Starting phenix.real_space_refine on Thu Feb 15 01:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2c_10368/02_2024/6t2c_10368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2c_10368/02_2024/6t2c_10368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2c_10368/02_2024/6t2c_10368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2c_10368/02_2024/6t2c_10368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2c_10368/02_2024/6t2c_10368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t2c_10368/02_2024/6t2c_10368.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 6670 2.51 5 N 1853 2.21 5 O 2082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10700 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4145 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain: "B" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4996 Classifications: {'peptide': 626} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 599} Chain breaks: 2 Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 941 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 617 Classifications: {'RNA': 29} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 7, 'rna3p': 21} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.02, per 1000 atoms: 0.84 Number of scatterers: 10700 At special positions: 0 Unit cell: (104.749, 116.281, 94.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 29 15.00 Mg 1 11.99 O 2082 8.00 N 1853 7.00 C 6670 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: 6.29 Conformation dependent library (CDL) restraints added in 2.1 seconds 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 13 sheets defined 47.2% alpha, 13.5% beta 5 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.643A pdb=" N SER A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.784A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.811A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 removed outlier: 3.752A pdb=" N GLU A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.614A pdb=" N ASN A 527 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 524 through 528' Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 577 through 596 removed outlier: 4.078A pdb=" N LEU A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.553A pdb=" N PHE A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 3.593A pdb=" N GLU A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 removed outlier: 3.617A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 713 removed outlier: 3.895A pdb=" N MET A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.762A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.521A pdb=" N VAL B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.787A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 4.008A pdb=" N SER B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.604A pdb=" N LEU B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.614A pdb=" N VAL B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 290 removed outlier: 4.230A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.602A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 326 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.747A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 376 removed outlier: 3.698A pdb=" N ASN B 372 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.124A pdb=" N TYR B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.513A pdb=" N LYS B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 471 Processing helix chain 'B' and resid 518 through 536 removed outlier: 3.605A pdb=" N ASP B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.886A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.651A pdb=" N ASN B 603 " --> pdb=" O ASN B 600 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 604 " --> pdb=" O LEU B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 604' Processing helix chain 'B' and resid 607 through 612 removed outlier: 3.570A pdb=" N LYS B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'C' and resid 43 through 53 removed outlier: 3.645A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.835A pdb=" N GLU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET C 66 " --> pdb=" O ILE C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 66' Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.077A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.756A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.001A pdb=" N LYS A 274 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.390A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 321 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 541 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LYS A 319 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N MET A 543 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 10.766A pdb=" N TRP A 317 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.219A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 475 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 373 removed outlier: 5.872A pdb=" N GLU A 372 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLN B 367 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.544A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.630A pdb=" N THR B 183 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 208 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.948A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130 457 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2892 1.33 - 1.45: 2066 1.45 - 1.57: 5864 1.57 - 1.69: 55 1.69 - 1.80: 112 Bond restraints: 10989 Sorted by residual: bond pdb=" C SER A 206 " pdb=" N TYR A 207 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.01e+01 bond pdb=" N ASP B 445 " pdb=" CA ASP B 445 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.21e+00 bond pdb=" N SER B 444 " pdb=" CA SER B 444 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.49e+00 bond pdb=" N SER B 443 " pdb=" CA SER B 443 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.49e+00 bond pdb=" CA SER B 443 " pdb=" CB SER B 443 " ideal model delta sigma weight residual 1.532 1.504 0.028 1.58e-02 4.01e+03 3.04e+00 ... (remaining 10984 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.16: 417 106.16 - 113.18: 5929 113.18 - 120.20: 4248 120.20 - 127.22: 4207 127.22 - 134.24: 177 Bond angle restraints: 14978 Sorted by residual: angle pdb=" N ASP B 445 " pdb=" CA ASP B 445 " pdb=" C ASP B 445 " ideal model delta sigma weight residual 112.54 104.50 8.04 1.51e+00 4.39e-01 2.83e+01 angle pdb=" N VAL C 109 " pdb=" CA VAL C 109 " pdb=" C VAL C 109 " ideal model delta sigma weight residual 113.71 109.15 4.56 9.50e-01 1.11e+00 2.31e+01 angle pdb=" N ASP B 446 " pdb=" CA ASP B 446 " pdb=" C ASP B 446 " ideal model delta sigma weight residual 109.07 116.34 -7.27 1.61e+00 3.86e-01 2.04e+01 angle pdb=" C ILE A 540 " pdb=" N GLY A 541 " pdb=" CA GLY A 541 " ideal model delta sigma weight residual 121.15 115.20 5.95 1.80e+00 3.09e-01 1.09e+01 angle pdb=" N ILE B 248 " pdb=" CA ILE B 248 " pdb=" CB ILE B 248 " ideal model delta sigma weight residual 112.15 107.32 4.83 1.47e+00 4.63e-01 1.08e+01 ... (remaining 14973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 5954 17.68 - 35.36: 509 35.36 - 53.04: 135 53.04 - 70.73: 57 70.73 - 88.41: 12 Dihedral angle restraints: 6667 sinusoidal: 3018 harmonic: 3649 Sorted by residual: dihedral pdb=" CA ILE A 481 " pdb=" C ILE A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 581 " pdb=" C LEU A 581 " pdb=" N GLN A 582 " pdb=" CA GLN A 582 " ideal model delta harmonic sigma weight residual 180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1296 0.059 - 0.118: 311 0.118 - 0.177: 42 0.177 - 0.236: 4 0.236 - 0.294: 1 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CA PHE B 447 " pdb=" N PHE B 447 " pdb=" C PHE B 447 " pdb=" CB PHE B 447 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 418 " pdb=" CA ILE A 418 " pdb=" CG1 ILE A 418 " pdb=" CG2 ILE A 418 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CG LEU B 258 " pdb=" CB LEU B 258 " pdb=" CD1 LEU B 258 " pdb=" CD2 LEU B 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1651 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 111 " 0.052 5.00e-02 4.00e+02 7.71e-02 9.52e+00 pdb=" N PRO C 112 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO A 620 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 584 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LEU A 584 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 584 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 585 " 0.014 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 221 2.66 - 3.22: 9032 3.22 - 3.78: 16295 3.78 - 4.34: 22418 4.34 - 4.90: 37425 Nonbonded interactions: 85391 Sorted by model distance: nonbonded pdb=" O ASP B 48 " pdb=" OD1 ASP B 48 " model vdw 2.097 3.040 nonbonded pdb=" OG SER B 374 " pdb=" OD1 ASP B 375 " model vdw 2.270 2.440 nonbonded pdb=" OD2 ASP B 446 " pdb="MG MG B 801 " model vdw 2.278 2.170 nonbonded pdb=" O LYS A 380 " pdb=" OH TYR B 380 " model vdw 2.280 2.440 nonbonded pdb=" O ASP B 120 " pdb=" OG1 THR B 123 " model vdw 2.295 2.440 ... (remaining 85386 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 9.480 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 38.350 Find NCS groups from input model: 0.250 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.008 0.069 10989 Z= 0.480 Angle : 0.756 8.541 14978 Z= 0.427 Chirality : 0.051 0.294 1654 Planarity : 0.007 0.077 1818 Dihedral : 15.430 88.408 4311 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 6.25 % Allowed : 8.06 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -3.65 (0.19), residues: 1243 helix: -2.33 (0.16), residues: 537 sheet: -1.15 (0.45), residues: 119 loop : -2.76 (0.21), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 438 HIS 0.005 0.001 HIS B 32 PHE 0.023 0.002 PHE B 490 TYR 0.017 0.002 TYR B 155 ARG 0.005 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 223 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9446 (m) cc_final: 0.9076 (t) REVERT: A 288 MET cc_start: 0.8489 (ttp) cc_final: 0.8281 (ttt) REVERT: A 356 LYS cc_start: 0.8287 (mttt) cc_final: 0.8037 (ttpp) REVERT: A 388 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8487 (m-10) REVERT: A 414 ASN cc_start: 0.7936 (m110) cc_final: 0.7701 (p0) REVERT: A 474 GLU cc_start: 0.7910 (mp0) cc_final: 0.7527 (mm-30) REVERT: A 585 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7916 (tp40) REVERT: A 598 LYS cc_start: 0.8753 (mmtt) cc_final: 0.7819 (tptm) REVERT: A 679 LYS cc_start: 0.8836 (mttt) cc_final: 0.8613 (mmtt) REVERT: A 707 LYS cc_start: 0.8569 (tttt) cc_final: 0.8367 (tptp) REVERT: B 15 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: B 54 ILE cc_start: 0.9299 (mt) cc_final: 0.8956 (pt) REVERT: B 120 ASP cc_start: 0.7326 (p0) cc_final: 0.7072 (p0) REVERT: B 157 LEU cc_start: 0.8417 (mt) cc_final: 0.7957 (mp) REVERT: B 169 ASP cc_start: 0.8008 (m-30) cc_final: 0.7665 (m-30) REVERT: B 171 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8914 (mm) REVERT: B 175 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: B 248 ILE cc_start: 0.9148 (tt) cc_final: 0.8761 (tp) REVERT: B 249 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6948 (mpt90) REVERT: B 256 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 353 ARG cc_start: 0.8398 (ptp-170) cc_final: 0.7949 (ptm-80) REVERT: B 468 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7701 (mtt180) REVERT: B 481 LYS cc_start: 0.8700 (mttt) cc_final: 0.8246 (mtmt) REVERT: C 47 MET cc_start: 0.8288 (tpp) cc_final: 0.7696 (tpt) REVERT: C 71 ASP cc_start: 0.7781 (m-30) cc_final: 0.7379 (m-30) REVERT: C 83 ASP cc_start: 0.8266 (t70) cc_final: 0.7301 (t70) REVERT: C 113 ARG cc_start: 0.4380 (OUTLIER) cc_final: 0.3863 (mpt180) outliers start: 69 outliers final: 35 residues processed: 278 average time/residue: 0.2841 time to fit residues: 105.3533 Evaluate side-chains 203 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 476 GLN B 47 HIS B 108 GLN B 276 ASN B 425 ASN B 567 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10989 Z= 0.158 Angle : 0.523 7.815 14978 Z= 0.274 Chirality : 0.038 0.142 1654 Planarity : 0.004 0.046 1818 Dihedral : 13.458 75.075 1879 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.10 % Rotamer: Outliers : 4.08 % Allowed : 12.41 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.72 (0.22), residues: 1243 helix: -0.07 (0.22), residues: 535 sheet: -0.94 (0.48), residues: 106 loop : -2.23 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 49 HIS 0.002 0.001 HIS A 360 PHE 0.015 0.001 PHE A 352 TYR 0.010 0.001 TYR B 555 ARG 0.005 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 178 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9388 (m) cc_final: 0.9035 (t) REVERT: A 388 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8545 (m-10) REVERT: A 414 ASN cc_start: 0.7925 (m-40) cc_final: 0.7721 (p0) REVERT: A 474 GLU cc_start: 0.7821 (mp0) cc_final: 0.7607 (mm-30) REVERT: A 568 ILE cc_start: 0.9064 (tp) cc_final: 0.8558 (pt) REVERT: A 585 GLN cc_start: 0.8363 (tt0) cc_final: 0.7940 (tp40) REVERT: A 597 VAL cc_start: 0.8411 (m) cc_final: 0.7963 (t) REVERT: A 598 LYS cc_start: 0.8809 (mmtt) cc_final: 0.7789 (tptm) REVERT: A 707 LYS cc_start: 0.8532 (tttt) cc_final: 0.8300 (tptp) REVERT: B 15 GLN cc_start: 0.9405 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: B 118 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7473 (tpp80) REVERT: B 157 LEU cc_start: 0.8363 (mt) cc_final: 0.8024 (mp) REVERT: B 169 ASP cc_start: 0.7880 (m-30) cc_final: 0.7636 (m-30) REVERT: B 175 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: B 256 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7774 (mm-30) REVERT: B 287 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7521 (mtmt) REVERT: B 353 ARG cc_start: 0.8309 (ptp-170) cc_final: 0.7837 (ptm-80) REVERT: B 468 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8000 (mtt180) REVERT: B 481 LYS cc_start: 0.8566 (mttt) cc_final: 0.8161 (mtmt) REVERT: B 577 LYS cc_start: 0.8324 (tptt) cc_final: 0.7930 (tppt) REVERT: C 47 MET cc_start: 0.8096 (tpp) cc_final: 0.7426 (tpt) REVERT: C 113 ARG cc_start: 0.4333 (OUTLIER) cc_final: 0.3730 (mpt180) outliers start: 45 outliers final: 29 residues processed: 215 average time/residue: 0.2823 time to fit residues: 81.8397 Evaluate side-chains 184 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10989 Z= 0.201 Angle : 0.510 6.915 14978 Z= 0.265 Chirality : 0.039 0.143 1654 Planarity : 0.004 0.041 1818 Dihedral : 12.814 78.464 1850 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.54 % Favored : 96.38 % Rotamer: Outliers : 3.99 % Allowed : 13.86 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.01 (0.23), residues: 1243 helix: 0.68 (0.23), residues: 542 sheet: -0.69 (0.46), residues: 116 loop : -2.03 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.016 0.001 PHE A 352 TYR 0.010 0.001 TYR B 555 ARG 0.005 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9367 (m) cc_final: 0.9055 (t) REVERT: A 544 GLU cc_start: 0.7271 (tm-30) cc_final: 0.7062 (tm-30) REVERT: A 568 ILE cc_start: 0.9095 (tp) cc_final: 0.8584 (pt) REVERT: A 585 GLN cc_start: 0.8400 (tt0) cc_final: 0.7994 (tp40) REVERT: A 597 VAL cc_start: 0.8402 (m) cc_final: 0.7997 (t) REVERT: A 598 LYS cc_start: 0.8792 (mmtt) cc_final: 0.7677 (tptm) REVERT: A 707 LYS cc_start: 0.8542 (tttt) cc_final: 0.8303 (tptp) REVERT: B 15 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.8075 (mp10) REVERT: B 157 LEU cc_start: 0.8415 (mt) cc_final: 0.8043 (mp) REVERT: B 169 ASP cc_start: 0.7883 (m-30) cc_final: 0.7646 (m-30) REVERT: B 175 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: B 256 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7786 (mm-30) REVERT: B 287 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7503 (mtmt) REVERT: B 353 ARG cc_start: 0.8384 (ptp-170) cc_final: 0.7861 (ptm-80) REVERT: B 442 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8503 (tp40) REVERT: B 468 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8073 (mtt180) REVERT: B 481 LYS cc_start: 0.8615 (mttt) cc_final: 0.8066 (ptpt) REVERT: C 47 MET cc_start: 0.8092 (tpp) cc_final: 0.7376 (tpt) REVERT: C 77 LEU cc_start: 0.8460 (mp) cc_final: 0.8172 (mp) REVERT: C 113 ARG cc_start: 0.4329 (OUTLIER) cc_final: 0.3738 (mpt180) outliers start: 44 outliers final: 33 residues processed: 201 average time/residue: 0.2506 time to fit residues: 69.6557 Evaluate side-chains 187 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 461 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10989 Z= 0.270 Angle : 0.528 6.768 14978 Z= 0.275 Chirality : 0.040 0.146 1654 Planarity : 0.004 0.040 1818 Dihedral : 12.652 84.739 1842 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.06 % Rotamer: Outliers : 4.62 % Allowed : 15.13 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.67 (0.24), residues: 1243 helix: 1.03 (0.23), residues: 539 sheet: -0.70 (0.47), residues: 121 loop : -1.88 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE A 352 TYR 0.012 0.001 TYR C 244 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9412 (m) cc_final: 0.9067 (t) REVERT: A 388 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8561 (m-10) REVERT: A 508 ASN cc_start: 0.8852 (m-40) cc_final: 0.8614 (m-40) REVERT: A 585 GLN cc_start: 0.8384 (tt0) cc_final: 0.8036 (tp40) REVERT: A 598 LYS cc_start: 0.8826 (mmtt) cc_final: 0.7703 (tptm) REVERT: A 707 LYS cc_start: 0.8549 (tttt) cc_final: 0.8318 (tptp) REVERT: B 157 LEU cc_start: 0.8432 (mt) cc_final: 0.7998 (mp) REVERT: B 169 ASP cc_start: 0.7972 (m-30) cc_final: 0.7683 (m-30) REVERT: B 175 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: B 287 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7512 (mtmt) REVERT: B 353 ARG cc_start: 0.8455 (ptp-170) cc_final: 0.7911 (ptm-80) REVERT: B 442 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8537 (tp40) REVERT: B 468 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7810 (mtt-85) REVERT: B 481 LYS cc_start: 0.8600 (mttt) cc_final: 0.8184 (mtmt) REVERT: C 47 MET cc_start: 0.8072 (tpp) cc_final: 0.7346 (tpt) REVERT: C 113 ARG cc_start: 0.4190 (OUTLIER) cc_final: 0.3626 (mpt180) outliers start: 51 outliers final: 38 residues processed: 199 average time/residue: 0.2572 time to fit residues: 70.2363 Evaluate side-chains 190 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 346 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10989 Z= 0.195 Angle : 0.487 8.222 14978 Z= 0.254 Chirality : 0.039 0.139 1654 Planarity : 0.003 0.039 1818 Dihedral : 12.456 85.829 1838 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.54 % Favored : 96.38 % Rotamer: Outliers : 4.08 % Allowed : 15.49 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.24), residues: 1243 helix: 1.35 (0.23), residues: 539 sheet: -0.51 (0.47), residues: 120 loop : -1.76 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 363 HIS 0.003 0.001 HIS A 360 PHE 0.020 0.001 PHE A 352 TYR 0.011 0.001 TYR B 555 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 1.264 Fit side-chains REVERT: A 218 SER cc_start: 0.9374 (m) cc_final: 0.9053 (t) REVERT: A 278 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8729 (tp-100) REVERT: A 508 ASN cc_start: 0.8802 (m-40) cc_final: 0.8561 (m110) REVERT: A 568 ILE cc_start: 0.9091 (tp) cc_final: 0.8574 (pt) REVERT: A 585 GLN cc_start: 0.8314 (tt0) cc_final: 0.7996 (tp40) REVERT: A 597 VAL cc_start: 0.8492 (m) cc_final: 0.8105 (t) REVERT: A 598 LYS cc_start: 0.8795 (mmtt) cc_final: 0.7664 (tptm) REVERT: A 707 LYS cc_start: 0.8534 (tttt) cc_final: 0.8301 (tptp) REVERT: B 15 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: B 157 LEU cc_start: 0.8424 (mt) cc_final: 0.7958 (mp) REVERT: B 169 ASP cc_start: 0.7950 (m-30) cc_final: 0.7578 (m-30) REVERT: B 175 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6060 (mp0) REVERT: B 256 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7821 (mm-30) REVERT: B 287 LYS cc_start: 0.7996 (tmtt) cc_final: 0.7477 (mtmt) REVERT: B 302 ILE cc_start: 0.9180 (mt) cc_final: 0.8952 (tt) REVERT: B 353 ARG cc_start: 0.8400 (ptp-170) cc_final: 0.7855 (ptm-80) REVERT: B 442 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8431 (tp40) REVERT: B 481 LYS cc_start: 0.8576 (mttt) cc_final: 0.8152 (mtmt) REVERT: C 47 MET cc_start: 0.8092 (tpp) cc_final: 0.7424 (tpt) outliers start: 45 outliers final: 33 residues processed: 202 average time/residue: 0.2455 time to fit residues: 69.0142 Evaluate side-chains 190 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN B 567 ASN C 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10989 Z= 0.354 Angle : 0.571 8.265 14978 Z= 0.296 Chirality : 0.042 0.152 1654 Planarity : 0.004 0.038 1818 Dihedral : 12.515 95.669 1827 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 4.80 % Allowed : 16.03 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.24), residues: 1243 helix: 1.29 (0.23), residues: 538 sheet: -0.40 (0.47), residues: 121 loop : -1.80 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.003 0.001 HIS B 465 PHE 0.021 0.002 PHE A 352 TYR 0.017 0.002 TYR A 475 ARG 0.004 0.000 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 155 time to evaluate : 1.370 Fit side-chains REVERT: A 218 SER cc_start: 0.9410 (m) cc_final: 0.9070 (t) REVERT: A 278 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8750 (tp-100) REVERT: A 585 GLN cc_start: 0.8381 (tt0) cc_final: 0.8041 (tp40) REVERT: A 598 LYS cc_start: 0.8823 (mmtt) cc_final: 0.7695 (tptm) REVERT: A 707 LYS cc_start: 0.8550 (tttt) cc_final: 0.8333 (tptp) REVERT: B 15 GLN cc_start: 0.9437 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: B 157 LEU cc_start: 0.8494 (mt) cc_final: 0.8022 (mp) REVERT: B 169 ASP cc_start: 0.8024 (m-30) cc_final: 0.7601 (m-30) REVERT: B 175 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6037 (mp0) REVERT: B 287 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7535 (mtmt) REVERT: B 442 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8572 (tp40) REVERT: B 481 LYS cc_start: 0.8672 (mttt) cc_final: 0.8211 (mtmt) REVERT: C 47 MET cc_start: 0.8110 (tpp) cc_final: 0.7458 (tpt) REVERT: C 113 ARG cc_start: 0.4152 (OUTLIER) cc_final: 0.3584 (mpt180) outliers start: 53 outliers final: 40 residues processed: 197 average time/residue: 0.2484 time to fit residues: 68.0692 Evaluate side-chains 193 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN B 310 ASN C 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10989 Z= 0.140 Angle : 0.466 8.502 14978 Z= 0.243 Chirality : 0.038 0.133 1654 Planarity : 0.003 0.037 1818 Dihedral : 12.242 92.503 1827 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.89 % Allowed : 17.48 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.04 (0.25), residues: 1243 helix: 1.59 (0.23), residues: 545 sheet: -0.06 (0.48), residues: 116 loop : -1.68 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.002 0.000 HIS A 360 PHE 0.022 0.001 PHE A 352 TYR 0.011 0.001 TYR B 555 ARG 0.004 0.000 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 168 time to evaluate : 1.240 Fit side-chains REVERT: A 218 SER cc_start: 0.9353 (m) cc_final: 0.9019 (t) REVERT: A 278 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8680 (tp-100) REVERT: A 508 ASN cc_start: 0.8733 (m-40) cc_final: 0.8491 (m110) REVERT: A 568 ILE cc_start: 0.9065 (tp) cc_final: 0.8560 (pt) REVERT: A 571 LYS cc_start: 0.8542 (tttt) cc_final: 0.8329 (tttp) REVERT: A 585 GLN cc_start: 0.8198 (tt0) cc_final: 0.7963 (tp40) REVERT: A 598 LYS cc_start: 0.8761 (mmtt) cc_final: 0.7626 (tptm) REVERT: B 15 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: B 157 LEU cc_start: 0.8398 (mt) cc_final: 0.7900 (mp) REVERT: B 169 ASP cc_start: 0.7936 (m-30) cc_final: 0.7525 (m-30) REVERT: B 175 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: B 256 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7783 (mm-30) REVERT: B 287 LYS cc_start: 0.7988 (tmtt) cc_final: 0.7505 (mtmt) REVERT: B 392 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8924 (tt) REVERT: B 442 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8351 (tp40) REVERT: B 481 LYS cc_start: 0.8585 (mttt) cc_final: 0.8016 (ptpt) REVERT: C 47 MET cc_start: 0.8081 (tpp) cc_final: 0.7493 (tpt) REVERT: C 113 ARG cc_start: 0.4132 (OUTLIER) cc_final: 0.3626 (mpt180) outliers start: 43 outliers final: 33 residues processed: 203 average time/residue: 0.2595 time to fit residues: 73.7890 Evaluate side-chains 197 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10989 Z= 0.150 Angle : 0.475 9.625 14978 Z= 0.245 Chirality : 0.038 0.133 1654 Planarity : 0.003 0.036 1818 Dihedral : 12.133 93.582 1825 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.99 % Allowed : 18.30 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.11 (0.24), residues: 1243 helix: 1.69 (0.23), residues: 547 sheet: 0.09 (0.50), residues: 114 loop : -1.59 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 363 HIS 0.003 0.000 HIS A 360 PHE 0.022 0.001 PHE A 352 TYR 0.010 0.001 TYR B 555 ARG 0.003 0.000 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.234 Fit side-chains REVERT: A 218 SER cc_start: 0.9334 (m) cc_final: 0.9036 (t) REVERT: A 278 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: A 508 ASN cc_start: 0.8754 (m-40) cc_final: 0.8545 (m110) REVERT: A 568 ILE cc_start: 0.9031 (tp) cc_final: 0.8556 (pt) REVERT: A 571 LYS cc_start: 0.8560 (tttt) cc_final: 0.8340 (tttp) REVERT: A 585 GLN cc_start: 0.8237 (tt0) cc_final: 0.8000 (tp40) REVERT: A 598 LYS cc_start: 0.8742 (mmtt) cc_final: 0.7603 (tptm) REVERT: B 157 LEU cc_start: 0.8363 (mt) cc_final: 0.7898 (mp) REVERT: B 169 ASP cc_start: 0.8000 (m-30) cc_final: 0.7570 (m-30) REVERT: B 175 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6035 (mp0) REVERT: B 256 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 287 LYS cc_start: 0.7991 (tmtt) cc_final: 0.7499 (mtmt) REVERT: B 442 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8425 (tp40) REVERT: B 481 LYS cc_start: 0.8542 (mttt) cc_final: 0.7974 (ptpt) REVERT: C 47 MET cc_start: 0.8090 (tpp) cc_final: 0.7479 (tpt) REVERT: C 113 ARG cc_start: 0.4099 (OUTLIER) cc_final: 0.3578 (mpt180) outliers start: 44 outliers final: 34 residues processed: 198 average time/residue: 0.2430 time to fit residues: 66.9258 Evaluate side-chains 193 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10989 Z= 0.266 Angle : 0.530 8.816 14978 Z= 0.272 Chirality : 0.040 0.161 1654 Planarity : 0.004 0.038 1818 Dihedral : 12.210 100.415 1821 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.62 % Allowed : 18.93 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.03 (0.24), residues: 1243 helix: 1.53 (0.23), residues: 549 sheet: 0.09 (0.49), residues: 119 loop : -1.65 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS B 47 PHE 0.023 0.001 PHE A 352 TYR 0.013 0.001 TYR A 475 ARG 0.003 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 1.188 Fit side-chains REVERT: A 218 SER cc_start: 0.9376 (m) cc_final: 0.9094 (t) REVERT: A 278 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8716 (tp-100) REVERT: A 508 ASN cc_start: 0.8808 (m-40) cc_final: 0.8580 (m110) REVERT: A 585 GLN cc_start: 0.8191 (tt0) cc_final: 0.7953 (tp40) REVERT: A 598 LYS cc_start: 0.8738 (mmtt) cc_final: 0.7602 (tptm) REVERT: B 157 LEU cc_start: 0.8495 (mt) cc_final: 0.7987 (mp) REVERT: B 169 ASP cc_start: 0.8011 (m-30) cc_final: 0.7580 (m-30) REVERT: B 175 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6022 (mp0) REVERT: B 287 LYS cc_start: 0.7958 (tmtt) cc_final: 0.7479 (mtmt) REVERT: B 442 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8519 (tp40) REVERT: B 481 LYS cc_start: 0.8626 (mttt) cc_final: 0.8051 (ptpt) REVERT: C 47 MET cc_start: 0.8128 (tpp) cc_final: 0.7539 (tpt) REVERT: C 113 ARG cc_start: 0.4098 (OUTLIER) cc_final: 0.3561 (mpt180) outliers start: 40 outliers final: 33 residues processed: 181 average time/residue: 0.2634 time to fit residues: 66.3620 Evaluate side-chains 185 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10989 Z= 0.274 Angle : 0.535 9.334 14978 Z= 0.275 Chirality : 0.041 0.133 1654 Planarity : 0.004 0.036 1818 Dihedral : 12.273 106.086 1821 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.53 % Allowed : 19.11 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.07 (0.24), residues: 1243 helix: 1.49 (0.23), residues: 548 sheet: 0.12 (0.49), residues: 119 loop : -1.68 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 438 HIS 0.004 0.001 HIS B 47 PHE 0.023 0.001 PHE A 352 TYR 0.014 0.001 TYR A 475 ARG 0.004 0.000 ARG B 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 1.160 Fit side-chains REVERT: A 218 SER cc_start: 0.9385 (m) cc_final: 0.9090 (t) REVERT: A 278 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8747 (tp-100) REVERT: A 508 ASN cc_start: 0.8792 (m-40) cc_final: 0.8554 (m-40) REVERT: A 585 GLN cc_start: 0.8195 (tt0) cc_final: 0.7968 (tp40) REVERT: A 598 LYS cc_start: 0.8728 (mmtt) cc_final: 0.7593 (tptm) REVERT: B 15 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: B 157 LEU cc_start: 0.8499 (mt) cc_final: 0.7981 (mp) REVERT: B 169 ASP cc_start: 0.8004 (m-30) cc_final: 0.7568 (m-30) REVERT: B 175 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6024 (mp0) REVERT: B 287 LYS cc_start: 0.7973 (tmtt) cc_final: 0.7492 (mtmt) REVERT: B 442 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8533 (tp40) REVERT: B 477 MET cc_start: 0.9096 (ttt) cc_final: 0.8776 (ttt) REVERT: B 481 LYS cc_start: 0.8674 (mttt) cc_final: 0.8158 (ptpt) REVERT: C 47 MET cc_start: 0.8128 (tpp) cc_final: 0.7540 (tpt) REVERT: C 113 ARG cc_start: 0.4111 (OUTLIER) cc_final: 0.3510 (mpt180) outliers start: 39 outliers final: 34 residues processed: 180 average time/residue: 0.2455 time to fit residues: 61.5434 Evaluate side-chains 187 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106255 restraints weight = 16319.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109252 restraints weight = 8589.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111232 restraints weight = 5665.620| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10989 Z= 0.165 Angle : 0.488 9.799 14978 Z= 0.250 Chirality : 0.038 0.146 1654 Planarity : 0.003 0.037 1818 Dihedral : 12.135 103.557 1821 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.35 % Allowed : 19.29 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.11 (0.24), residues: 1243 helix: 1.67 (0.23), residues: 547 sheet: 0.28 (0.53), residues: 105 loop : -1.60 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.021 0.001 PHE A 352 TYR 0.010 0.001 TYR B 555 ARG 0.003 0.000 ARG B 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.42 seconds wall clock time: 42 minutes 46.31 seconds (2566.31 seconds total)