 PHE 0.009 0.001 PHE A 649 TYR 0.012 0.001 TYR A 374 ARG 0.004 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 297 time to evaluate : 1.896 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: D 293 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: D 471 ASP cc_start: 0.8288 (t0) cc_final: 0.7987 (t0) REVERT: B 214 MET cc_start: 0.6043 (ptp) cc_final: 0.5592 (tpt) REVERT: B 308 MET cc_start: 0.8548 (tpp) cc_final: 0.8252 (tpp) REVERT: B 363 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6243 (ttt90) REVERT: B 412 MET cc_start: 0.9230 (mtm) cc_final: 0.9015 (mtp) REVERT: B 443 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8853 (mp) REVERT: C 308 MET cc_start: 0.8605 (tpp) cc_final: 0.8400 (tpp) REVERT: C 356 GLU cc_start: 0.7216 (tt0) cc_final: 0.6907 (tp30) REVERT: C 471 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7876 (t70) REVERT: C 639 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8484 (mttt) outliers start: 63 outliers final: 28 residues processed: 329 average time/residue: 1.0901 time to fit residues: 407.3039 Evaluate side-chains 326 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 293 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 152 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 393 ASN B 354 GLN B 393 ASN C 393 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17963 Z= 0.252 Angle : 0.537 13.388 24285 Z= 0.277 Chirality : 0.039 0.236 2727 Planarity : 0.004 0.043 2975 Dihedral : 9.063 64.498 2587 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.73 % Allowed : 12.88 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.16 (0.18), residues: 2099 helix: 1.83 (0.14), residues: 1299 sheet: 1.57 (0.50), residues: 56 loop : -1.28 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 372 HIS 0.004 0.001 HIS D 320 PHE 0.015 0.001 PHE C 438 TYR 0.016 0.001 TYR A 309 ARG 0.003 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 285 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8607 (tpp) cc_final: 0.8232 (tpp) REVERT: A 343 SER cc_start: 0.8976 (m) cc_final: 0.8633 (p) REVERT: A 443 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8887 (mp) REVERT: D 293 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: D 471 ASP cc_start: 0.8263 (t0) cc_final: 0.7964 (t0) REVERT: B 308 MET cc_start: 0.8459 (tpp) cc_final: 0.8202 (tpp) REVERT: B 343 SER cc_start: 0.9009 (m) cc_final: 0.8644 (p) REVERT: B 363 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6244 (ttt90) REVERT: B 443 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8872 (mp) REVERT: B 471 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7984 (t70) REVERT: C 356 GLU cc_start: 0.7239 (tt0) cc_final: 0.6942 (tp30) REVERT: C 443 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8872 (mp) REVERT: C 471 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7971 (t70) REVERT: C 639 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8541 (mttt) outliers start: 70 outliers final: 29 residues processed: 321 average time/residue: 1.0621 time to fit residues: 387.4789 Evaluate side-chains 306 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 269 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 205 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 393 ASN B 354 GLN B 393 ASN C 393 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17963 Z= 0.225 Angle : 0.540 13.386 24285 Z= 0.278 Chirality : 0.039 0.220 2727 Planarity : 0.004 0.044 2975 Dihedral : 8.943 66.386 2587 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.51 % Allowed : 13.73 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.12 (0.18), residues: 2099 helix: 1.82 (0.14), residues: 1296 sheet: 1.60 (0.50), residues: 56 loop : -1.32 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 697 HIS 0.004 0.001 HIS D 320 PHE 0.012 0.001 PHE C 438 TYR 0.014 0.001 TYR B 309 ARG 0.004 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 280 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8489 (tpp) cc_final: 0.8160 (tpp) REVERT: A 343 SER cc_start: 0.8990 (m) cc_final: 0.8637 (p) REVERT: A 412 MET cc_start: 0.9263 (mtm) cc_final: 0.9041 (mtp) REVERT: A 443 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8872 (mp) REVERT: D 293 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: D 343 SER cc_start: 0.8881 (m) cc_final: 0.8549 (p) REVERT: B 308 MET cc_start: 0.8433 (tpp) cc_final: 0.8191 (tpp) REVERT: B 343 SER cc_start: 0.8990 (m) cc_final: 0.8627 (p) REVERT: B 363 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6188 (ttt90) REVERT: B 443 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8863 (mp) REVERT: B 471 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8056 (t70) REVERT: C 356 GLU cc_start: 0.7251 (tt0) cc_final: 0.6953 (tp30) REVERT: C 412 MET cc_start: 0.9254 (mtm) cc_final: 0.9038 (mtp) REVERT: C 443 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8851 (mp) REVERT: C 639 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8498 (mttt) outliers start: 66 outliers final: 34 residues processed: 319 average time/residue: 1.0685 time to fit residues: 387.6785 Evaluate side-chains 319 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 278 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 204 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN B 354 GLN B 393 ASN C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17963 Z= 0.195 Angle : 0.529 13.750 24285 Z= 0.273 Chirality : 0.039 0.208 2727 Planarity : 0.004 0.044 2975 Dihedral : 8.756 67.496 2581 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.14 % Allowed : 14.10 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.12 (0.18), residues: 2099 helix: 1.83 (0.14), residues: 1296 sheet: 1.62 (0.51), residues: 56 loop : -1.34 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 697 HIS 0.003 0.001 HIS D 320 PHE 0.010 0.001 PHE C 438 TYR 0.012 0.001 TYR B 309 ARG 0.004 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 282 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8480 (tpp) cc_final: 0.8251 (tpp) REVERT: A 343 SER cc_start: 0.9002 (m) cc_final: 0.8646 (p) REVERT: A 412 MET cc_start: 0.9261 (mtm) cc_final: 0.9021 (mtp) REVERT: A 443 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8879 (mp) REVERT: D 293 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: B 308 MET cc_start: 0.8391 (tpp) cc_final: 0.8185 (tpp) REVERT: B 343 SER cc_start: 0.8977 (m) cc_final: 0.8635 (p) REVERT: B 363 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.6162 (ttt90) REVERT: B 443 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8861 (mp) REVERT: B 471 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8080 (t70) REVERT: C 356 GLU cc_start: 0.7232 (tt0) cc_final: 0.6933 (tp30) REVERT: C 412 MET cc_start: 0.9264 (mtm) cc_final: 0.9024 (mtp) REVERT: C 443 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8848 (mp) REVERT: C 471 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8060 (t70) REVERT: C 639 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8486 (mttt) outliers start: 59 outliers final: 34 residues processed: 316 average time/residue: 1.1026 time to fit residues: 395.3198 Evaluate side-chains 321 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 279 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 393 ASN B 232 ASN B 393 ASN B 498 GLN C 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 17963 Z= 0.329 Angle : 0.589 13.322 24285 Z= 0.303 Chirality : 0.041 0.239 2727 Planarity : 0.004 0.044 2975 Dihedral : 9.015 65.202 2581 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.98 % Allowed : 14.48 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.89 (0.18), residues: 2099 helix: 1.59 (0.14), residues: 1299 sheet: 1.61 (0.51), residues: 56 loop : -1.33 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 372 HIS 0.003 0.001 HIS A 289 PHE 0.017 0.002 PHE C 438 TYR 0.016 0.002 TYR C 627 ARG 0.004 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 279 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8459 (tpp) cc_final: 0.8199 (tpp) REVERT: A 343 SER cc_start: 0.9054 (m) cc_final: 0.8681 (p) REVERT: A 412 MET cc_start: 0.9272 (mtm) cc_final: 0.9053 (mtp) REVERT: A 443 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8874 (mp) REVERT: D 293 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: D 343 SER cc_start: 0.8969 (m) cc_final: 0.8628 (p) REVERT: B 343 SER cc_start: 0.8999 (m) cc_final: 0.8653 (p) REVERT: B 363 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.6043 (ttt90) REVERT: B 443 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8872 (mp) REVERT: B 471 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8091 (t70) REVERT: C 356 GLU cc_start: 0.7269 (tt0) cc_final: 0.6977 (tp30) REVERT: C 412 MET cc_start: 0.9281 (mtm) cc_final: 0.9080 (mtp) REVERT: C 443 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8870 (mp) REVERT: C 471 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8127 (t70) outliers start: 56 outliers final: 32 residues processed: 313 average time/residue: 1.1252 time to fit residues: 398.9472 Evaluate side-chains 313 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 274 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 0.4980 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 172 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 498 GLN B 354 GLN B 393 ASN B 498 GLN C 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 17963 Z= 0.163 Angle : 0.534 14.444 24285 Z= 0.275 Chirality : 0.038 0.194 2727 Planarity : 0.004 0.043 2975 Dihedral : 8.730 72.093 2581 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.34 % Allowed : 15.70 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.09 (0.19), residues: 2099 helix: 1.79 (0.14), residues: 1299 sheet: 1.67 (0.51), residues: 56 loop : -1.35 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 697 HIS 0.003 0.001 HIS D 320 PHE 0.009 0.001 PHE C 649 TYR 0.011 0.001 TYR C 309 ARG 0.004 0.000 ARG D 500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 288 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8481 (tpp) cc_final: 0.8142 (tpp) REVERT: A 343 SER cc_start: 0.9020 (m) cc_final: 0.8653 (p) REVERT: A 412 MET cc_start: 0.9228 (mtm) cc_final: 0.9010 (mtp) REVERT: A 443 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8873 (mp) REVERT: D 293 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: D 343 SER cc_start: 0.8942 (m) cc_final: 0.8613 (p) REVERT: B 303 LYS cc_start: 0.8767 (tppt) cc_final: 0.8545 (mtpt) REVERT: B 308 MET cc_start: 0.8478 (tpp) cc_final: 0.8275 (tpp) REVERT: B 343 SER cc_start: 0.8930 (m) cc_final: 0.8592 (p) REVERT: B 363 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.6070 (ttt90) REVERT: B 443 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8859 (mp) REVERT: B 471 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8109 (t0) REVERT: C 356 GLU cc_start: 0.7250 (tt0) cc_final: 0.6943 (tp30) REVERT: C 443 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8851 (mp) REVERT: C 471 ASP cc_start: 0.8325 (t70) cc_final: 0.8112 (t70) outliers start: 44 outliers final: 23 residues processed: 314 average time/residue: 1.1233 time to fit residues: 400.9289 Evaluate side-chains 312 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 283 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 707 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 95 optimal weight: 0.0060 chunk 139 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 393 ASN A 498 GLN D 285 ASN B 393 ASN B 498 GLN C 393 ASN C 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17963 Z= 0.172 Angle : 0.544 14.013 24285 Z= 0.280 Chirality : 0.038 0.193 2727 Planarity : 0.004 0.043 2975 Dihedral : 8.660 77.170 2581 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.81 % Allowed : 16.50 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.10 (0.19), residues: 2099 helix: 1.81 (0.14), residues: 1299 sheet: 1.76 (0.53), residues: 56 loop : -1.37 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 697 HIS 0.003 0.001 HIS D 320 PHE 0.010 0.001 PHE A 649 TYR 0.012 0.001 TYR B 309 ARG 0.007 0.000 ARG B 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 290 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 SER cc_start: 0.9015 (m) cc_final: 0.8657 (p) REVERT: A 412 MET cc_start: 0.9220 (mtm) cc_final: 0.8984 (mtp) REVERT: A 443 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8854 (mp) REVERT: D 293 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7777 (mt-10) REVERT: D 343 SER cc_start: 0.8915 (m) cc_final: 0.8596 (p) REVERT: B 303 LYS cc_start: 0.8735 (tppt) cc_final: 0.8519 (mtpt) REVERT: B 308 MET cc_start: 0.8488 (tpp) cc_final: 0.8281 (tpp) REVERT: B 343 SER cc_start: 0.8919 (m) cc_final: 0.8586 (p) REVERT: B 363 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6103 (ttt90) REVERT: B 443 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8867 (mp) REVERT: C 356 GLU cc_start: 0.7257 (tt0) cc_final: 0.6953 (tp30) REVERT: C 443 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8858 (mp) REVERT: C 709 GLU cc_start: 0.8136 (tt0) cc_final: 0.7602 (mt-10) REVERT: C 746 GLU cc_start: 0.7965 (tt0) cc_final: 0.7491 (pm20) outliers start: 34 outliers final: 22 residues processed: 312 average time/residue: 1.0801 time to fit residues: 383.2026 Evaluate side-chains 305 residues out of total 1879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 279 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 707 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.0070 chunk 168 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 393 ASN A 498 GLN B 393 ASN B 498 GLN C 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112384 restraints weight = 21880.724| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.15 r_work: 0.3121 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17963 Z= 0.166 Angle : 0.533 14.386 24285 Z= 0.274 Chirality : 0.038 0.184 2727 Planarity : 0.004 0.043 2975 Dihedral : 8.656 84.071 2581 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.54 % Allowed : 16.92 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.11 (0.19), residues: 2099 helix: 1.83 (0.14), residues: 1298 sheet: 1.86 (0.53), residues: 56 loop : -1.39 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 697 HIS 0.003 0.001 HIS D 320 PHE 0.009 0.001 PHE C 649 TYR 0.011 0.001 TYR B 309 ARG 0.007 0.000 ARG B 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7151.08 seconds wall clock time: 127 minutes 5.43 seconds (7625.43 seconds total)