Starting phenix.real_space_refine on Sun Apr 7 20:25:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t56_25696/04_2024/7t56_25696_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t56_25696/04_2024/7t56_25696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t56_25696/04_2024/7t56_25696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t56_25696/04_2024/7t56_25696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t56_25696/04_2024/7t56_25696_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t56_25696/04_2024/7t56_25696_updated.pdb" } resolution = 3.7 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= 0.033 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 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 7382 2.51 5 N 1870 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B PHE 715": "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: 11460 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.42, per 1000 atoms: 0.56 Number of scatterers: 11460 At special positions: 0 Unit cell: (109.18, 107.12, 138.02, 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 60 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1870 7.00 C 7382 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 Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 2.2 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 8 sheets defined 55.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 155 through 162 removed outlier: 4.051A pdb=" N GLY A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 195 removed outlier: 4.335A pdb=" N PHE A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 252 removed outlier: 4.228A pdb=" N PHE A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 263 through 271 removed outlier: 3.892A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 282 through 304 removed outlier: 3.899A pdb=" N ILE A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 353 removed outlier: 3.654A pdb=" N ILE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 4.079A pdb=" N GLN A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 364 through 416 Processing helix chain 'A' and resid 422 through 434 removed outlier: 4.104A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 459 removed outlier: 4.090A pdb=" N GLN A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix removed outlier: 3.720A pdb=" N ARG A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 555 through 558 No H-bonds generated for 'chain 'A' and resid 555 through 558' Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 625 through 638 removed outlier: 4.239A pdb=" N ARG A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'B' and resid 22 through 33 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.845A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU B 162 " --> pdb=" O PHE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 195 removed outlier: 4.357A pdb=" N PHE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 252 removed outlier: 4.248A pdb=" N PHE B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 263 through 270 removed outlier: 3.952A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 282 through 304 removed outlier: 3.912A pdb=" N ILE B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 353 removed outlier: 3.670A pdb=" N ILE B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 4.049A pdb=" N GLN B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 364 through 416 removed outlier: 3.712A pdb=" N GLU B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 434 removed outlier: 4.144A pdb=" N ALA B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 459 removed outlier: 4.067A pdb=" N GLN B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.612A pdb=" N ARG B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 525 through 532 removed outlier: 3.846A pdb=" N ALA B 529 " --> pdb=" O LYS B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 589 through 599 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.680A pdb=" N PHE B 604 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 625 through 639 removed outlier: 3.638A pdb=" N ARG B 630 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 682 through 684 No H-bonds generated for 'chain 'B' and resid 682 through 684' Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 714 through 721 Processing helix chain 'D' and resid 15 through 20 Processing sheet with id= A, first strand: chain 'A' and resid 67 through 72 Processing sheet with id= B, first strand: chain 'A' and resid 87 through 93 removed outlier: 4.027A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 102 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 507 through 509 removed outlier: 4.072A pdb=" N LEU A 507 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 700 through 702 removed outlier: 3.832A pdb=" N GLU A 700 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 674 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE A 517 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 676 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N GLY A 519 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA A 678 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 67 through 72 Processing sheet with id= F, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.035A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 102 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 506 through 509 Processing sheet with id= H, first strand: chain 'B' and resid 697 through 702 removed outlier: 6.835A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1761 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: 3.39 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3576 1.34 - 1.46: 1485 1.46 - 1.57: 6460 1.57 - 1.69: 11 1.69 - 1.81: 104 Bond restraints: 11636 Sorted by residual: bond pdb=" N MET A 533 " pdb=" CA MET A 533 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.26e-02 6.30e+03 9.59e+00 bond pdb=" N VAL A 672 " pdb=" CA VAL A 672 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.19e-02 7.06e+03 8.51e+00 bond pdb=" N VAL A 501 " pdb=" CA VAL A 501 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.59e+00 bond pdb=" N LEU A 502 " pdb=" CA LEU A 502 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.22e-02 6.72e+03 7.43e+00 bond pdb=" N ILE A 505 " pdb=" CA ILE A 505 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.19e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 98.36 - 106.67: 190 106.67 - 114.97: 7218 114.97 - 123.27: 7991 123.27 - 131.57: 285 131.57 - 139.87: 12 Bond angle restraints: 15696 Sorted by residual: angle pdb=" N GLU A 470 " pdb=" CA GLU A 470 " pdb=" C GLU A 470 " ideal model delta sigma weight residual 111.28 120.78 -9.50 1.09e+00 8.42e-01 7.59e+01 angle pdb=" N LYS A 469 " pdb=" CA LYS A 469 " pdb=" C LYS A 469 " ideal model delta sigma weight residual 111.28 120.68 -9.40 1.09e+00 8.42e-01 7.44e+01 angle pdb=" N GLU B 470 " pdb=" CA GLU B 470 " pdb=" C GLU B 470 " ideal model delta sigma weight residual 111.28 119.74 -8.46 1.09e+00 8.42e-01 6.02e+01 angle pdb=" N LYS B 469 " pdb=" CA LYS B 469 " pdb=" C LYS B 469 " ideal model delta sigma weight residual 111.28 119.01 -7.73 1.09e+00 8.42e-01 5.02e+01 angle pdb=" N GLU B 468 " pdb=" CA GLU B 468 " pdb=" C GLU B 468 " ideal model delta sigma weight residual 111.28 117.62 -6.34 1.09e+00 8.42e-01 3.38e+01 ... (remaining 15691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6392 17.66 - 35.32: 525 35.32 - 52.97: 120 52.97 - 70.63: 25 70.63 - 88.29: 6 Dihedral angle restraints: 7068 sinusoidal: 2846 harmonic: 4222 Sorted by residual: dihedral pdb=" N SER A 651 " pdb=" C SER A 651 " pdb=" CA SER A 651 " pdb=" CB SER A 651 " ideal model delta harmonic sigma weight residual 122.80 131.50 -8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C SER A 651 " pdb=" N SER A 651 " pdb=" CA SER A 651 " pdb=" CB SER A 651 " ideal model delta harmonic sigma weight residual -122.60 -130.77 8.17 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CA ASP A 94 " pdb=" CB ASP A 94 " pdb=" CG ASP A 94 " pdb=" OD1 ASP A 94 " ideal model delta sinusoidal sigma weight residual -30.00 -84.84 54.84 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1642 0.068 - 0.136: 189 0.136 - 0.204: 14 0.204 - 0.271: 3 0.271 - 0.339: 4 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA LYS A 469 " pdb=" N LYS A 469 " pdb=" C LYS A 469 " pdb=" CB LYS A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA SER A 651 " pdb=" N SER A 651 " pdb=" C SER A 651 " pdb=" CB SER A 651 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA GLU A 470 " pdb=" N GLU A 470 " pdb=" C GLU A 470 " pdb=" CB GLU A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1849 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 532 " -0.028 2.00e-02 2.50e+03 5.52e-02 3.04e+01 pdb=" C LEU A 532 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU A 532 " -0.036 2.00e-02 2.50e+03 pdb=" N MET A 533 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LEU A 710 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 710 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 711 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 328 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 329 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.025 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 13 2.36 - 2.99: 6083 2.99 - 3.63: 17002 3.63 - 4.26: 24175 4.26 - 4.90: 41037 Nonbonded interactions: 88310 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.719 2.170 nonbonded pdb=" OE1 GLN A 567 " pdb="MG MG A 802 " model vdw 1.823 2.170 nonbonded pdb=" O1B ATP A 801 " pdb="MG MG A 802 " model vdw 1.824 2.170 nonbonded pdb=" OD1 ASP B 647 " pdb=" N GLU B 648 " model vdw 2.116 2.520 nonbonded pdb=" N GLU A 669 " pdb=" OE1 GLU A 669 " model vdw 2.197 2.520 ... (remaining 88305 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 6.190 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.730 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 0.048 11636 Z= 0.247 Angle : 0.682 9.498 15696 Z= 0.433 Chirality : 0.047 0.339 1852 Planarity : 0.003 0.055 1944 Dihedral : 13.819 88.290 4356 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 0.72 % Allowed : 0.64 % Favored : 98.64 % 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: 0.18 (0.22), residues: 1456 helix: 1.42 (0.19), residues: 832 sheet: -1.15 (0.42), residues: 138 loop : -1.81 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 132 HIS 0.005 0.001 HIS A 249 PHE 0.015 0.002 PHE A 83 TYR 0.013 0.001 TYR B 389 ARG 0.007 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 432 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.8092 (m-40) cc_final: 0.7519 (t0) REVERT: C 19 MET cc_start: 0.6545 (mmp) cc_final: 0.6144 (mmp) REVERT: B 39 LEU cc_start: 0.8705 (tp) cc_final: 0.8442 (tp) REVERT: B 518 VAL cc_start: 0.8792 (p) cc_final: 0.8563 (m) REVERT: B 598 MET cc_start: 0.7849 (mtp) cc_final: 0.7547 (mtt) outliers start: 9 outliers final: 1 residues processed: 439 average time/residue: 0.2542 time to fit residues: 154.7726 Evaluate side-chains 271 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS A 305 ASN A 424 GLN A 450 GLN A 490 ASN A 629 GLN A 704 HIS B 99 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11636 Z= 0.253 Angle : 0.587 6.892 15696 Z= 0.307 Chirality : 0.041 0.152 1852 Planarity : 0.004 0.068 1944 Dihedral : 7.043 88.448 1622 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.37 % Allowed : 15.97 % Favored : 80.66 % 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: 0.62 (0.22), residues: 1456 helix: 1.80 (0.19), residues: 818 sheet: -1.07 (0.42), residues: 138 loop : -1.54 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 718 HIS 0.004 0.001 HIS B 660 PHE 0.015 0.002 PHE A 428 TYR 0.012 0.001 TYR B 319 ARG 0.015 0.001 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 269 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.7569 (p0) cc_final: 0.7264 (p0) REVERT: A 194 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7720 (t80) REVERT: A 335 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6486 (ptp-110) REVERT: B 99 HIS cc_start: 0.7745 (t70) cc_final: 0.7460 (t70) REVERT: B 694 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7427 (ttpt) outliers start: 42 outliers final: 33 residues processed: 298 average time/residue: 0.2051 time to fit residues: 89.7251 Evaluate side-chains 262 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 99 HIS A 278 GLN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN B 429 ASN B 660 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11636 Z= 0.170 Angle : 0.538 7.113 15696 Z= 0.279 Chirality : 0.040 0.148 1852 Planarity : 0.003 0.058 1944 Dihedral : 6.069 74.192 1622 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.01 % Allowed : 19.50 % Favored : 76.48 % 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: 0.71 (0.22), residues: 1456 helix: 1.85 (0.19), residues: 818 sheet: -0.92 (0.43), residues: 138 loop : -1.49 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 132 HIS 0.003 0.001 HIS B 660 PHE 0.012 0.001 PHE A 428 TYR 0.010 0.001 TYR A 179 ARG 0.005 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 246 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.7422 (p0) cc_final: 0.7172 (p0) REVERT: A 194 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7676 (t80) REVERT: A 340 ASP cc_start: 0.8464 (t0) cc_final: 0.8175 (t0) REVERT: A 420 MET cc_start: 0.6206 (ttm) cc_final: 0.5925 (mtp) REVERT: B 239 ASP cc_start: 0.8136 (t0) cc_final: 0.7829 (t0) REVERT: D 18 LEU cc_start: 0.8655 (mt) cc_final: 0.8417 (mm) outliers start: 50 outliers final: 32 residues processed: 278 average time/residue: 0.2063 time to fit residues: 85.0706 Evaluate side-chains 257 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 0.0020 chunk 139 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS A 304 GLN A 419 ASN B 99 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11636 Z= 0.305 Angle : 0.609 7.649 15696 Z= 0.311 Chirality : 0.041 0.134 1852 Planarity : 0.003 0.048 1944 Dihedral : 5.884 67.179 1622 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.30 % Allowed : 20.63 % Favored : 74.08 % 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: 0.78 (0.22), residues: 1456 helix: 1.90 (0.19), residues: 796 sheet: -0.76 (0.42), residues: 136 loop : -1.34 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 718 HIS 0.005 0.001 HIS A 249 PHE 0.019 0.002 PHE B 715 TYR 0.011 0.001 TYR A 225 ARG 0.012 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 232 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.7558 (p0) cc_final: 0.7257 (p0) REVERT: A 317 LEU cc_start: 0.9177 (tp) cc_final: 0.8875 (tt) REVERT: A 340 ASP cc_start: 0.8445 (t0) cc_final: 0.8173 (t0) REVERT: A 450 GLN cc_start: 0.8167 (tp40) cc_final: 0.7954 (tp40) REVERT: B 633 ILE cc_start: 0.8881 (mp) cc_final: 0.8639 (mp) REVERT: D 18 LEU cc_start: 0.8698 (mt) cc_final: 0.8444 (mm) outliers start: 66 outliers final: 51 residues processed: 275 average time/residue: 0.2275 time to fit residues: 92.2565 Evaluate side-chains 272 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 221 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 715 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.0870 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 249 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11636 Z= 0.186 Angle : 0.564 13.319 15696 Z= 0.283 Chirality : 0.040 0.136 1852 Planarity : 0.003 0.046 1944 Dihedral : 5.560 58.851 1622 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.41 % Allowed : 23.03 % Favored : 72.55 % 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: 0.91 (0.22), residues: 1456 helix: 2.06 (0.19), residues: 792 sheet: -0.65 (0.41), residues: 158 loop : -1.39 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.014 0.002 HIS B 660 PHE 0.016 0.001 PHE B 715 TYR 0.010 0.001 TYR A 225 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.7513 (p0) cc_final: 0.7218 (p0) REVERT: A 293 MET cc_start: 0.7338 (ttm) cc_final: 0.7133 (mtp) REVERT: A 340 ASP cc_start: 0.8347 (t0) cc_final: 0.8132 (t0) REVERT: A 420 MET cc_start: 0.6261 (ttm) cc_final: 0.5784 (mtp) REVERT: B 239 ASP cc_start: 0.8159 (t0) cc_final: 0.7880 (t0) REVERT: D 18 LEU cc_start: 0.8729 (mt) cc_final: 0.8484 (mm) outliers start: 55 outliers final: 44 residues processed: 270 average time/residue: 0.2205 time to fit residues: 86.5087 Evaluate side-chains 264 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 457 ASN Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS A 278 GLN A 450 GLN B 51 GLN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11636 Z= 0.302 Angle : 0.633 14.759 15696 Z= 0.317 Chirality : 0.041 0.138 1852 Planarity : 0.003 0.039 1944 Dihedral : 5.649 59.071 1622 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.90 % Allowed : 23.76 % Favored : 71.35 % 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: 0.77 (0.22), residues: 1456 helix: 1.87 (0.19), residues: 808 sheet: -0.93 (0.41), residues: 138 loop : -1.33 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.012 0.002 HIS B 99 PHE 0.019 0.002 PHE B 428 TYR 0.011 0.001 TYR A 225 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 227 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.7533 (p0) cc_final: 0.7320 (p0) REVERT: A 317 LEU cc_start: 0.9202 (tp) cc_final: 0.8934 (tt) REVERT: A 340 ASP cc_start: 0.8393 (t0) cc_final: 0.8178 (t0) REVERT: A 420 MET cc_start: 0.6429 (ttm) cc_final: 0.6011 (mtp) REVERT: D 18 LEU cc_start: 0.8804 (mt) cc_final: 0.8562 (mm) outliers start: 61 outliers final: 48 residues processed: 269 average time/residue: 0.2163 time to fit residues: 86.0478 Evaluate side-chains 264 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 278 GLN A 304 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11636 Z= 0.173 Angle : 0.588 13.650 15696 Z= 0.292 Chirality : 0.040 0.155 1852 Planarity : 0.003 0.039 1944 Dihedral : 5.391 57.081 1622 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.21 % Allowed : 25.92 % Favored : 70.87 % 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: 0.90 (0.22), residues: 1456 helix: 2.00 (0.19), residues: 802 sheet: -0.67 (0.40), residues: 154 loop : -1.34 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.009 0.001 HIS B 660 PHE 0.026 0.001 PHE B 715 TYR 0.012 0.001 TYR A 150 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 228 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.7477 (tt0) cc_final: 0.7150 (tt0) REVERT: A 340 ASP cc_start: 0.8330 (t0) cc_final: 0.8106 (t0) REVERT: A 420 MET cc_start: 0.6348 (ttm) cc_final: 0.5904 (mtp) REVERT: B 173 PHE cc_start: 0.7732 (t80) cc_final: 0.7518 (t80) REVERT: B 239 ASP cc_start: 0.8153 (t0) cc_final: 0.7904 (t0) REVERT: D 18 LEU cc_start: 0.8760 (mt) cc_final: 0.8539 (mm) outliers start: 40 outliers final: 30 residues processed: 254 average time/residue: 0.2235 time to fit residues: 84.1120 Evaluate side-chains 244 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS A 146 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN B 51 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11636 Z= 0.211 Angle : 0.608 13.429 15696 Z= 0.299 Chirality : 0.041 0.183 1852 Planarity : 0.003 0.037 1944 Dihedral : 5.375 57.068 1622 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.93 % Allowed : 25.44 % Favored : 70.63 % 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: 0.92 (0.22), residues: 1456 helix: 2.03 (0.19), residues: 802 sheet: -0.67 (0.40), residues: 154 loop : -1.36 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.009 0.001 HIS B 660 PHE 0.024 0.001 PHE A 428 TYR 0.011 0.001 TYR A 225 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.7472 (tt0) cc_final: 0.7154 (tt0) REVERT: A 420 MET cc_start: 0.6308 (ttm) cc_final: 0.5906 (mtp) REVERT: B 239 ASP cc_start: 0.8179 (t0) cc_final: 0.7941 (t0) REVERT: B 251 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9064 (mm) REVERT: D 18 LEU cc_start: 0.8784 (mt) cc_final: 0.8574 (mm) outliers start: 49 outliers final: 39 residues processed: 252 average time/residue: 0.2203 time to fit residues: 82.6379 Evaluate side-chains 254 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 214 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11636 Z= 0.187 Angle : 0.618 14.554 15696 Z= 0.303 Chirality : 0.041 0.161 1852 Planarity : 0.003 0.037 1944 Dihedral : 5.357 58.264 1622 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.77 % Allowed : 25.92 % Favored : 70.30 % 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: 0.90 (0.22), residues: 1456 helix: 2.02 (0.19), residues: 802 sheet: -0.59 (0.41), residues: 150 loop : -1.43 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.010 0.001 HIS B 660 PHE 0.024 0.001 PHE A 478 TYR 0.011 0.001 TYR A 225 ARG 0.007 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 221 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.7445 (tt0) cc_final: 0.7160 (tt0) REVERT: A 340 ASP cc_start: 0.8156 (t0) cc_final: 0.7934 (t0) REVERT: A 420 MET cc_start: 0.6377 (ttm) cc_final: 0.5949 (mtp) REVERT: C 16 GLU cc_start: 0.8384 (tp30) cc_final: 0.7948 (tp30) REVERT: B 239 ASP cc_start: 0.8194 (t0) cc_final: 0.7965 (t0) REVERT: B 251 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9031 (mm) outliers start: 47 outliers final: 40 residues processed: 252 average time/residue: 0.2189 time to fit residues: 81.5215 Evaluate side-chains 251 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 99 HIS ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11636 Z= 0.233 Angle : 0.652 14.884 15696 Z= 0.319 Chirality : 0.041 0.160 1852 Planarity : 0.003 0.069 1944 Dihedral : 5.429 59.522 1622 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.61 % Allowed : 26.65 % Favored : 69.74 % 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 (0.22), residues: 1456 helix: 2.01 (0.19), residues: 806 sheet: -0.68 (0.41), residues: 140 loop : -1.40 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 718 HIS 0.015 0.001 HIS B 660 PHE 0.023 0.002 PHE A 428 TYR 0.011 0.001 TYR A 225 ARG 0.008 0.001 ARG B 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 220 GLN cc_start: 0.7497 (tt0) cc_final: 0.7215 (tt0) REVERT: A 236 MET cc_start: 0.7397 (mtp) cc_final: 0.7186 (mtp) REVERT: C 16 GLU cc_start: 0.8415 (tp30) cc_final: 0.7524 (tp30) REVERT: B 239 ASP cc_start: 0.8197 (t0) cc_final: 0.7955 (t0) REVERT: B 251 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9055 (mm) outliers start: 45 outliers final: 39 residues processed: 241 average time/residue: 0.2126 time to fit residues: 77.3127 Evaluate side-chains 251 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 211 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 117 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 HIS ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS A 450 GLN ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 429 ASN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.134179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110391 restraints weight = 26763.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113244 restraints weight = 13418.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.114983 restraints weight = 8356.537| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11636 Z= 0.176 Angle : 0.651 14.655 15696 Z= 0.319 Chirality : 0.041 0.176 1852 Planarity : 0.003 0.045 1944 Dihedral : 5.268 59.752 1622 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.05 % Allowed : 27.53 % Favored : 69.42 % 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: 0.94 (0.22), residues: 1456 helix: 2.00 (0.19), residues: 818 sheet: -0.63 (0.41), residues: 142 loop : -1.40 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 718 HIS 0.015 0.001 HIS B 660 PHE 0.022 0.001 PHE A 428 TYR 0.016 0.001 TYR A 150 ARG 0.008 0.001 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.05 seconds wall clock time: 48 minutes 2.82 seconds (2882.82 seconds total)