Starting phenix.real_space_refine on Thu Feb 15 08:47:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2r_20240/02_2024/6p2r_20240_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 62 5.16 5 C 7721 2.51 5 N 1888 2.21 5 O 2038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 27": "NH1" <-> "NH2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11712 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5879 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 31, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5605 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 31, 'TRANS': 658} Chain breaks: 1 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'CPL': 1, 'NAG': 1, 'NNM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'CPL': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.68, per 1000 atoms: 0.57 Number of scatterers: 11712 At special positions: 0 Unit cell: (109.074, 107.016, 108.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 3 15.00 O 2038 8.00 N 1888 7.00 C 7721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 511 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 390 " " NAG B1001 " - " ASN B 131 " Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2654 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 13 sheets defined 45.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.886A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 159 removed outlier: 4.479A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 184 Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 214 through 231 Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.647A pdb=" N VAL A 244 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 251 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 252 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 295 removed outlier: 4.163A pdb=" N VAL A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 533 through 549 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 587 through 612 removed outlier: 4.328A pdb=" N ALA A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 653 through 655 No H-bonds generated for 'chain 'A' and resid 653 through 655' Processing helix chain 'A' and resid 657 through 676 removed outlier: 3.719A pdb=" N PHE A 662 " --> pdb=" O PRO A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 703 Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 715 through 721 removed outlier: 3.917A pdb=" N LYS A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 741 removed outlier: 3.594A pdb=" N TYR A 741 " --> pdb=" O LEU A 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'B' and resid 58 through 79 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.652A pdb=" N LYS B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 removed outlier: 3.946A pdb=" N ALA B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 203 through 223 removed outlier: 4.006A pdb=" N GLN B 223 " --> pdb=" O MET B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.584A pdb=" N LEU B 254 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 255 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 256 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 257 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 260 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 295 through 311 removed outlier: 3.503A pdb=" N PHE B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 385 through 387 No H-bonds generated for 'chain 'B' and resid 385 through 387' Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 548 through 566 Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 611 through 622 Processing helix chain 'B' and resid 625 through 633 Processing helix chain 'B' and resid 642 through 651 Processing helix chain 'B' and resid 653 through 668 Proline residue: B 665 - end of helix Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 679 through 694 removed outlier: 3.719A pdb=" N TYR B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 684 " --> pdb=" O PRO B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 701 No H-bonds generated for 'chain 'B' and resid 699 through 701' Processing helix chain 'B' and resid 704 through 727 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.516A pdb=" N SER B 732 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing sheet with id= A, first strand: chain 'A' and resid 21 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 334 through 337 Processing sheet with id= C, first strand: chain 'A' and resid 373 through 377 Processing sheet with id= D, first strand: chain 'A' and resid 443 through 447 Processing sheet with id= E, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.938A pdb=" N HIS A 348 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 360 " --> pdb=" O HIS A 348 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 478 through 486 removed outlier: 4.356A pdb=" N HIS A 482 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU A 495 " --> pdb=" O HIS A 482 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 484 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN A 493 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 571 through 576 removed outlier: 6.352A pdb=" N VAL A 581 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY A 575 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 360 through 362 Processing sheet with id= I, first strand: chain 'B' and resid 389 through 392 Processing sheet with id= J, first strand: chain 'B' and resid 491 through 494 removed outlier: 3.584A pdb=" N VAL B 510 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 348 through 353 removed outlier: 3.803A pdb=" N SER B 350 " --> pdb=" O THR B 528 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 528 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS B 352 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE B 526 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 426 through 433 removed outlier: 4.307A pdb=" N GLU B 442 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 458 through 465 removed outlier: 3.635A pdb=" N LYS B 484 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 480 " --> pdb=" O MET B 463 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1263 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: 3.32 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1747 1.30 - 1.43: 3697 1.43 - 1.56: 6513 1.56 - 1.69: 13 1.69 - 1.82: 105 Bond restraints: 12075 Sorted by residual: bond pdb=" C18 NNM A1003 " pdb=" C19 NNM A1003 " ideal model delta sigma weight residual 1.332 1.562 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C27 NNM A1003 " pdb=" C28 NNM A1003 " ideal model delta sigma weight residual 1.577 1.347 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C7 NNM A1003 " pdb=" C8 NNM A1003 " ideal model delta sigma weight residual 1.547 1.329 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C38 NNM A1003 " pdb=" C39 NNM A1003 " ideal model delta sigma weight residual 1.327 1.544 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C12 NNM A1003 " pdb=" C13 NNM A1003 " ideal model delta sigma weight residual 1.569 1.355 0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 12070 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.14: 242 105.14 - 112.37: 5867 112.37 - 119.60: 4131 119.60 - 126.83: 5892 126.83 - 134.06: 256 Bond angle restraints: 16388 Sorted by residual: angle pdb=" C17 NNM A1003 " pdb=" C18 NNM A1003 " pdb=" C20 NNM A1003 " ideal model delta sigma weight residual 74.54 123.70 -49.16 3.00e+00 1.11e-01 2.69e+02 angle pdb=" C22 NNM A1003 " pdb=" C23 NNM A1003 " pdb=" C25 NNM A1003 " ideal model delta sigma weight residual 74.54 121.28 -46.74 3.00e+00 1.11e-01 2.43e+02 angle pdb=" C27 NNM A1003 " pdb=" C28 NNM A1003 " pdb=" C30 NNM A1003 " ideal model delta sigma weight residual 74.53 120.18 -45.65 3.00e+00 1.11e-01 2.32e+02 angle pdb=" C37 NNM A1003 " pdb=" C38 NNM A1003 " pdb=" C40 NNM A1003 " ideal model delta sigma weight residual 74.52 119.88 -45.36 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C12 NNM A1003 " pdb=" C13 NNM A1003 " pdb=" C15 NNM A1003 " ideal model delta sigma weight residual 74.49 119.75 -45.26 3.00e+00 1.11e-01 2.28e+02 ... (remaining 16383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 6870 35.34 - 70.68: 101 70.68 - 106.01: 13 106.01 - 141.35: 0 141.35 - 176.69: 2 Dihedral angle restraints: 6986 sinusoidal: 2844 harmonic: 4142 Sorted by residual: dihedral pdb=" CA PRO A 530 " pdb=" C PRO A 530 " pdb=" N ALA A 531 " pdb=" CA ALA A 531 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA GLY A 160 " pdb=" C GLY A 160 " pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta harmonic sigma weight residual 180.00 -152.98 -27.02 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA TRP B 583 " pdb=" C TRP B 583 " pdb=" N PRO B 584 " pdb=" CA PRO B 584 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 6983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1144 0.048 - 0.097: 447 0.097 - 0.145: 115 0.145 - 0.193: 32 0.193 - 0.241: 8 Chirality restraints: 1746 Sorted by residual: chirality pdb=" CG LEU B 59 " pdb=" CB LEU B 59 " pdb=" CD1 LEU B 59 " pdb=" CD2 LEU B 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2 CPL B1003 " pdb=" C1 CPL B1003 " pdb=" C3 CPL B1003 " pdb=" O2 CPL B1003 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 30 " pdb=" CA ILE A 30 " pdb=" CG1 ILE A 30 " pdb=" CG2 ILE A 30 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1743 not shown) Planarity restraints: 2029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 727 " 0.036 2.00e-02 2.50e+03 2.32e-02 1.34e+01 pdb=" CG TRP A 727 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 727 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 727 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 727 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 727 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 727 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 727 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 727 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 727 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 654 " -0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO B 655 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 655 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 655 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 590 " 0.026 2.00e-02 2.50e+03 1.91e-02 9.16e+00 pdb=" CG TRP A 590 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 590 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 590 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 590 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 590 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 590 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 590 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 590 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 590 " -0.003 2.00e-02 2.50e+03 ... (remaining 2026 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2301 2.77 - 3.30: 10909 3.30 - 3.83: 20421 3.83 - 4.37: 24318 4.37 - 4.90: 41425 Nonbonded interactions: 99374 Sorted by model distance: nonbonded pdb=" OE2 GLU B 93 " pdb=" OH TYR B 142 " model vdw 2.236 2.440 nonbonded pdb=" O LEU A 151 " pdb=" OG1 THR A 155 " model vdw 2.249 2.440 nonbonded pdb=" O PHE A 139 " pdb=" OG SER A 143 " model vdw 2.259 2.440 nonbonded pdb=" O ASN B 191 " pdb=" OG1 THR B 195 " model vdw 2.267 2.440 nonbonded pdb=" O PRO B 68 " pdb=" OG1 THR B 72 " model vdw 2.280 2.440 ... (remaining 99369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.720 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 34.480 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.011 0.230 12075 Z= 0.671 Angle : 1.476 49.164 16388 Z= 0.648 Chirality : 0.057 0.241 1746 Planarity : 0.008 0.086 2027 Dihedral : 13.101 176.689 4329 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.57 % Allowed : 5.01 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.16), residues: 1413 helix: -3.27 (0.12), residues: 655 sheet: -3.24 (0.45), residues: 102 loop : -2.61 (0.19), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP A 727 HIS 0.026 0.002 HIS A 632 PHE 0.040 0.004 PHE B 301 TYR 0.042 0.003 TYR A 573 ARG 0.011 0.001 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 271 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8457 (tp) cc_final: 0.8178 (tp) REVERT: A 48 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7784 (tttp) REVERT: A 148 THR cc_start: 0.8947 (t) cc_final: 0.8722 (m) REVERT: A 229 MET cc_start: 0.8397 (ttm) cc_final: 0.8010 (mtp) REVERT: A 264 LYS cc_start: 0.8139 (tmtp) cc_final: 0.7827 (tptp) REVERT: A 315 LYS cc_start: 0.8103 (mtpm) cc_final: 0.7899 (mmtp) REVERT: A 340 THR cc_start: 0.8859 (m) cc_final: 0.8534 (p) REVERT: A 364 TYR cc_start: 0.7322 (t80) cc_final: 0.6582 (t80) REVERT: A 370 ASN cc_start: 0.7506 (m-40) cc_final: 0.7159 (m-40) REVERT: A 398 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6632 (mtt90) REVERT: A 407 ARG cc_start: 0.7645 (mmt90) cc_final: 0.7387 (mmt-90) REVERT: A 474 MET cc_start: 0.8288 (mmm) cc_final: 0.7889 (mtp) REVERT: A 525 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7645 (mmt-90) REVERT: A 538 ILE cc_start: 0.8408 (mm) cc_final: 0.8190 (mt) REVERT: A 588 ILE cc_start: 0.8541 (tt) cc_final: 0.8275 (mt) REVERT: A 603 ILE cc_start: 0.7454 (tp) cc_final: 0.7034 (pt) REVERT: A 687 TYR cc_start: 0.8059 (m-10) cc_final: 0.7801 (m-80) REVERT: A 717 LEU cc_start: 0.7518 (tp) cc_final: 0.7007 (mt) REVERT: B 80 MET cc_start: 0.8218 (mpp) cc_final: 0.7852 (mtm) REVERT: B 219 MET cc_start: 0.8577 (mmt) cc_final: 0.8255 (mmt) REVERT: B 543 TYR cc_start: 0.6925 (m-80) cc_final: 0.6604 (m-80) REVERT: B 699 LYS cc_start: 0.7945 (mttt) cc_final: 0.7658 (mptt) REVERT: B 753 ILE cc_start: 0.8266 (tt) cc_final: 0.7426 (tt) outliers start: 7 outliers final: 4 residues processed: 276 average time/residue: 0.2512 time to fit residues: 95.9376 Evaluate side-chains 154 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 611 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 59 optimal weight: 0.0270 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 111 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 350 HIS A 458 GLN A 482 HIS A 546 HIS A 586 ASN A 715 GLN A 719 GLN A 732 ASN B 106 HIS B 110 HIS B 221 HIS B 308 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN B 633 GLN B 741 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12075 Z= 0.185 Angle : 0.933 25.537 16388 Z= 0.393 Chirality : 0.042 0.160 1746 Planarity : 0.005 0.055 2027 Dihedral : 12.364 178.861 1744 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.18 % Allowed : 10.34 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.19), residues: 1413 helix: -1.04 (0.17), residues: 644 sheet: -2.79 (0.50), residues: 93 loop : -2.20 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 727 HIS 0.008 0.001 HIS A 632 PHE 0.024 0.002 PHE B 301 TYR 0.016 0.001 TYR A 734 ARG 0.006 0.000 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8571 (tp) cc_final: 0.8259 (mm) REVERT: A 148 THR cc_start: 0.8959 (t) cc_final: 0.8694 (m) REVERT: A 264 LYS cc_start: 0.8279 (tmtp) cc_final: 0.7955 (tptp) REVERT: A 315 LYS cc_start: 0.8231 (mtpm) cc_final: 0.7920 (mmtp) REVERT: A 370 ASN cc_start: 0.7377 (m-40) cc_final: 0.6884 (m-40) REVERT: A 425 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7129 (ttpt) REVERT: A 446 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 459 GLU cc_start: 0.8224 (pt0) cc_final: 0.7939 (pm20) REVERT: A 474 MET cc_start: 0.8208 (mmm) cc_final: 0.7872 (mtp) REVERT: A 610 SER cc_start: 0.8750 (t) cc_final: 0.8474 (p) REVERT: A 622 LYS cc_start: 0.8721 (mttp) cc_final: 0.8498 (mtmm) REVERT: B 202 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7842 (pp) REVERT: B 527 GLU cc_start: 0.6804 (tp30) cc_final: 0.6501 (tp30) REVERT: B 590 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8398 (tp) outliers start: 27 outliers final: 11 residues processed: 190 average time/residue: 0.2356 time to fit residues: 65.3968 Evaluate side-chains 156 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 0.0010 chunk 87 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN B 86 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12075 Z= 0.345 Angle : 0.957 23.196 16388 Z= 0.404 Chirality : 0.044 0.149 1746 Planarity : 0.005 0.053 2027 Dihedral : 11.708 176.223 1741 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.80 % Allowed : 10.82 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.21), residues: 1413 helix: -0.20 (0.19), residues: 668 sheet: -2.71 (0.51), residues: 90 loop : -1.91 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 727 HIS 0.011 0.001 HIS A 632 PHE 0.019 0.002 PHE B 301 TYR 0.017 0.002 TYR A 633 ARG 0.007 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 144 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8570 (tp) cc_final: 0.8354 (mm) REVERT: A 101 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8482 (tp) REVERT: A 315 LYS cc_start: 0.8092 (mtpm) cc_final: 0.7801 (mmtp) REVERT: A 370 ASN cc_start: 0.7756 (m-40) cc_final: 0.7425 (m-40) REVERT: A 396 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8412 (ttpt) REVERT: A 398 ARG cc_start: 0.6988 (mtt180) cc_final: 0.6517 (mtt90) REVERT: A 425 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7213 (ttpt) REVERT: A 447 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 459 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: A 474 MET cc_start: 0.8194 (mmm) cc_final: 0.7852 (mtp) REVERT: A 495 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 610 SER cc_start: 0.8760 (t) cc_final: 0.8509 (p) REVERT: A 622 LYS cc_start: 0.8706 (mttp) cc_final: 0.8495 (mtmm) REVERT: A 672 ASP cc_start: 0.8117 (t70) cc_final: 0.7893 (t70) REVERT: B 126 TYR cc_start: 0.8506 (t80) cc_final: 0.8261 (t80) REVERT: B 202 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7974 (pp) REVERT: B 322 MET cc_start: 0.8740 (mmm) cc_final: 0.8186 (mmm) REVERT: B 527 GLU cc_start: 0.6988 (tp30) cc_final: 0.6565 (tp30) REVERT: B 590 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8462 (tp) REVERT: B 656 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8342 (tp) REVERT: B 672 VAL cc_start: 0.8778 (t) cc_final: 0.8501 (p) outliers start: 47 outliers final: 24 residues processed: 181 average time/residue: 0.2009 time to fit residues: 55.4317 Evaluate side-chains 157 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 114 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS B 327 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12075 Z= 0.203 Angle : 0.908 23.431 16388 Z= 0.372 Chirality : 0.041 0.146 1746 Planarity : 0.004 0.048 2027 Dihedral : 11.148 174.353 1741 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.80 % Allowed : 11.87 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1413 helix: 0.36 (0.20), residues: 670 sheet: -2.38 (0.53), residues: 87 loop : -1.75 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 727 HIS 0.007 0.001 HIS A 346 PHE 0.014 0.001 PHE B 301 TYR 0.018 0.001 TYR A 364 ARG 0.004 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 146 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 148 THR cc_start: 0.8977 (t) cc_final: 0.8653 (m) REVERT: A 233 SER cc_start: 0.9024 (p) cc_final: 0.8797 (p) REVERT: A 315 LYS cc_start: 0.8064 (mtpm) cc_final: 0.7776 (mmtp) REVERT: A 364 TYR cc_start: 0.7427 (t80) cc_final: 0.6604 (t80) REVERT: A 368 ASP cc_start: 0.7375 (m-30) cc_final: 0.6023 (m-30) REVERT: A 396 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8544 (ttpt) REVERT: A 398 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6466 (mtt90) REVERT: A 447 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 459 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: A 474 MET cc_start: 0.8210 (mmm) cc_final: 0.7815 (mtp) REVERT: A 478 TYR cc_start: 0.7826 (m-80) cc_final: 0.7393 (m-10) REVERT: A 495 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6715 (tm-30) REVERT: A 610 SER cc_start: 0.8685 (t) cc_final: 0.8471 (p) REVERT: B 126 TYR cc_start: 0.8525 (t80) cc_final: 0.8212 (t80) REVERT: B 202 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7926 (pp) REVERT: B 259 MET cc_start: 0.8418 (tmm) cc_final: 0.7576 (ttp) REVERT: B 322 MET cc_start: 0.8791 (mmm) cc_final: 0.8256 (mmm) REVERT: B 527 GLU cc_start: 0.6993 (tp30) cc_final: 0.6541 (tp30) REVERT: B 605 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8284 (pt) REVERT: B 616 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8340 (t) REVERT: B 650 MET cc_start: 0.8657 (mmm) cc_final: 0.8364 (tpp) REVERT: B 656 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 672 VAL cc_start: 0.8698 (t) cc_final: 0.8428 (p) outliers start: 47 outliers final: 18 residues processed: 183 average time/residue: 0.2231 time to fit residues: 62.9515 Evaluate side-chains 154 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 713 TRP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12075 Z= 0.349 Angle : 0.941 23.064 16388 Z= 0.393 Chirality : 0.044 0.165 1746 Planarity : 0.004 0.052 2027 Dihedral : 10.925 170.437 1741 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.04 % Allowed : 12.68 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1413 helix: 0.46 (0.20), residues: 667 sheet: -2.35 (0.53), residues: 90 loop : -1.57 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 727 HIS 0.008 0.001 HIS A 632 PHE 0.016 0.002 PHE A 81 TYR 0.011 0.002 TYR A 364 ARG 0.004 0.001 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 130 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7479 (mp0) REVERT: A 233 SER cc_start: 0.9073 (p) cc_final: 0.8844 (p) REVERT: A 315 LYS cc_start: 0.8031 (mtpm) cc_final: 0.7724 (mmtp) REVERT: A 359 GLN cc_start: 0.5960 (pt0) cc_final: 0.5737 (pt0) REVERT: A 398 ARG cc_start: 0.7228 (mtt180) cc_final: 0.6417 (mtt-85) REVERT: A 425 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7294 (ttpt) REVERT: A 459 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 478 TYR cc_start: 0.7815 (m-80) cc_final: 0.7325 (m-10) REVERT: A 610 SER cc_start: 0.8800 (t) cc_final: 0.8578 (p) REVERT: B 202 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7994 (pp) REVERT: B 322 MET cc_start: 0.8846 (mmm) cc_final: 0.8337 (mmm) REVERT: B 527 GLU cc_start: 0.7206 (tp30) cc_final: 0.6755 (tp30) REVERT: B 605 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8349 (pt) REVERT: B 616 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8421 (t) REVERT: B 656 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8396 (tp) REVERT: B 672 VAL cc_start: 0.8842 (t) cc_final: 0.8575 (p) REVERT: B 686 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8672 (mt) outliers start: 50 outliers final: 30 residues processed: 170 average time/residue: 0.1926 time to fit residues: 50.7117 Evaluate side-chains 159 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 712 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS A 612 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12075 Z= 0.271 Angle : 0.918 23.061 16388 Z= 0.380 Chirality : 0.043 0.258 1746 Planarity : 0.004 0.052 2027 Dihedral : 10.609 169.399 1739 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.39 % Allowed : 14.38 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1413 helix: 0.64 (0.20), residues: 661 sheet: -2.27 (0.53), residues: 90 loop : -1.49 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 727 HIS 0.007 0.001 HIS A 632 PHE 0.014 0.002 PHE A 537 TYR 0.017 0.001 TYR A 364 ARG 0.003 0.000 ARG B 702 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 315 LYS cc_start: 0.8023 (mtpm) cc_final: 0.7686 (mmtp) REVERT: A 364 TYR cc_start: 0.7422 (t80) cc_final: 0.6346 (t80) REVERT: A 396 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8444 (tttt) REVERT: A 398 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6323 (mtt-85) REVERT: A 459 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: A 478 TYR cc_start: 0.7799 (m-80) cc_final: 0.7247 (m-10) REVERT: A 610 SER cc_start: 0.8779 (t) cc_final: 0.8569 (p) REVERT: B 202 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7982 (pp) REVERT: B 322 MET cc_start: 0.8833 (mmm) cc_final: 0.8363 (mmm) REVERT: B 527 GLU cc_start: 0.7216 (tp30) cc_final: 0.6769 (tp30) REVERT: B 605 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8314 (pt) REVERT: B 650 MET cc_start: 0.8813 (mmm) cc_final: 0.8571 (mmp) REVERT: B 656 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8398 (tp) REVERT: B 672 VAL cc_start: 0.8777 (t) cc_final: 0.8523 (p) outliers start: 42 outliers final: 27 residues processed: 166 average time/residue: 0.1957 time to fit residues: 50.1582 Evaluate side-chains 156 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 712 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12075 Z= 0.211 Angle : 0.902 22.642 16388 Z= 0.370 Chirality : 0.042 0.195 1746 Planarity : 0.004 0.051 2027 Dihedral : 10.419 168.208 1739 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.63 % Allowed : 14.62 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1413 helix: 0.85 (0.20), residues: 659 sheet: -2.27 (0.51), residues: 94 loop : -1.38 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 727 HIS 0.016 0.001 HIS A 546 PHE 0.013 0.001 PHE A 537 TYR 0.015 0.001 TYR A 364 ARG 0.004 0.000 ARG B 702 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 132 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.8939 (t) cc_final: 0.8633 (m) REVERT: A 315 LYS cc_start: 0.8029 (mtpm) cc_final: 0.7704 (mmtp) REVERT: A 364 TYR cc_start: 0.7408 (t80) cc_final: 0.6427 (t80) REVERT: A 396 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8408 (ttpt) REVERT: A 398 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6283 (mtt-85) REVERT: A 459 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: A 478 TYR cc_start: 0.7817 (m-80) cc_final: 0.7254 (m-10) REVERT: B 202 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7895 (pp) REVERT: B 322 MET cc_start: 0.8845 (mmm) cc_final: 0.8361 (mmm) REVERT: B 527 GLU cc_start: 0.7303 (tp30) cc_final: 0.6882 (tp30) REVERT: B 605 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8277 (pt) REVERT: B 656 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 672 VAL cc_start: 0.8751 (t) cc_final: 0.8489 (p) outliers start: 45 outliers final: 29 residues processed: 164 average time/residue: 0.1968 time to fit residues: 49.9985 Evaluate side-chains 160 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 752 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 41 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12075 Z= 0.211 Angle : 0.898 22.232 16388 Z= 0.368 Chirality : 0.041 0.154 1746 Planarity : 0.004 0.049 2027 Dihedral : 10.218 166.581 1739 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.96 % Allowed : 14.94 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1413 helix: 0.95 (0.20), residues: 661 sheet: -2.15 (0.47), residues: 108 loop : -1.35 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 727 HIS 0.006 0.001 HIS A 346 PHE 0.013 0.001 PHE A 537 TYR 0.014 0.001 TYR A 364 ARG 0.003 0.000 ARG B 702 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 132 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.8931 (t) cc_final: 0.8620 (m) REVERT: A 315 LYS cc_start: 0.8040 (mtpm) cc_final: 0.7745 (mmtp) REVERT: A 364 TYR cc_start: 0.7423 (t80) cc_final: 0.6436 (t80) REVERT: A 368 ASP cc_start: 0.7251 (m-30) cc_final: 0.5633 (m-30) REVERT: A 396 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8419 (ttpt) REVERT: A 398 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6491 (mtt90) REVERT: A 459 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: A 478 TYR cc_start: 0.7796 (m-80) cc_final: 0.7317 (m-10) REVERT: A 546 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.6700 (m-70) REVERT: B 202 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7897 (pp) REVERT: B 322 MET cc_start: 0.8863 (mmm) cc_final: 0.8370 (mmm) REVERT: B 527 GLU cc_start: 0.7350 (tp30) cc_final: 0.6871 (tp30) REVERT: B 605 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8221 (pt) REVERT: B 656 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8415 (tp) REVERT: B 672 VAL cc_start: 0.8733 (t) cc_final: 0.8469 (p) outliers start: 49 outliers final: 33 residues processed: 167 average time/residue: 0.1938 time to fit residues: 50.5341 Evaluate side-chains 163 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 752 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 131 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12075 Z= 0.241 Angle : 0.907 22.094 16388 Z= 0.372 Chirality : 0.042 0.156 1746 Planarity : 0.004 0.050 2027 Dihedral : 10.190 165.802 1739 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.55 % Allowed : 15.35 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1413 helix: 0.97 (0.20), residues: 662 sheet: -2.01 (0.46), residues: 120 loop : -1.22 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 727 HIS 0.014 0.001 HIS A 546 PHE 0.015 0.001 PHE B 552 TYR 0.016 0.001 TYR A 364 ARG 0.004 0.000 ARG B 702 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.8926 (t) cc_final: 0.8604 (m) REVERT: A 315 LYS cc_start: 0.7994 (mtpm) cc_final: 0.7725 (mmtp) REVERT: A 364 TYR cc_start: 0.7489 (t80) cc_final: 0.6481 (t80) REVERT: A 368 ASP cc_start: 0.7296 (m-30) cc_final: 0.5741 (m-30) REVERT: A 398 ARG cc_start: 0.6952 (mtt180) cc_final: 0.6212 (mtt-85) REVERT: A 459 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: A 478 TYR cc_start: 0.7801 (m-80) cc_final: 0.7306 (m-10) REVERT: A 546 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.6840 (m-70) REVERT: B 202 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7912 (pp) REVERT: B 322 MET cc_start: 0.8870 (mmm) cc_final: 0.8372 (mmm) REVERT: B 527 GLU cc_start: 0.7353 (tp30) cc_final: 0.6882 (tp30) REVERT: B 605 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8230 (pt) REVERT: B 656 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 672 VAL cc_start: 0.8748 (t) cc_final: 0.8481 (p) outliers start: 44 outliers final: 36 residues processed: 158 average time/residue: 0.1989 time to fit residues: 48.9531 Evaluate side-chains 165 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 546 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 752 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0970 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 112 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 89 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12075 Z= 0.176 Angle : 0.895 21.997 16388 Z= 0.364 Chirality : 0.041 0.153 1746 Planarity : 0.004 0.049 2027 Dihedral : 10.058 164.467 1739 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.99 % Allowed : 15.91 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1413 helix: 1.04 (0.20), residues: 664 sheet: -1.96 (0.46), residues: 120 loop : -1.19 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 727 HIS 0.025 0.001 HIS A 546 PHE 0.014 0.001 PHE B 552 TYR 0.019 0.001 TYR A 364 ARG 0.004 0.000 ARG B 702 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.8897 (t) cc_final: 0.8607 (m) REVERT: A 315 LYS cc_start: 0.8039 (mtpm) cc_final: 0.7745 (mmtp) REVERT: A 364 TYR cc_start: 0.7481 (t80) cc_final: 0.6647 (t80) REVERT: A 368 ASP cc_start: 0.7261 (m-30) cc_final: 0.5751 (m-30) REVERT: A 370 ASN cc_start: 0.7508 (m110) cc_final: 0.7103 (m-40) REVERT: A 396 LYS cc_start: 0.8671 (tttt) cc_final: 0.8433 (tttt) REVERT: A 398 ARG cc_start: 0.6903 (mtt180) cc_final: 0.6158 (mtt-85) REVERT: A 459 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: A 478 TYR cc_start: 0.7782 (m-80) cc_final: 0.7275 (m-10) REVERT: A 546 HIS cc_start: 0.7771 (t-170) cc_final: 0.6948 (m-70) REVERT: A 719 GLN cc_start: 0.7526 (mm110) cc_final: 0.7307 (mm-40) REVERT: B 202 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7820 (pp) REVERT: B 322 MET cc_start: 0.8862 (mmm) cc_final: 0.8377 (mmm) REVERT: B 527 GLU cc_start: 0.7390 (tp30) cc_final: 0.6920 (tp30) REVERT: B 543 TYR cc_start: 0.7076 (m-80) cc_final: 0.6819 (m-80) REVERT: B 605 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8180 (pt) REVERT: B 656 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8380 (tp) REVERT: B 672 VAL cc_start: 0.8710 (t) cc_final: 0.8445 (p) outliers start: 37 outliers final: 30 residues processed: 160 average time/residue: 0.2020 time to fit residues: 50.1982 Evaluate side-chains 159 residues out of total 1238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 752 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS A 359 GLN A 360 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS A 612 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.170032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118936 restraints weight = 14489.271| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.00 r_work: 0.2983 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12075 Z= 0.307 Angle : 0.922 21.854 16388 Z= 0.381 Chirality : 0.044 0.156 1746 Planarity : 0.004 0.050 2027 Dihedral : 10.178 163.550 1739 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.07 % Allowed : 16.07 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1413 helix: 0.96 (0.20), residues: 658 sheet: -1.95 (0.45), residues: 119 loop : -1.12 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 727 HIS 0.007 0.001 HIS B 221 PHE 0.015 0.002 PHE A 121 TYR 0.017 0.001 TYR A 364 ARG 0.004 0.000 ARG B 702 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2568.28 seconds wall clock time: 47 minutes 54.04 seconds (2874.04 seconds total)