Starting phenix.real_space_refine on Mon Apr 8 08:23:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x05_32917/04_2024/7x05_32917_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x05_32917/04_2024/7x05_32917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x05_32917/04_2024/7x05_32917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x05_32917/04_2024/7x05_32917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x05_32917/04_2024/7x05_32917_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x05_32917/04_2024/7x05_32917_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.003 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 Mn 2 7.51 5 P 4 5.49 5 S 72 5.16 5 C 8420 2.51 5 N 2156 2.21 5 O 2346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13000 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6431 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 30, 'TRANS': 770} Chain breaks: 1 Chain: "B" Number of atoms: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6431 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 30, 'TRANS': 770} Chain breaks: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.53, per 1000 atoms: 0.50 Number of scatterers: 13000 At special positions: 0 Unit cell: (118.77, 114.49, 127.33, 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) Mn 2 24.99 S 72 16.00 P 4 15.00 O 2346 8.00 N 2156 7.00 C 8420 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 - 3.50 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " NAG C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.2 seconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 6 sheets defined 59.7% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.566A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 114 through 132 removed outlier: 4.347A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 161 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 392 through 402 Processing helix chain 'A' and resid 424 through 446 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 481 through 484 No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.546A pdb=" N VAL A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 559 removed outlier: 5.470A pdb=" N GLY A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 604 removed outlier: 3.710A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 588 " --> pdb=" O PHE A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 620 through 646 removed outlier: 4.064A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 680 Processing helix chain 'A' and resid 685 through 705 removed outlier: 5.329A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 5.051A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 720 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 735 Processing helix chain 'A' and resid 765 through 818 Processing helix chain 'A' and resid 821 through 856 Proline residue: A 826 - end of helix removed outlier: 4.998A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 Processing helix chain 'B' and resid 77 through 90 removed outlier: 3.567A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 114 through 132 removed outlier: 4.349A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 161 Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 243 through 262 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 358 through 373 Processing helix chain 'B' and resid 392 through 402 Processing helix chain 'B' and resid 424 through 446 Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 475 through 478 No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 481 through 484 No H-bonds generated for 'chain 'B' and resid 481 through 484' Processing helix chain 'B' and resid 486 through 489 No H-bonds generated for 'chain 'B' and resid 486 through 489' Processing helix chain 'B' and resid 495 through 504 removed outlier: 3.547A pdb=" N VAL B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 559 removed outlier: 5.470A pdb=" N GLY B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG B 556 " --> pdb=" O TRP B 552 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR B 558 " --> pdb=" O TRP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 604 removed outlier: 3.710A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 588 " --> pdb=" O PHE B 584 " (cutoff:3.500A) Proline residue: B 589 - end of helix Processing helix chain 'B' and resid 620 through 646 removed outlier: 4.064A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 680 Processing helix chain 'B' and resid 685 through 705 removed outlier: 5.329A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 removed outlier: 5.051A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 720 " --> pdb=" O THR B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 735 Processing helix chain 'B' and resid 765 through 818 Processing helix chain 'B' and resid 821 through 856 Proline residue: B 826 - end of helix removed outlier: 4.998A pdb=" N GLY B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 177 through 180 removed outlier: 7.773A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 326 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR A 377 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N CYS A 235 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA A 379 " --> pdb=" O CYS A 235 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR A 237 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N MET A 381 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.193A pdb=" N ALA A 521 " --> pdb=" O THR A 413 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 405 through 409 removed outlier: 6.453A pdb=" N THR A 512 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 408 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 514 " --> pdb=" O ALA A 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 177 through 180 removed outlier: 7.773A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 326 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR B 377 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N CYS B 235 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA B 379 " --> pdb=" O CYS B 235 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR B 237 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET B 381 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 412 through 414 removed outlier: 6.193A pdb=" N ALA B 521 " --> pdb=" O THR B 413 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 405 through 409 removed outlier: 6.453A pdb=" N THR B 512 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 408 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS B 514 " --> pdb=" O ALA B 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 728 hydrogen bonds defined for protein. 2160 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: 4.16 Time building geometry restraints manager: 5.61 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: 2032 1.31 - 1.43: 3909 1.43 - 1.56: 7289 1.56 - 1.68: 6 1.68 - 1.81: 112 Bond restraints: 13348 Sorted by residual: bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C7 NAG C 1 " pdb=" N2 NAG C 1 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C7 NAG C 3 " pdb=" N2 NAG C 3 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C7 NAG D 3 " pdb=" N2 NAG D 3 " ideal model delta sigma weight residual 1.346 1.450 -0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C7 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 13343 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 376 106.67 - 113.50: 7187 113.50 - 120.33: 5106 120.33 - 127.15: 5307 127.15 - 133.98: 156 Bond angle restraints: 18132 Sorted by residual: angle pdb=" O1B UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3A UDP A1001 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.42e+01 angle pdb=" O1B UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3A UDP B1001 " ideal model delta sigma weight residual 102.95 112.12 -9.17 1.00e+00 1.00e+00 8.41e+01 angle pdb=" O3A UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3B UDP A1001 " ideal model delta sigma weight residual 112.01 103.03 8.98 1.00e+00 1.00e+00 8.07e+01 angle pdb=" O3A UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3B UDP B1001 " ideal model delta sigma weight residual 112.01 103.08 8.93 1.00e+00 1.00e+00 7.97e+01 angle pdb=" O5' UDP A1001 " pdb=" PA UDP A1001 " pdb=" O1A UDP A1001 " ideal model delta sigma weight residual 106.70 111.06 -4.36 1.00e+00 1.00e+00 1.90e+01 ... (remaining 18127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 7485 16.84 - 33.69: 325 33.69 - 50.53: 88 50.53 - 67.38: 14 67.38 - 84.22: 6 Dihedral angle restraints: 7918 sinusoidal: 3226 harmonic: 4692 Sorted by residual: dihedral pdb=" CA GLN B 602 " pdb=" C GLN B 602 " pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLN A 602 " pdb=" C GLN A 602 " pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" N ARG B 780 " pdb=" CA ARG B 780 " pdb=" CB ARG B 780 " pdb=" CG ARG B 780 " ideal model delta sinusoidal sigma weight residual -180.00 -124.30 -55.70 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 7915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1175 0.026 - 0.051: 525 0.051 - 0.077: 187 0.077 - 0.103: 73 0.103 - 0.129: 46 Chirality restraints: 2006 Sorted by residual: chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.62 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.62 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" C5 NAG D 3 " pdb=" C4 NAG D 3 " pdb=" C6 NAG D 3 " pdb=" O5 NAG D 3 " both_signs ideal model delta sigma weight residual False -2.41 -2.54 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2003 not shown) Planarity restraints: 2278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 598 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C PHE B 598 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE B 598 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE B 599 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C PHE A 598 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 599 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C ILE B 599 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 599 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 600 " 0.012 2.00e-02 2.50e+03 ... (remaining 2275 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1220 2.74 - 3.28: 12523 3.28 - 3.82: 21090 3.82 - 4.36: 22354 4.36 - 4.90: 41800 Nonbonded interactions: 98987 Sorted by model distance: nonbonded pdb=" PB UDP B1001 " pdb="MN MN B1002 " model vdw 2.204 2.680 nonbonded pdb=" PB UDP A1001 " pdb="MN MN A1002 " model vdw 2.204 2.680 nonbonded pdb=" OH TYR B 593 " pdb=" OD1 ASN B 630 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR A 593 " pdb=" OD1 ASN A 630 " model vdw 2.289 2.440 nonbonded pdb=" O SER A 390 " pdb=" ND1 HIS A 394 " model vdw 2.291 2.520 ... (remaining 98982 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.760 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: 0.020 Extract box with map and model: 6.130 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.860 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 0.105 13348 Z= 0.243 Angle : 0.523 9.177 18132 Z= 0.298 Chirality : 0.038 0.129 2006 Planarity : 0.003 0.026 2278 Dihedral : 10.756 84.223 4906 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: 2.05 (0.22), residues: 1594 helix: 2.87 (0.17), residues: 958 sheet: 0.08 (0.43), residues: 156 loop : -1.51 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 804 HIS 0.002 0.001 HIS A 403 PHE 0.012 0.001 PHE B 601 TYR 0.009 0.001 TYR B 365 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7671 (m90) cc_final: 0.7035 (m90) REVERT: A 179 ILE cc_start: 0.8950 (pt) cc_final: 0.8718 (mp) REVERT: A 201 MET cc_start: 0.7951 (ptm) cc_final: 0.7652 (ppp) REVERT: A 207 TYR cc_start: 0.8082 (t80) cc_final: 0.7578 (t80) REVERT: A 233 MET cc_start: 0.8580 (mtp) cc_final: 0.8264 (mtp) REVERT: A 523 THR cc_start: 0.9554 (p) cc_final: 0.9229 (t) REVERT: A 607 ASN cc_start: 0.7617 (t0) cc_final: 0.7397 (p0) REVERT: B 95 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7352 (tm-30) REVERT: B 152 ASN cc_start: 0.8165 (m-40) cc_final: 0.7960 (m110) REVERT: B 336 SER cc_start: 0.8419 (t) cc_final: 0.8201 (p) REVERT: B 390 SER cc_start: 0.7996 (m) cc_final: 0.7346 (p) REVERT: B 457 PHE cc_start: 0.7602 (t80) cc_final: 0.7253 (t80) REVERT: B 492 TYR cc_start: 0.8499 (t80) cc_final: 0.7709 (t80) REVERT: B 493 LEU cc_start: 0.8923 (mt) cc_final: 0.8643 (mt) REVERT: B 607 ASN cc_start: 0.7430 (t0) cc_final: 0.7142 (t0) REVERT: B 850 ILE cc_start: 0.8639 (tt) cc_final: 0.8437 (tt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2465 time to fit residues: 106.5894 Evaluate side-chains 181 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 145 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 605 GLN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13348 Z= 0.232 Angle : 0.533 6.771 18132 Z= 0.275 Chirality : 0.039 0.131 2006 Planarity : 0.004 0.053 2278 Dihedral : 6.432 58.445 1954 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.27 % Allowed : 11.61 % Favored : 85.12 % 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: 1.96 (0.22), residues: 1594 helix: 2.81 (0.17), residues: 954 sheet: 0.29 (0.44), residues: 148 loop : -1.58 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 554 HIS 0.003 0.001 HIS A 403 PHE 0.014 0.001 PHE A 397 TYR 0.021 0.001 TYR B 575 ARG 0.006 0.000 ARG A 856 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 182 time to evaluate : 1.505 Fit side-chains REVERT: A 179 ILE cc_start: 0.8930 (pt) cc_final: 0.8676 (mp) REVERT: A 201 MET cc_start: 0.7954 (ptm) cc_final: 0.7583 (ppp) REVERT: A 207 TYR cc_start: 0.8159 (t80) cc_final: 0.7770 (t80) REVERT: A 233 MET cc_start: 0.8654 (mtp) cc_final: 0.8258 (mtp) REVERT: A 318 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8873 (m-40) REVERT: A 397 PHE cc_start: 0.8212 (t80) cc_final: 0.7472 (t80) REVERT: A 607 ASN cc_start: 0.7426 (t0) cc_final: 0.7079 (t0) REVERT: A 665 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7531 (tp) REVERT: A 694 THR cc_start: 0.8546 (t) cc_final: 0.8103 (p) REVERT: B 95 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 336 SER cc_start: 0.8489 (t) cc_final: 0.8248 (p) REVERT: B 390 SER cc_start: 0.8056 (m) cc_final: 0.7419 (p) REVERT: B 492 TYR cc_start: 0.8503 (t80) cc_final: 0.7790 (t80) REVERT: B 493 LEU cc_start: 0.9027 (mt) cc_final: 0.8329 (mt) REVERT: B 607 ASN cc_start: 0.7443 (t0) cc_final: 0.7083 (t0) REVERT: B 850 ILE cc_start: 0.8599 (tt) cc_final: 0.8326 (tt) outliers start: 45 outliers final: 30 residues processed: 211 average time/residue: 0.2227 time to fit residues: 73.0481 Evaluate side-chains 198 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 844 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 175 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 318 ASN B 851 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13348 Z= 0.187 Angle : 0.519 10.419 18132 Z= 0.262 Chirality : 0.039 0.126 2006 Planarity : 0.004 0.042 2278 Dihedral : 6.054 58.232 1954 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.12 % Allowed : 13.43 % Favored : 83.45 % 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: 1.99 (0.22), residues: 1594 helix: 2.85 (0.17), residues: 952 sheet: -0.09 (0.44), residues: 152 loop : -1.47 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 153 HIS 0.007 0.001 HIS A 169 PHE 0.014 0.001 PHE B 601 TYR 0.024 0.001 TYR B 88 ARG 0.004 0.000 ARG B 538 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 178 time to evaluate : 1.348 Fit side-chains REVERT: A 201 MET cc_start: 0.7940 (ptm) cc_final: 0.7651 (ppp) REVERT: A 233 MET cc_start: 0.8616 (mtp) cc_final: 0.8254 (mtp) REVERT: A 390 SER cc_start: 0.8268 (m) cc_final: 0.7462 (p) REVERT: A 607 ASN cc_start: 0.7341 (t0) cc_final: 0.6984 (t0) REVERT: A 665 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7650 (tp) REVERT: A 669 LEU cc_start: 0.8604 (tt) cc_final: 0.8348 (tp) REVERT: A 694 THR cc_start: 0.8575 (t) cc_final: 0.8196 (p) REVERT: A 831 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7715 (t80) REVERT: B 95 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 233 MET cc_start: 0.8462 (mtp) cc_final: 0.8246 (mtp) REVERT: B 336 SER cc_start: 0.8502 (t) cc_final: 0.8253 (p) REVERT: B 390 SER cc_start: 0.8081 (m) cc_final: 0.7454 (p) REVERT: B 607 ASN cc_start: 0.7454 (t0) cc_final: 0.7106 (t0) REVERT: B 850 ILE cc_start: 0.8582 (tt) cc_final: 0.8380 (tt) outliers start: 43 outliers final: 25 residues processed: 210 average time/residue: 0.2132 time to fit residues: 69.4327 Evaluate side-chains 193 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 831 PHE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 800 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 0.0070 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 372 GLN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13348 Z= 0.174 Angle : 0.510 12.480 18132 Z= 0.257 Chirality : 0.038 0.134 2006 Planarity : 0.004 0.040 2278 Dihedral : 5.891 57.346 1954 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.56 % Allowed : 15.31 % Favored : 81.13 % 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: 2.03 (0.22), residues: 1594 helix: 2.88 (0.17), residues: 948 sheet: 0.04 (0.45), residues: 144 loop : -1.43 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.003 0.001 HIS B 403 PHE 0.025 0.001 PHE A 611 TYR 0.032 0.001 TYR B 88 ARG 0.006 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 1.488 Fit side-chains REVERT: A 207 TYR cc_start: 0.8272 (t80) cc_final: 0.8034 (t80) REVERT: A 233 MET cc_start: 0.8603 (mtp) cc_final: 0.8250 (mtp) REVERT: A 390 SER cc_start: 0.8307 (m) cc_final: 0.7448 (p) REVERT: A 607 ASN cc_start: 0.7341 (t0) cc_final: 0.6964 (t0) REVERT: A 694 THR cc_start: 0.8442 (t) cc_final: 0.8057 (p) REVERT: A 831 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7776 (t80) REVERT: B 95 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 336 SER cc_start: 0.8511 (t) cc_final: 0.8250 (p) REVERT: B 390 SER cc_start: 0.8077 (m) cc_final: 0.7430 (p) REVERT: B 492 TYR cc_start: 0.8669 (t80) cc_final: 0.8420 (t80) REVERT: B 607 ASN cc_start: 0.7550 (t0) cc_final: 0.7210 (t0) REVERT: B 856 ARG cc_start: 0.6065 (ttp80) cc_final: 0.5764 (tpt90) outliers start: 49 outliers final: 37 residues processed: 209 average time/residue: 0.2036 time to fit residues: 67.4882 Evaluate side-chains 202 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 831 PHE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 800 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 318 ASN B 851 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 13348 Z= 0.453 Angle : 0.698 13.331 18132 Z= 0.360 Chirality : 0.045 0.152 2006 Planarity : 0.005 0.040 2278 Dihedral : 6.106 47.781 1954 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.99 % Allowed : 16.33 % Favored : 79.68 % 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: 1.27 (0.22), residues: 1594 helix: 2.08 (0.17), residues: 986 sheet: -0.28 (0.42), residues: 150 loop : -1.58 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 804 HIS 0.007 0.002 HIS B 403 PHE 0.027 0.002 PHE B 597 TYR 0.028 0.002 TYR A 732 ARG 0.007 0.001 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 1.508 Fit side-chains REVERT: A 233 MET cc_start: 0.8752 (mtp) cc_final: 0.8550 (mtp) REVERT: A 390 SER cc_start: 0.8440 (m) cc_final: 0.7711 (p) REVERT: A 397 PHE cc_start: 0.8570 (t80) cc_final: 0.8276 (t80) REVERT: A 492 TYR cc_start: 0.8687 (t80) cc_final: 0.8399 (t80) REVERT: A 607 ASN cc_start: 0.7376 (t0) cc_final: 0.7089 (t0) REVERT: B 95 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7652 (tm-30) REVERT: B 357 SER cc_start: 0.9151 (p) cc_final: 0.8722 (t) REVERT: B 390 SER cc_start: 0.8342 (m) cc_final: 0.7646 (p) REVERT: B 495 GLU cc_start: 0.8552 (mp0) cc_final: 0.8322 (mp0) REVERT: B 607 ASN cc_start: 0.7622 (t0) cc_final: 0.7342 (t0) outliers start: 55 outliers final: 42 residues processed: 211 average time/residue: 0.1960 time to fit residues: 65.1288 Evaluate side-chains 198 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.0070 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 851 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13348 Z= 0.173 Angle : 0.538 11.687 18132 Z= 0.273 Chirality : 0.039 0.127 2006 Planarity : 0.004 0.037 2278 Dihedral : 5.773 51.489 1954 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.92 % Allowed : 17.85 % Favored : 78.23 % 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: 1.69 (0.22), residues: 1594 helix: 2.54 (0.17), residues: 962 sheet: -0.16 (0.44), residues: 148 loop : -1.52 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 804 HIS 0.008 0.001 HIS B 851 PHE 0.024 0.001 PHE A 611 TYR 0.033 0.001 TYR B 88 ARG 0.006 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 168 time to evaluate : 1.494 Fit side-chains REVERT: A 57 ILE cc_start: 0.8907 (mm) cc_final: 0.8572 (mt) REVERT: A 207 TYR cc_start: 0.8530 (t80) cc_final: 0.8245 (t80) REVERT: A 233 MET cc_start: 0.8698 (mtp) cc_final: 0.8413 (mtp) REVERT: A 390 SER cc_start: 0.8314 (m) cc_final: 0.7608 (p) REVERT: A 397 PHE cc_start: 0.8425 (t80) cc_final: 0.8119 (t80) REVERT: A 607 ASN cc_start: 0.7239 (t0) cc_final: 0.6946 (t0) REVERT: A 694 THR cc_start: 0.8350 (t) cc_final: 0.8105 (p) REVERT: B 95 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 357 SER cc_start: 0.9128 (p) cc_final: 0.8680 (t) REVERT: B 390 SER cc_start: 0.8251 (m) cc_final: 0.7594 (p) REVERT: B 492 TYR cc_start: 0.8748 (t80) cc_final: 0.8542 (t80) REVERT: B 607 ASN cc_start: 0.7593 (t0) cc_final: 0.7263 (t0) outliers start: 54 outliers final: 40 residues processed: 206 average time/residue: 0.2041 time to fit residues: 66.7525 Evaluate side-chains 194 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 736 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 851 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13348 Z= 0.249 Angle : 0.570 11.817 18132 Z= 0.287 Chirality : 0.040 0.130 2006 Planarity : 0.004 0.037 2278 Dihedral : 5.706 50.491 1954 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.92 % Allowed : 18.80 % Favored : 77.29 % 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: 1.64 (0.22), residues: 1594 helix: 2.51 (0.17), residues: 966 sheet: -0.32 (0.44), residues: 144 loop : -1.52 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.009 0.001 HIS B 851 PHE 0.025 0.001 PHE A 611 TYR 0.028 0.001 TYR B 88 ARG 0.007 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 156 time to evaluate : 1.425 Fit side-chains REVERT: A 57 ILE cc_start: 0.8933 (mm) cc_final: 0.8594 (mt) REVERT: A 207 TYR cc_start: 0.8591 (t80) cc_final: 0.8264 (t80) REVERT: A 233 MET cc_start: 0.8668 (mtp) cc_final: 0.8282 (mtp) REVERT: A 390 SER cc_start: 0.8327 (m) cc_final: 0.7655 (p) REVERT: A 397 PHE cc_start: 0.8463 (t80) cc_final: 0.8187 (t80) REVERT: A 607 ASN cc_start: 0.7289 (t0) cc_final: 0.7005 (t0) REVERT: A 610 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 694 THR cc_start: 0.8425 (t) cc_final: 0.8177 (p) REVERT: B 95 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 357 SER cc_start: 0.9141 (p) cc_final: 0.8684 (t) REVERT: B 390 SER cc_start: 0.8213 (m) cc_final: 0.7531 (p) REVERT: B 492 TYR cc_start: 0.8767 (t80) cc_final: 0.8563 (t80) REVERT: B 607 ASN cc_start: 0.7570 (t0) cc_final: 0.7224 (t0) outliers start: 54 outliers final: 45 residues processed: 198 average time/residue: 0.1911 time to fit residues: 60.7788 Evaluate side-chains 199 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 154 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 851 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13348 Z= 0.269 Angle : 0.583 13.775 18132 Z= 0.293 Chirality : 0.040 0.296 2006 Planarity : 0.004 0.035 2278 Dihedral : 5.676 51.180 1954 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.99 % Allowed : 18.87 % Favored : 77.14 % 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: 1.59 (0.22), residues: 1594 helix: 2.46 (0.17), residues: 968 sheet: -0.38 (0.44), residues: 144 loop : -1.53 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.011 0.001 HIS B 851 PHE 0.026 0.001 PHE A 611 TYR 0.024 0.001 TYR B 88 ARG 0.006 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 161 time to evaluate : 1.417 Fit side-chains REVERT: A 57 ILE cc_start: 0.8956 (mm) cc_final: 0.8618 (mt) REVERT: A 207 TYR cc_start: 0.8596 (t80) cc_final: 0.8320 (t80) REVERT: A 233 MET cc_start: 0.8648 (mtp) cc_final: 0.8223 (mtp) REVERT: A 390 SER cc_start: 0.8342 (m) cc_final: 0.7674 (p) REVERT: A 397 PHE cc_start: 0.8476 (t80) cc_final: 0.8170 (t80) REVERT: A 607 ASN cc_start: 0.7249 (t0) cc_final: 0.6982 (t0) REVERT: A 610 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8333 (mm-30) REVERT: B 95 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 357 SER cc_start: 0.9152 (p) cc_final: 0.8682 (t) REVERT: B 390 SER cc_start: 0.8248 (m) cc_final: 0.7567 (p) REVERT: B 492 TYR cc_start: 0.8764 (t80) cc_final: 0.8557 (t80) REVERT: B 607 ASN cc_start: 0.7587 (t0) cc_final: 0.7253 (t0) outliers start: 55 outliers final: 50 residues processed: 204 average time/residue: 0.1891 time to fit residues: 62.5307 Evaluate side-chains 205 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 831 PHE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 851 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13348 Z= 0.180 Angle : 0.557 12.297 18132 Z= 0.275 Chirality : 0.039 0.282 2006 Planarity : 0.003 0.036 2278 Dihedral : 5.545 51.835 1954 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.48 % Allowed : 19.67 % Favored : 76.85 % 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: 1.66 (0.22), residues: 1594 helix: 2.55 (0.17), residues: 964 sheet: -0.32 (0.44), residues: 144 loop : -1.56 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 554 HIS 0.016 0.001 HIS B 851 PHE 0.025 0.001 PHE A 611 TYR 0.032 0.001 TYR B 88 ARG 0.007 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 161 time to evaluate : 1.403 Fit side-chains REVERT: A 57 ILE cc_start: 0.8944 (mm) cc_final: 0.8616 (mt) REVERT: A 207 TYR cc_start: 0.8559 (t80) cc_final: 0.8297 (t80) REVERT: A 390 SER cc_start: 0.8295 (m) cc_final: 0.7645 (p) REVERT: A 397 PHE cc_start: 0.8428 (t80) cc_final: 0.8128 (t80) REVERT: A 443 LEU cc_start: 0.9450 (tp) cc_final: 0.9172 (tp) REVERT: A 607 ASN cc_start: 0.7226 (t0) cc_final: 0.6944 (t0) REVERT: A 610 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 694 THR cc_start: 0.8414 (t) cc_final: 0.8211 (p) REVERT: B 95 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 168 LYS cc_start: 0.7914 (mmmm) cc_final: 0.7446 (tptt) REVERT: B 357 SER cc_start: 0.9133 (p) cc_final: 0.8678 (t) REVERT: B 390 SER cc_start: 0.8194 (m) cc_final: 0.7540 (p) REVERT: B 492 TYR cc_start: 0.8776 (t80) cc_final: 0.8560 (t80) REVERT: B 607 ASN cc_start: 0.7576 (t0) cc_final: 0.7223 (t0) outliers start: 48 outliers final: 42 residues processed: 196 average time/residue: 0.1907 time to fit residues: 60.6588 Evaluate side-chains 199 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 0.0370 chunk 159 optimal weight: 0.0770 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 372 GLN B 851 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13348 Z= 0.155 Angle : 0.548 13.375 18132 Z= 0.269 Chirality : 0.038 0.271 2006 Planarity : 0.003 0.037 2278 Dihedral : 5.403 52.308 1954 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.98 % Allowed : 20.32 % Favored : 76.71 % 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: 1.77 (0.22), residues: 1594 helix: 2.66 (0.17), residues: 962 sheet: -0.24 (0.45), residues: 144 loop : -1.54 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 554 HIS 0.014 0.001 HIS B 851 PHE 0.025 0.001 PHE A 611 TYR 0.026 0.001 TYR B 88 ARG 0.006 0.000 ARG A 522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 1.491 Fit side-chains REVERT: A 57 ILE cc_start: 0.8944 (mm) cc_final: 0.8616 (mt) REVERT: A 207 TYR cc_start: 0.8541 (t80) cc_final: 0.8336 (t80) REVERT: A 390 SER cc_start: 0.8271 (m) cc_final: 0.7623 (p) REVERT: A 443 LEU cc_start: 0.9424 (tp) cc_final: 0.9172 (tp) REVERT: A 607 ASN cc_start: 0.7267 (t0) cc_final: 0.6968 (t0) REVERT: A 610 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8353 (mm-30) REVERT: B 95 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 168 LYS cc_start: 0.7909 (mmmm) cc_final: 0.7470 (tptt) REVERT: B 357 SER cc_start: 0.9175 (p) cc_final: 0.8672 (t) REVERT: B 390 SER cc_start: 0.8184 (m) cc_final: 0.7557 (p) REVERT: B 492 TYR cc_start: 0.8743 (t80) cc_final: 0.8502 (t80) REVERT: B 495 GLU cc_start: 0.8412 (mp0) cc_final: 0.8100 (mp0) REVERT: B 607 ASN cc_start: 0.7580 (t0) cc_final: 0.7209 (t0) outliers start: 41 outliers final: 38 residues processed: 200 average time/residue: 0.1914 time to fit residues: 62.7349 Evaluate side-chains 197 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 851 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101934 restraints weight = 18825.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103139 restraints weight = 14820.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104394 restraints weight = 11794.175| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13348 Z= 0.190 Angle : 0.553 13.049 18132 Z= 0.272 Chirality : 0.039 0.270 2006 Planarity : 0.004 0.039 2278 Dihedral : 5.346 52.369 1954 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.12 % Allowed : 20.39 % Favored : 76.49 % 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: 1.77 (0.22), residues: 1594 helix: 2.63 (0.17), residues: 964 sheet: -0.25 (0.44), residues: 144 loop : -1.51 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 554 HIS 0.003 0.001 HIS A 403 PHE 0.025 0.001 PHE A 611 TYR 0.026 0.001 TYR A 732 ARG 0.006 0.000 ARG A 522 =============================================================================== Job complete usr+sys time: 2413.22 seconds wall clock time: 45 minutes 8.38 seconds (2708.38 seconds total)