Starting phenix.real_space_refine on Wed May 8 22:58:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/05_2024/8p23_17357_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/05_2024/8p23_17357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/05_2024/8p23_17357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/05_2024/8p23_17357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/05_2024/8p23_17357_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/05_2024/8p23_17357_updated.pdb" } resolution = 3.17 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= 0.002 sd= 0.031 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 Zn 1 6.06 5 P 15 5.49 5 S 71 5.16 5 C 7126 2.51 5 N 2000 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 646": "OD1" <-> "OD2" Residue "B ASP 648": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11399 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5510 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 665} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5735 Classifications: {'peptide': 715} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 693} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' ZN': 1, 'ATP': 2, 'CTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10830 SG CYS B 683 16.674 87.785 61.025 1.00102.46 S ATOM 10921 SG CYS B 695 14.070 86.300 63.500 1.00104.69 S ATOM 10943 SG CYS B 698 14.686 84.344 61.636 1.00105.10 S Time building chain proxies: 7.26, per 1000 atoms: 0.64 Number of scatterers: 11399 At special positions: 0 Unit cell: (82.422, 137.948, 118.861, 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) Zn 1 29.99 S 71 16.00 P 15 15.00 O 2186 8.00 N 2000 7.00 C 7126 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: 4.92 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 698 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 683 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 695 " 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 5 sheets defined 44.3% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.782A pdb=" N GLN A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 71 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.979A pdb=" N TYR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 122 through 138 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 197 through 214 removed outlier: 3.625A pdb=" N CYS A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 246 Proline residue: A 230 - end of helix removed outlier: 4.223A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 300 removed outlier: 3.720A pdb=" N HIS A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.066A pdb=" N CYS A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 487 removed outlier: 4.122A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 496 through 499 No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 514 through 519 removed outlier: 4.310A pdb=" N ASN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 514 through 519' Processing helix chain 'A' and resid 546 through 569 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.623A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 634 Proline residue: A 630 - end of helix removed outlier: 4.472A pdb=" N ASP A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 654 through 665 Processing helix chain 'A' and resid 722 through 730 removed outlier: 4.222A pdb=" N ALA A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 28 removed outlier: 3.670A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 57 through 69 removed outlier: 4.095A pdb=" N ASP B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 104 removed outlier: 3.801A pdb=" N ALA B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR B 95 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 141 removed outlier: 3.784A pdb=" N MET B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 161 through 166 Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 197 through 210 removed outlier: 3.852A pdb=" N CYS B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 230 through 246 removed outlier: 4.142A pdb=" N MET B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 removed outlier: 3.901A pdb=" N ASN B 286 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 287 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 removed outlier: 3.615A pdb=" N ARG B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.832A pdb=" N LEU B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.873A pdb=" N CYS B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 487 removed outlier: 3.579A pdb=" N ASP B 472 " --> pdb=" O ASP B 468 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 473 " --> pdb=" O ASN B 469 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 532 through 535 No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 545 through 569 removed outlier: 4.252A pdb=" N GLU B 549 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'B' and resid 621 through 633 Proline residue: B 630 - end of helix removed outlier: 4.625A pdb=" N ASP B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 655 through 665 removed outlier: 3.597A pdb=" N VAL B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 728 No H-bonds generated for 'chain 'B' and resid 725 through 728' Processing sheet with id= A, first strand: chain 'A' and resid 156 through 158 removed outlier: 7.714A pdb=" N THR A 521 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE A 438 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 523 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N THR A 440 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY A 525 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASN A 442 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 527 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.907A pdb=" N ALA A 220 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 350 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR A 317 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A 352 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN A 385 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LYS A 355 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 387 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 643 through 645 Processing sheet with id= D, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.518A pdb=" N THR B 521 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY B 523 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE B 438 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY B 525 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR B 440 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE B 527 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN B 442 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 526 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.504A pdb=" N ILE B 350 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N TYR B 317 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 352 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN B 385 " --> pdb=" O TRP B 353 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS B 355 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 387 " --> pdb=" O LYS B 355 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1050 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: 3.37 Time building geometry restraints manager: 5.25 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: 1921 1.31 - 1.43: 3075 1.43 - 1.56: 6483 1.56 - 1.68: 25 1.68 - 1.81: 121 Bond restraints: 11625 Sorted by residual: bond pdb=" C TYR B 371 " pdb=" O TYR B 371 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.15e-02 7.56e+03 2.19e+01 bond pdb=" C VAL B 659 " pdb=" O VAL B 659 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.19e-02 7.06e+03 1.97e+01 bond pdb=" C ALA B 374 " pdb=" O ALA B 374 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.26e-02 6.30e+03 1.57e+01 bond pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 1.531 1.477 0.053 1.37e-02 5.33e+03 1.52e+01 bond pdb=" N ILE B 735 " pdb=" CA ILE B 735 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.30e-02 5.92e+03 1.34e+01 ... (remaining 11620 not shown) Histogram of bond angle deviations from ideal: 98.47 - 106.75: 364 106.75 - 115.03: 6990 115.03 - 123.31: 7924 123.31 - 131.59: 411 131.59 - 139.87: 25 Bond angle restraints: 15714 Sorted by residual: angle pdb=" N GLN B 212 " pdb=" CA GLN B 212 " pdb=" C GLN B 212 " ideal model delta sigma weight residual 112.57 98.47 14.10 1.13e+00 7.83e-01 1.56e+02 angle pdb=" N HIS B 734 " pdb=" CA HIS B 734 " pdb=" C HIS B 734 " ideal model delta sigma weight residual 110.24 100.41 9.83 1.47e+00 4.63e-01 4.47e+01 angle pdb=" C ARG B 305 " pdb=" CA ARG B 305 " pdb=" CB ARG B 305 " ideal model delta sigma weight residual 109.80 99.24 10.56 1.61e+00 3.86e-01 4.30e+01 angle pdb=" N ASN B 213 " pdb=" CA ASN B 213 " pdb=" C ASN B 213 " ideal model delta sigma weight residual 112.54 103.50 9.04 1.51e+00 4.39e-01 3.59e+01 angle pdb=" N THR B 650 " pdb=" CA THR B 650 " pdb=" C THR B 650 " ideal model delta sigma weight residual 113.38 106.21 7.17 1.23e+00 6.61e-01 3.40e+01 ... (remaining 15709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 6559 17.25 - 34.50: 354 34.50 - 51.75: 112 51.75 - 69.00: 40 69.00 - 86.25: 13 Dihedral angle restraints: 7078 sinusoidal: 2991 harmonic: 4087 Sorted by residual: dihedral pdb=" C CYS B 327 " pdb=" N CYS B 327 " pdb=" CA CYS B 327 " pdb=" CB CYS B 327 " ideal model delta harmonic sigma weight residual -122.60 -108.55 -14.05 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" C ARG B 305 " pdb=" N ARG B 305 " pdb=" CA ARG B 305 " pdb=" CB ARG B 305 " ideal model delta harmonic sigma weight residual -122.60 -109.48 -13.12 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" CA VAL B 714 " pdb=" C VAL B 714 " pdb=" N GLY B 715 " pdb=" CA GLY B 715 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1582 0.091 - 0.182: 98 0.182 - 0.273: 11 0.273 - 0.363: 11 0.363 - 0.454: 1 Chirality restraints: 1703 Sorted by residual: chirality pdb=" CA LYS B 33 " pdb=" N LYS B 33 " pdb=" C LYS B 33 " pdb=" CB LYS B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA CYS B 327 " pdb=" N CYS B 327 " pdb=" C CYS B 327 " pdb=" CB CYS B 327 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA HIS B 734 " pdb=" N HIS B 734 " pdb=" C HIS B 734 " pdb=" CB HIS B 734 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1700 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 302 " -0.031 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C ILE B 302 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE B 302 " -0.040 2.00e-02 2.50e+03 pdb=" N HIS B 303 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 326 " -0.394 9.50e-02 1.11e+02 1.77e-01 1.91e+01 pdb=" NE ARG B 326 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 326 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 326 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 326 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 403 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO B 404 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " -0.041 5.00e-02 4.00e+02 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 257 2.65 - 3.21: 11128 3.21 - 3.78: 16272 3.78 - 4.34: 22243 4.34 - 4.90: 36917 Nonbonded interactions: 86817 Sorted by model distance: nonbonded pdb=" N CYS B 698 " pdb="ZN ZN B 804 " model vdw 2.090 2.310 nonbonded pdb=" O ALA A 391 " pdb=" OG1 THR A 392 " model vdw 2.139 2.440 nonbonded pdb=" O PHE B 526 " pdb=" OG SER B 610 " model vdw 2.155 2.440 nonbonded pdb=" O ASP B 403 " pdb=" N GLU B 405 " model vdw 2.203 2.520 nonbonded pdb=" OD1 ASP B 633 " pdb=" NH2 ARG B 636 " model vdw 2.207 2.520 ... (remaining 86812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 33 or resid 36 through 49 or resid 55 through 71 \ or resid 75 through 735 or resid 801)) selection = (chain 'B' and (resid 2 through 184 or resid 193 through 303 or resid 310 throug \ h 676 or (resid 705 and (name N or name CA or name C or name O or name CB )) or \ resid 706 through 707 or (resid 708 and (name N or name CA or name C or name O o \ r name CB )) or resid 713 through 735 or resid 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.000 Extract box with map and model: 7.920 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 36.200 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 0.054 11625 Z= 0.242 Angle : 0.692 14.103 15714 Z= 0.426 Chirality : 0.051 0.454 1703 Planarity : 0.006 0.177 2015 Dihedral : 13.197 86.251 4442 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.81 % Favored : 93.68 % Rotamer: Outliers : 4.71 % Allowed : 7.77 % Favored : 87.52 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 7.50 % 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 (0.24), residues: 1377 helix: 1.35 (0.22), residues: 627 sheet: 0.03 (0.52), residues: 113 loop : -2.99 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 720 HIS 0.003 0.001 HIS B 303 PHE 0.010 0.001 PHE A 224 TYR 0.026 0.001 TYR B 371 ARG 0.006 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 349 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.7766 (m-70) cc_final: 0.7203 (m-70) REVERT: A 100 MET cc_start: 0.6549 (tmm) cc_final: 0.6284 (tmm) REVERT: A 117 MET cc_start: 0.6051 (mtp) cc_final: 0.5674 (mtp) REVERT: A 138 VAL cc_start: 0.8220 (p) cc_final: 0.8014 (m) REVERT: A 140 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6759 (p0) REVERT: A 238 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6853 (mm-30) REVERT: A 239 GLU cc_start: 0.6886 (tp30) cc_final: 0.6609 (mm-30) REVERT: A 241 LYS cc_start: 0.7557 (tppp) cc_final: 0.7295 (ttmt) REVERT: A 244 GLU cc_start: 0.7225 (tm-30) cc_final: 0.7011 (tm-30) REVERT: A 271 GLN cc_start: 0.7487 (pp30) cc_final: 0.7151 (pp30) REVERT: A 313 SER cc_start: 0.7493 (p) cc_final: 0.7158 (m) REVERT: A 316 ASN cc_start: 0.7722 (m-40) cc_final: 0.7441 (m-40) REVERT: A 342 ASN cc_start: 0.7132 (t0) cc_final: 0.6793 (t0) REVERT: A 352 ILE cc_start: 0.8582 (pp) cc_final: 0.8347 (pt) REVERT: A 360 ASN cc_start: 0.7690 (t0) cc_final: 0.7106 (t0) REVERT: A 476 LYS cc_start: 0.7965 (tppp) cc_final: 0.7636 (tppt) REVERT: A 564 GLU cc_start: 0.6230 (pt0) cc_final: 0.5972 (pt0) REVERT: A 594 GLN cc_start: 0.7287 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 603 ASP cc_start: 0.6924 (t70) cc_final: 0.6668 (t0) REVERT: A 622 LEU cc_start: 0.8041 (mt) cc_final: 0.7791 (mm) REVERT: A 642 TYR cc_start: 0.7449 (m-80) cc_final: 0.6816 (t80) REVERT: A 674 ASN cc_start: 0.7271 (m110) cc_final: 0.6870 (m-40) REVERT: A 719 ARG cc_start: 0.6654 (mtp180) cc_final: 0.6123 (mtp180) REVERT: B 21 MET cc_start: 0.7287 (ptm) cc_final: 0.6987 (ptm) REVERT: B 86 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 145 GLU cc_start: 0.7423 (pm20) cc_final: 0.7218 (pm20) REVERT: B 148 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7631 (mtm110) REVERT: B 214 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 238 GLU cc_start: 0.7018 (tp30) cc_final: 0.6817 (tp30) REVERT: B 239 GLU cc_start: 0.7989 (tp30) cc_final: 0.7402 (tp30) REVERT: B 299 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6136 (mpm) REVERT: B 301 THR cc_start: 0.8207 (m) cc_final: 0.7853 (m) REVERT: B 303 HIS cc_start: 0.6394 (m90) cc_final: 0.6163 (m90) REVERT: B 376 LYS cc_start: 0.7872 (tppt) cc_final: 0.7635 (ttpp) REVERT: B 397 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7220 (tm-30) REVERT: B 429 THR cc_start: 0.8086 (t) cc_final: 0.7726 (p) REVERT: B 483 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7789 (mm-40) REVERT: B 511 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6447 (tm-30) REVERT: B 560 ASP cc_start: 0.7436 (m-30) cc_final: 0.7231 (m-30) REVERT: B 603 ASP cc_start: 0.7154 (t0) cc_final: 0.6776 (t0) REVERT: B 611 ASN cc_start: 0.6347 (p0) cc_final: 0.6054 (p0) REVERT: B 654 SER cc_start: 0.6162 (OUTLIER) cc_final: 0.5518 (p) REVERT: B 729 HIS cc_start: 0.7526 (t70) cc_final: 0.7274 (t-170) outliers start: 57 outliers final: 26 residues processed: 384 average time/residue: 0.2862 time to fit residues: 147.1023 Evaluate side-chains 337 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 308 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 0.0070 chunk 108 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 86 GLN A 114 ASN A 182 HIS A 242 ASN A 300 ASN A 395 GLN A 506 ASN A 676 ASN B 78 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 548 GLN B 572 ASN B 611 ASN B 652 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11625 Z= 0.163 Angle : 0.567 6.819 15714 Z= 0.296 Chirality : 0.043 0.229 1703 Planarity : 0.004 0.073 2015 Dihedral : 12.250 84.875 1741 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.39 % Favored : 93.25 % Rotamer: Outliers : 4.46 % Allowed : 14.13 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 (0.23), residues: 1377 helix: 1.25 (0.22), residues: 629 sheet: 0.16 (0.51), residues: 115 loop : -2.84 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 501 HIS 0.004 0.001 HIS B 540 PHE 0.016 0.001 PHE A 383 TYR 0.011 0.001 TYR B 164 ARG 0.004 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 316 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8099 (mtpp) REVERT: A 21 MET cc_start: 0.6396 (mpt) cc_final: 0.5862 (mtp) REVERT: A 25 ARG cc_start: 0.7361 (mpt-90) cc_final: 0.7117 (mpt-90) REVERT: A 30 HIS cc_start: 0.7779 (m-70) cc_final: 0.7474 (m-70) REVERT: A 45 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6720 (m-30) REVERT: A 100 MET cc_start: 0.6598 (tmm) cc_final: 0.6314 (tmm) REVERT: A 117 MET cc_start: 0.6066 (mtp) cc_final: 0.5671 (mtp) REVERT: A 140 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6775 (p0) REVERT: A 238 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 241 LYS cc_start: 0.7592 (tppp) cc_final: 0.7303 (ttmt) REVERT: A 244 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6955 (tm-30) REVERT: A 264 GLU cc_start: 0.7090 (pm20) cc_final: 0.6581 (pm20) REVERT: A 313 SER cc_start: 0.7611 (p) cc_final: 0.7332 (m) REVERT: A 342 ASN cc_start: 0.7180 (t0) cc_final: 0.6819 (t0) REVERT: A 352 ILE cc_start: 0.8600 (pp) cc_final: 0.8360 (pt) REVERT: A 360 ASN cc_start: 0.7509 (t0) cc_final: 0.6878 (t0) REVERT: A 364 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6722 (tm-30) REVERT: A 380 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7608 (ttp-170) REVERT: A 590 LYS cc_start: 0.7447 (mppt) cc_final: 0.7101 (mppt) REVERT: A 594 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7027 (tm-30) REVERT: A 603 ASP cc_start: 0.6941 (t70) cc_final: 0.6689 (t0) REVERT: A 622 LEU cc_start: 0.7862 (mt) cc_final: 0.7599 (mt) REVERT: A 626 GLN cc_start: 0.7614 (mt0) cc_final: 0.7373 (mt0) REVERT: A 642 TYR cc_start: 0.7437 (m-80) cc_final: 0.6757 (t80) REVERT: A 674 ASN cc_start: 0.7354 (m110) cc_final: 0.6858 (m110) REVERT: A 719 ARG cc_start: 0.6411 (mtp180) cc_final: 0.6193 (mtp180) REVERT: A 725 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7774 (mt) REVERT: B 21 MET cc_start: 0.7195 (ptm) cc_final: 0.6823 (ptm) REVERT: B 24 ILE cc_start: 0.8191 (mm) cc_final: 0.7820 (mm) REVERT: B 28 MET cc_start: 0.5983 (mmm) cc_final: 0.5666 (mmm) REVERT: B 86 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 145 GLU cc_start: 0.7436 (pm20) cc_final: 0.7164 (pm20) REVERT: B 148 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7580 (mtp85) REVERT: B 214 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7619 (mt-10) REVERT: B 239 GLU cc_start: 0.7921 (tp30) cc_final: 0.7497 (tp30) REVERT: B 299 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6410 (mpm) REVERT: B 301 THR cc_start: 0.8102 (m) cc_final: 0.7867 (m) REVERT: B 372 LYS cc_start: 0.8649 (tppt) cc_final: 0.8117 (tppt) REVERT: B 397 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 398 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8493 (mtmt) REVERT: B 429 THR cc_start: 0.8213 (t) cc_final: 0.7903 (p) REVERT: B 483 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7816 (mm-40) REVERT: B 511 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6454 (tm-30) REVERT: B 560 ASP cc_start: 0.7456 (m-30) cc_final: 0.7088 (m-30) REVERT: B 603 ASP cc_start: 0.7183 (t0) cc_final: 0.6779 (t0) REVERT: B 654 SER cc_start: 0.5969 (OUTLIER) cc_final: 0.5281 (p) REVERT: B 657 GLU cc_start: 0.7075 (tp30) cc_final: 0.6789 (tp30) outliers start: 54 outliers final: 29 residues processed: 349 average time/residue: 0.2915 time to fit residues: 138.2491 Evaluate side-chains 330 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.2980 chunk 39 optimal weight: 0.0670 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 101 optimal weight: 0.0040 overall best weight: 0.3330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 242 ASN A 298 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 729 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11625 Z= 0.148 Angle : 0.539 6.962 15714 Z= 0.285 Chirality : 0.042 0.259 1703 Planarity : 0.004 0.072 2015 Dihedral : 11.640 84.913 1727 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.95 % Favored : 93.68 % Rotamer: Outliers : 4.46 % Allowed : 14.71 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.83 (0.23), residues: 1377 helix: 1.25 (0.22), residues: 629 sheet: 0.32 (0.50), residues: 115 loop : -2.78 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 399 HIS 0.011 0.001 HIS B 541 PHE 0.025 0.001 PHE A 526 TYR 0.009 0.001 TYR A 606 ARG 0.005 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 305 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8129 (mtpp) REVERT: A 21 MET cc_start: 0.6408 (mpt) cc_final: 0.5984 (mtp) REVERT: A 25 ARG cc_start: 0.7399 (mpt-90) cc_final: 0.7195 (mpt-90) REVERT: A 30 HIS cc_start: 0.7757 (m-70) cc_final: 0.7522 (m-70) REVERT: A 100 MET cc_start: 0.6608 (tmm) cc_final: 0.6369 (tmm) REVERT: A 117 MET cc_start: 0.6059 (mtp) cc_final: 0.5633 (mtp) REVERT: A 140 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6779 (p0) REVERT: A 238 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6830 (mm-30) REVERT: A 239 GLU cc_start: 0.6865 (tp30) cc_final: 0.6627 (tp30) REVERT: A 241 LYS cc_start: 0.7533 (tppp) cc_final: 0.7282 (ttmt) REVERT: A 244 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 261 ASP cc_start: 0.6927 (p0) cc_final: 0.6702 (p0) REVERT: A 263 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7430 (mp) REVERT: A 264 GLU cc_start: 0.7061 (pm20) cc_final: 0.6680 (pm20) REVERT: A 319 THR cc_start: 0.7162 (m) cc_final: 0.6635 (t) REVERT: A 342 ASN cc_start: 0.7180 (t0) cc_final: 0.6878 (t0) REVERT: A 352 ILE cc_start: 0.8594 (pp) cc_final: 0.8327 (pt) REVERT: A 360 ASN cc_start: 0.7539 (t0) cc_final: 0.6885 (t0) REVERT: A 364 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6708 (tm-30) REVERT: A 380 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7448 (ttp-170) REVERT: A 414 MET cc_start: 0.6682 (tmm) cc_final: 0.6410 (tmm) REVERT: A 533 LEU cc_start: 0.7819 (pp) cc_final: 0.7540 (pp) REVERT: A 590 LYS cc_start: 0.7487 (mppt) cc_final: 0.7182 (mppt) REVERT: A 594 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 603 ASP cc_start: 0.6945 (t70) cc_final: 0.6701 (t0) REVERT: A 622 LEU cc_start: 0.7865 (mt) cc_final: 0.7596 (mt) REVERT: A 626 GLN cc_start: 0.7580 (mt0) cc_final: 0.7326 (mt0) REVERT: A 719 ARG cc_start: 0.6389 (mtp180) cc_final: 0.6143 (mtp180) REVERT: A 725 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 7 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7054 (mtpp) REVERT: B 21 MET cc_start: 0.7138 (ptm) cc_final: 0.6778 (ptm) REVERT: B 24 ILE cc_start: 0.8238 (mm) cc_final: 0.7664 (mm) REVERT: B 28 MET cc_start: 0.6160 (mmm) cc_final: 0.5714 (mmm) REVERT: B 86 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 132 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6710 (mm-30) REVERT: B 145 GLU cc_start: 0.7384 (pm20) cc_final: 0.7173 (pm20) REVERT: B 148 ARG cc_start: 0.7838 (ttt-90) cc_final: 0.7479 (mtp85) REVERT: B 239 GLU cc_start: 0.7864 (tp30) cc_final: 0.7384 (tp30) REVERT: B 299 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6548 (mpm) REVERT: B 372 LYS cc_start: 0.8617 (tppt) cc_final: 0.8055 (tppt) REVERT: B 397 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7199 (tm-30) REVERT: B 398 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8477 (mtpp) REVERT: B 429 THR cc_start: 0.8191 (t) cc_final: 0.7899 (p) REVERT: B 483 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7812 (mm-40) REVERT: B 511 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6466 (tm-30) REVERT: B 560 ASP cc_start: 0.7449 (m-30) cc_final: 0.7134 (m-30) REVERT: B 603 ASP cc_start: 0.7141 (t0) cc_final: 0.6735 (t0) REVERT: B 657 GLU cc_start: 0.7005 (tp30) cc_final: 0.6685 (mm-30) outliers start: 54 outliers final: 39 residues processed: 334 average time/residue: 0.2868 time to fit residues: 129.0029 Evaluate side-chains 338 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 294 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 134 optimal weight: 0.0370 chunk 66 optimal weight: 7.9990 chunk 120 optimal weight: 0.0870 chunk 36 optimal weight: 0.2980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11625 Z= 0.163 Angle : 0.537 7.516 15714 Z= 0.284 Chirality : 0.042 0.244 1703 Planarity : 0.004 0.071 2015 Dihedral : 11.251 88.619 1718 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.66 % Favored : 93.97 % Rotamer: Outliers : 4.55 % Allowed : 16.53 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.79 (0.23), residues: 1377 helix: 1.25 (0.22), residues: 629 sheet: 0.60 (0.51), residues: 106 loop : -2.72 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 720 HIS 0.012 0.001 HIS B 541 PHE 0.012 0.001 PHE A 382 TYR 0.010 0.001 TYR B 164 ARG 0.003 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8071 (mtpp) REVERT: A 21 MET cc_start: 0.6435 (mpt) cc_final: 0.6146 (mtp) REVERT: A 25 ARG cc_start: 0.7393 (mpt-90) cc_final: 0.7185 (mpt-90) REVERT: A 45 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: A 100 MET cc_start: 0.6650 (tmm) cc_final: 0.6413 (tmm) REVERT: A 117 MET cc_start: 0.6053 (mtp) cc_final: 0.5612 (mtp) REVERT: A 140 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6836 (p0) REVERT: A 238 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 239 GLU cc_start: 0.6865 (tp30) cc_final: 0.6648 (tp30) REVERT: A 241 LYS cc_start: 0.7552 (tppp) cc_final: 0.7267 (ttmt) REVERT: A 244 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6984 (tm-30) REVERT: A 263 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7434 (mp) REVERT: A 264 GLU cc_start: 0.7061 (pm20) cc_final: 0.6707 (pm20) REVERT: A 319 THR cc_start: 0.7159 (m) cc_final: 0.6650 (t) REVERT: A 334 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7356 (mp10) REVERT: A 342 ASN cc_start: 0.7184 (t0) cc_final: 0.6897 (t0) REVERT: A 352 ILE cc_start: 0.8589 (pp) cc_final: 0.8343 (pt) REVERT: A 360 ASN cc_start: 0.7472 (t0) cc_final: 0.6781 (t0) REVERT: A 364 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6686 (tm-30) REVERT: A 380 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7457 (ttp80) REVERT: A 414 MET cc_start: 0.6671 (tmm) cc_final: 0.6352 (tmm) REVERT: A 590 LYS cc_start: 0.7513 (mppt) cc_final: 0.7249 (mppt) REVERT: A 594 GLN cc_start: 0.7463 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 603 ASP cc_start: 0.6955 (t70) cc_final: 0.6701 (t0) REVERT: A 622 LEU cc_start: 0.7895 (mt) cc_final: 0.7597 (mt) REVERT: A 626 GLN cc_start: 0.7602 (mt0) cc_final: 0.7334 (mt0) REVERT: A 642 TYR cc_start: 0.7399 (m-80) cc_final: 0.6802 (t80) REVERT: A 719 ARG cc_start: 0.6401 (mtp180) cc_final: 0.6121 (mtp180) REVERT: A 725 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7725 (mt) REVERT: B 7 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6886 (mtpp) REVERT: B 21 MET cc_start: 0.7179 (ptm) cc_final: 0.6818 (ptm) REVERT: B 24 ILE cc_start: 0.8237 (mm) cc_final: 0.7646 (mm) REVERT: B 28 MET cc_start: 0.6300 (mmm) cc_final: 0.5815 (mmm) REVERT: B 86 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 132 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6764 (mm-30) REVERT: B 148 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.7491 (mtp85) REVERT: B 345 THR cc_start: 0.8051 (t) cc_final: 0.7850 (p) REVERT: B 397 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7190 (tm-30) REVERT: B 429 THR cc_start: 0.8207 (t) cc_final: 0.7900 (p) REVERT: B 511 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6503 (tm-30) REVERT: B 578 THR cc_start: 0.8062 (m) cc_final: 0.7690 (p) REVERT: B 603 ASP cc_start: 0.7176 (t0) cc_final: 0.6767 (t0) REVERT: B 611 ASN cc_start: 0.6851 (p0) cc_final: 0.6629 (p0) REVERT: B 705 LYS cc_start: 0.8185 (mppt) cc_final: 0.7745 (mppt) outliers start: 55 outliers final: 37 residues processed: 324 average time/residue: 0.3138 time to fit residues: 135.7932 Evaluate side-chains 328 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 286 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 120 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11625 Z= 0.181 Angle : 0.544 7.171 15714 Z= 0.289 Chirality : 0.042 0.250 1703 Planarity : 0.004 0.070 2015 Dihedral : 10.679 88.696 1711 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.17 % Favored : 93.46 % Rotamer: Outliers : 4.13 % Allowed : 17.27 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.84 (0.23), residues: 1377 helix: 1.17 (0.21), residues: 631 sheet: 0.35 (0.50), residues: 110 loop : -2.68 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 720 HIS 0.003 0.001 HIS B 541 PHE 0.027 0.001 PHE A 526 TYR 0.012 0.001 TYR B 164 ARG 0.004 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 303 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8140 (mtpp) REVERT: A 45 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6625 (m-30) REVERT: A 100 MET cc_start: 0.6646 (tmm) cc_final: 0.6378 (tmm) REVERT: A 117 MET cc_start: 0.6086 (mtp) cc_final: 0.5569 (mtp) REVERT: A 140 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.6921 (p0) REVERT: A 238 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 241 LYS cc_start: 0.7548 (tppp) cc_final: 0.7274 (ttmt) REVERT: A 244 GLU cc_start: 0.7269 (tm-30) cc_final: 0.7002 (tm-30) REVERT: A 261 ASP cc_start: 0.6976 (p0) cc_final: 0.6726 (p0) REVERT: A 263 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7542 (mp) REVERT: A 264 GLU cc_start: 0.7079 (pm20) cc_final: 0.6726 (pm20) REVERT: A 271 GLN cc_start: 0.7589 (pp30) cc_final: 0.7220 (pp30) REVERT: A 292 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7597 (mmm) REVERT: A 319 THR cc_start: 0.7202 (m) cc_final: 0.6617 (t) REVERT: A 342 ASN cc_start: 0.7206 (t0) cc_final: 0.6894 (t0) REVERT: A 352 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8343 (pt) REVERT: A 360 ASN cc_start: 0.7481 (t0) cc_final: 0.6782 (t0) REVERT: A 364 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6693 (tm-30) REVERT: A 414 MET cc_start: 0.6673 (tmm) cc_final: 0.6316 (tmm) REVERT: A 476 LYS cc_start: 0.7997 (tppp) cc_final: 0.7628 (tppt) REVERT: A 533 LEU cc_start: 0.7827 (pp) cc_final: 0.7538 (pp) REVERT: A 590 LYS cc_start: 0.7522 (mppt) cc_final: 0.7289 (mppt) REVERT: A 594 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 603 ASP cc_start: 0.6951 (t70) cc_final: 0.6696 (t0) REVERT: A 719 ARG cc_start: 0.6392 (mtp180) cc_final: 0.6112 (mtp180) REVERT: A 725 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7743 (mt) REVERT: B 21 MET cc_start: 0.7207 (ptm) cc_final: 0.6851 (ptm) REVERT: B 24 ILE cc_start: 0.8260 (mm) cc_final: 0.7624 (mm) REVERT: B 28 MET cc_start: 0.6390 (mmm) cc_final: 0.5887 (mmm) REVERT: B 86 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 132 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6782 (mm-30) REVERT: B 148 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7511 (mtp85) REVERT: B 239 GLU cc_start: 0.7849 (tp30) cc_final: 0.7519 (tp30) REVERT: B 397 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 429 THR cc_start: 0.8203 (t) cc_final: 0.7893 (p) REVERT: B 511 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6514 (tm-30) REVERT: B 560 ASP cc_start: 0.7514 (m-30) cc_final: 0.7226 (m-30) REVERT: B 578 THR cc_start: 0.8091 (m) cc_final: 0.7728 (p) REVERT: B 603 ASP cc_start: 0.7198 (t0) cc_final: 0.6832 (t0) REVERT: B 611 ASN cc_start: 0.6963 (p0) cc_final: 0.6636 (p0) REVERT: B 705 LYS cc_start: 0.8205 (mppt) cc_final: 0.7756 (mppt) outliers start: 50 outliers final: 37 residues processed: 329 average time/residue: 0.2877 time to fit residues: 127.1244 Evaluate side-chains 329 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 chunk 111 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 overall best weight: 0.1628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11625 Z= 0.137 Angle : 0.522 8.509 15714 Z= 0.276 Chirality : 0.041 0.247 1703 Planarity : 0.004 0.068 2015 Dihedral : 10.009 84.824 1709 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.23 % Favored : 94.41 % Rotamer: Outliers : 4.30 % Allowed : 17.93 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.68 (0.23), residues: 1377 helix: 1.29 (0.22), residues: 632 sheet: 0.58 (0.51), residues: 109 loop : -2.62 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 399 HIS 0.002 0.000 HIS A 675 PHE 0.011 0.001 PHE A 393 TYR 0.014 0.001 TYR B 371 ARG 0.009 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 297 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8016 (mtpp) REVERT: A 45 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: A 100 MET cc_start: 0.6622 (tmm) cc_final: 0.6361 (tmm) REVERT: A 117 MET cc_start: 0.6085 (mtp) cc_final: 0.5583 (mtp) REVERT: A 140 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6898 (p0) REVERT: A 238 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 241 LYS cc_start: 0.7548 (tppp) cc_final: 0.7271 (ttmt) REVERT: A 244 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 261 ASP cc_start: 0.6869 (p0) cc_final: 0.6658 (p0) REVERT: A 263 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7445 (mp) REVERT: A 264 GLU cc_start: 0.7040 (pm20) cc_final: 0.6678 (pm20) REVERT: A 271 GLN cc_start: 0.7553 (pp30) cc_final: 0.7171 (pp30) REVERT: A 360 ASN cc_start: 0.7354 (t0) cc_final: 0.6635 (t0) REVERT: A 364 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6659 (tm-30) REVERT: A 414 MET cc_start: 0.6615 (tmm) cc_final: 0.6318 (tmm) REVERT: A 590 LYS cc_start: 0.7474 (mppt) cc_final: 0.7274 (mppt) REVERT: A 594 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7101 (tt0) REVERT: A 603 ASP cc_start: 0.6933 (t70) cc_final: 0.6688 (t0) REVERT: A 719 ARG cc_start: 0.6382 (mtp180) cc_final: 0.6129 (mtp180) REVERT: A 725 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7764 (mt) REVERT: B 7 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6849 (mtpp) REVERT: B 21 MET cc_start: 0.7115 (ptm) cc_final: 0.6755 (ptm) REVERT: B 24 ILE cc_start: 0.8279 (mm) cc_final: 0.7621 (mm) REVERT: B 28 MET cc_start: 0.6457 (mmm) cc_final: 0.5935 (mmm) REVERT: B 67 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 86 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 132 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6767 (mm-30) REVERT: B 148 ARG cc_start: 0.7797 (ttt-90) cc_final: 0.7427 (mtp85) REVERT: B 397 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7188 (tm-30) REVERT: B 429 THR cc_start: 0.8176 (t) cc_final: 0.7827 (p) REVERT: B 511 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6480 (tm-30) REVERT: B 537 ILE cc_start: 0.5820 (OUTLIER) cc_final: 0.5462 (mt) REVERT: B 560 ASP cc_start: 0.7540 (m-30) cc_final: 0.7209 (m-30) REVERT: B 564 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 578 THR cc_start: 0.8052 (m) cc_final: 0.7724 (p) REVERT: B 603 ASP cc_start: 0.7141 (t0) cc_final: 0.6781 (t0) REVERT: B 705 LYS cc_start: 0.8227 (mppt) cc_final: 0.7777 (mppt) outliers start: 52 outliers final: 36 residues processed: 327 average time/residue: 0.3004 time to fit residues: 131.7829 Evaluate side-chains 332 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 290 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 83 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 611 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11625 Z= 0.184 Angle : 0.557 8.592 15714 Z= 0.296 Chirality : 0.043 0.251 1703 Planarity : 0.004 0.068 2015 Dihedral : 9.839 82.911 1707 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.25 % Favored : 93.32 % Rotamer: Outliers : 4.63 % Allowed : 19.34 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.69 (0.23), residues: 1377 helix: 1.24 (0.21), residues: 635 sheet: 0.53 (0.51), residues: 109 loop : -2.58 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 409 HIS 0.003 0.000 HIS A 675 PHE 0.013 0.001 PHE A 393 TYR 0.011 0.001 TYR B 164 ARG 0.005 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 299 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8128 (mtpp) REVERT: A 45 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: A 100 MET cc_start: 0.6654 (tmm) cc_final: 0.6389 (tmm) REVERT: A 140 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6927 (p0) REVERT: A 238 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6852 (mm-30) REVERT: A 239 GLU cc_start: 0.6912 (tp30) cc_final: 0.6708 (tp30) REVERT: A 241 LYS cc_start: 0.7561 (tppp) cc_final: 0.7298 (ttmt) REVERT: A 244 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 263 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7496 (mp) REVERT: A 264 GLU cc_start: 0.7051 (pm20) cc_final: 0.6777 (pm20) REVERT: A 271 GLN cc_start: 0.7613 (pp30) cc_final: 0.7229 (pp30) REVERT: A 319 THR cc_start: 0.7102 (m) cc_final: 0.6660 (t) REVERT: A 342 ASN cc_start: 0.7207 (t0) cc_final: 0.6849 (t0) REVERT: A 360 ASN cc_start: 0.7400 (t0) cc_final: 0.6712 (t0) REVERT: A 364 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6652 (tm-30) REVERT: A 410 GLU cc_start: 0.7764 (pt0) cc_final: 0.7484 (pt0) REVERT: A 590 LYS cc_start: 0.7563 (mppt) cc_final: 0.7345 (mppt) REVERT: A 594 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 603 ASP cc_start: 0.6969 (t70) cc_final: 0.6719 (t0) REVERT: A 725 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7739 (mt) REVERT: B 21 MET cc_start: 0.7223 (ptm) cc_final: 0.6854 (ptm) REVERT: B 24 ILE cc_start: 0.8287 (mm) cc_final: 0.7605 (mm) REVERT: B 28 MET cc_start: 0.6602 (mmm) cc_final: 0.6048 (mmm) REVERT: B 86 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 132 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6773 (mm-30) REVERT: B 148 ARG cc_start: 0.7767 (ttt-90) cc_final: 0.7495 (mtp85) REVERT: B 239 GLU cc_start: 0.7783 (tp30) cc_final: 0.7546 (tp30) REVERT: B 397 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 398 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8403 (mtmm) REVERT: B 429 THR cc_start: 0.8193 (t) cc_final: 0.7892 (p) REVERT: B 511 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6490 (tm-30) REVERT: B 537 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5636 (mt) REVERT: B 560 ASP cc_start: 0.7561 (m-30) cc_final: 0.7208 (m-30) REVERT: B 578 THR cc_start: 0.8097 (m) cc_final: 0.7734 (p) REVERT: B 603 ASP cc_start: 0.7226 (t0) cc_final: 0.6853 (t0) REVERT: B 705 LYS cc_start: 0.8221 (mppt) cc_final: 0.7775 (mppt) outliers start: 56 outliers final: 40 residues processed: 331 average time/residue: 0.3038 time to fit residues: 133.9895 Evaluate side-chains 329 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 284 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 91 optimal weight: 0.0050 chunk 66 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11625 Z= 0.165 Angle : 0.577 8.610 15714 Z= 0.300 Chirality : 0.043 0.253 1703 Planarity : 0.004 0.066 2015 Dihedral : 9.672 81.203 1707 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.95 % Favored : 93.68 % Rotamer: Outliers : 3.64 % Allowed : 20.74 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.66 (0.23), residues: 1377 helix: 1.26 (0.22), residues: 635 sheet: 0.44 (0.51), residues: 110 loop : -2.54 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.003 0.000 HIS A 675 PHE 0.012 0.001 PHE A 393 TYR 0.010 0.001 TYR B 371 ARG 0.005 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 291 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8018 (mtpp) REVERT: A 45 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: A 100 MET cc_start: 0.6661 (tmm) cc_final: 0.6393 (tmm) REVERT: A 140 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6944 (p0) REVERT: A 238 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6852 (mm-30) REVERT: A 239 GLU cc_start: 0.6899 (tp30) cc_final: 0.6691 (tp30) REVERT: A 241 LYS cc_start: 0.7550 (tppp) cc_final: 0.7289 (ttmt) REVERT: A 244 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 264 GLU cc_start: 0.7059 (pm20) cc_final: 0.6772 (pm20) REVERT: A 271 GLN cc_start: 0.7597 (pp30) cc_final: 0.7224 (pp30) REVERT: A 319 THR cc_start: 0.7139 (m) cc_final: 0.6679 (t) REVERT: A 342 ASN cc_start: 0.7219 (t0) cc_final: 0.6860 (t0) REVERT: A 360 ASN cc_start: 0.7328 (t0) cc_final: 0.6651 (t0) REVERT: A 364 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6657 (tm-30) REVERT: A 410 GLU cc_start: 0.7746 (pt0) cc_final: 0.7490 (pt0) REVERT: A 590 LYS cc_start: 0.7566 (mppt) cc_final: 0.7346 (mppt) REVERT: A 594 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 603 ASP cc_start: 0.7008 (t70) cc_final: 0.6741 (t0) REVERT: A 623 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7634 (mtpp) REVERT: A 725 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7756 (mt) REVERT: B 15 PHE cc_start: 0.6669 (t80) cc_final: 0.5780 (t80) REVERT: B 21 MET cc_start: 0.7213 (ptm) cc_final: 0.6844 (ptm) REVERT: B 24 ILE cc_start: 0.8295 (mm) cc_final: 0.7593 (mm) REVERT: B 28 MET cc_start: 0.6517 (mmm) cc_final: 0.5936 (mmm) REVERT: B 86 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7650 (tm-30) REVERT: B 127 MET cc_start: 0.7549 (tpp) cc_final: 0.7276 (mmm) REVERT: B 132 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6772 (mm-30) REVERT: B 148 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7549 (mtp85) REVERT: B 397 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 398 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8560 (mtmt) REVERT: B 429 THR cc_start: 0.8205 (t) cc_final: 0.7881 (p) REVERT: B 511 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6478 (tm-30) REVERT: B 537 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5614 (mt) REVERT: B 560 ASP cc_start: 0.7551 (m-30) cc_final: 0.7173 (m-30) REVERT: B 564 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6825 (mm-30) REVERT: B 578 THR cc_start: 0.8065 (m) cc_final: 0.7740 (p) REVERT: B 603 ASP cc_start: 0.7218 (t0) cc_final: 0.6861 (t0) REVERT: B 705 LYS cc_start: 0.8234 (mppt) cc_final: 0.7793 (mppt) outliers start: 44 outliers final: 34 residues processed: 315 average time/residue: 0.2962 time to fit residues: 124.3895 Evaluate side-chains 326 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 288 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 81 optimal weight: 1.9990 chunk 132 optimal weight: 0.1980 overall best weight: 0.4220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11625 Z= 0.163 Angle : 0.570 8.855 15714 Z= 0.299 Chirality : 0.042 0.250 1703 Planarity : 0.004 0.066 2015 Dihedral : 9.408 78.806 1707 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.25 % Favored : 93.39 % Rotamer: Outliers : 3.72 % Allowed : 20.91 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.59 (0.23), residues: 1377 helix: 1.29 (0.22), residues: 635 sheet: 0.58 (0.51), residues: 108 loop : -2.49 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 720 HIS 0.006 0.000 HIS B 612 PHE 0.014 0.001 PHE B 15 TYR 0.018 0.001 TYR A 262 ARG 0.004 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 295 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8027 (mtpp) REVERT: A 45 ASP cc_start: 0.7018 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: A 100 MET cc_start: 0.6660 (tmm) cc_final: 0.6378 (tmm) REVERT: A 238 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6847 (mm-30) REVERT: A 239 GLU cc_start: 0.6893 (tp30) cc_final: 0.6693 (tp30) REVERT: A 241 LYS cc_start: 0.7551 (tppp) cc_final: 0.7296 (ttmt) REVERT: A 244 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6972 (tm-30) REVERT: A 264 GLU cc_start: 0.7223 (pm20) cc_final: 0.6897 (pm20) REVERT: A 271 GLN cc_start: 0.7592 (pp30) cc_final: 0.7209 (pp30) REVERT: A 319 THR cc_start: 0.7141 (m) cc_final: 0.6665 (t) REVERT: A 360 ASN cc_start: 0.7400 (t0) cc_final: 0.6703 (t0) REVERT: A 364 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6665 (tm-30) REVERT: A 410 GLU cc_start: 0.7733 (pt0) cc_final: 0.7477 (pt0) REVERT: A 590 LYS cc_start: 0.7571 (mppt) cc_final: 0.7354 (mppt) REVERT: A 594 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 603 ASP cc_start: 0.7010 (t70) cc_final: 0.6742 (t0) REVERT: A 623 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7634 (mtpp) REVERT: A 725 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7748 (mt) REVERT: B 21 MET cc_start: 0.7238 (ptm) cc_final: 0.6906 (ptm) REVERT: B 24 ILE cc_start: 0.8285 (mm) cc_final: 0.7542 (mm) REVERT: B 28 MET cc_start: 0.6615 (mmm) cc_final: 0.6078 (mmm) REVERT: B 67 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 86 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 109 ASP cc_start: 0.7213 (t70) cc_final: 0.6899 (t0) REVERT: B 127 MET cc_start: 0.7499 (tpp) cc_final: 0.7180 (mmt) REVERT: B 132 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6761 (mm-30) REVERT: B 148 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7369 (mtp85) REVERT: B 397 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7179 (tm-30) REVERT: B 398 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8563 (mtmt) REVERT: B 429 THR cc_start: 0.8202 (t) cc_final: 0.7874 (p) REVERT: B 511 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6488 (tm-30) REVERT: B 537 ILE cc_start: 0.5953 (OUTLIER) cc_final: 0.5607 (mt) REVERT: B 560 ASP cc_start: 0.7559 (m-30) cc_final: 0.7169 (m-30) REVERT: B 564 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6808 (mm-30) REVERT: B 578 THR cc_start: 0.8062 (m) cc_final: 0.7751 (p) REVERT: B 603 ASP cc_start: 0.7230 (t0) cc_final: 0.6869 (t0) REVERT: B 623 LYS cc_start: 0.7597 (ttpp) cc_final: 0.7350 (ttpp) REVERT: B 705 LYS cc_start: 0.8236 (mppt) cc_final: 0.7790 (mppt) outliers start: 45 outliers final: 32 residues processed: 320 average time/residue: 0.3002 time to fit residues: 128.7060 Evaluate side-chains 329 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 294 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 127 optimal weight: 0.0370 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 117 optimal weight: 0.0670 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 300 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11625 Z= 0.149 Angle : 0.570 9.280 15714 Z= 0.295 Chirality : 0.042 0.250 1703 Planarity : 0.004 0.064 2015 Dihedral : 8.926 75.602 1703 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.37 % Favored : 94.26 % Rotamer: Outliers : 2.89 % Allowed : 22.23 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.49 (0.23), residues: 1377 helix: 1.38 (0.22), residues: 633 sheet: 0.71 (0.51), residues: 108 loop : -2.45 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 399 HIS 0.002 0.000 HIS A 675 PHE 0.010 0.001 PHE B 421 TYR 0.012 0.001 TYR B 371 ARG 0.005 0.000 ARG A 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 293 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8009 (mtpp) REVERT: A 45 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: A 100 MET cc_start: 0.6643 (tmm) cc_final: 0.6358 (tmm) REVERT: A 241 LYS cc_start: 0.7555 (tppp) cc_final: 0.7308 (ttmt) REVERT: A 244 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6976 (tm-30) REVERT: A 264 GLU cc_start: 0.7176 (pm20) cc_final: 0.6879 (pm20) REVERT: A 319 THR cc_start: 0.7027 (m) cc_final: 0.6558 (t) REVERT: A 360 ASN cc_start: 0.7290 (t0) cc_final: 0.6581 (t0) REVERT: A 364 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6629 (tm-30) REVERT: A 533 LEU cc_start: 0.7708 (pp) cc_final: 0.7410 (pp) REVERT: A 590 LYS cc_start: 0.7565 (mppt) cc_final: 0.7337 (mppt) REVERT: A 594 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7089 (tt0) REVERT: A 623 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7593 (mtpp) REVERT: A 725 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7734 (mt) REVERT: B 21 MET cc_start: 0.7211 (ptm) cc_final: 0.6878 (ptm) REVERT: B 24 ILE cc_start: 0.8268 (mm) cc_final: 0.7541 (mm) REVERT: B 28 MET cc_start: 0.6576 (mmm) cc_final: 0.6000 (mmm) REVERT: B 86 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 127 MET cc_start: 0.7442 (tpp) cc_final: 0.7109 (mmt) REVERT: B 132 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6760 (mm-30) REVERT: B 148 ARG cc_start: 0.7731 (ttt-90) cc_final: 0.7365 (mtp85) REVERT: B 397 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7165 (tm-30) REVERT: B 398 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8477 (mtmt) REVERT: B 511 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6507 (tm-30) REVERT: B 537 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.5561 (mt) REVERT: B 560 ASP cc_start: 0.7552 (m-30) cc_final: 0.7158 (m-30) REVERT: B 578 THR cc_start: 0.8003 (m) cc_final: 0.7698 (p) REVERT: B 603 ASP cc_start: 0.7163 (t0) cc_final: 0.6823 (t0) REVERT: B 705 LYS cc_start: 0.8248 (mppt) cc_final: 0.7794 (mppt) outliers start: 35 outliers final: 27 residues processed: 312 average time/residue: 0.2659 time to fit residues: 111.4295 Evaluate side-chains 313 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 283 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: