Starting phenix.real_space_refine on Sat Mar 16 01:44:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/03_2024/8h8x_34551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/03_2024/8h8x_34551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/03_2024/8h8x_34551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/03_2024/8h8x_34551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/03_2024/8h8x_34551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8x_34551/03_2024/8h8x_34551.pdb" } resolution = 3.92 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 4274 2.51 5 N 1166 2.21 5 O 1262 1.98 5 H 6667 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 748": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13418 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 13418 Classifications: {'peptide': 850} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 39, 'TRANS': 810} Chain breaks: 1 Time building chain proxies: 6.14, per 1000 atoms: 0.46 Number of scatterers: 13418 At special positions: 0 Unit cell: (75.5392, 100.433, 156.229, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 1262 8.00 N 1166 7.00 C 4274 6.00 H 6667 1.00 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: 10.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 63.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 removed outlier: 4.401A pdb=" N LEU A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 4.182A pdb=" N TYR A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.546A pdb=" N ILE A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.934A pdb=" N LEU A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.986A pdb=" N LEU A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.529A pdb=" N LEU A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.523A pdb=" N GLN A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 208 removed outlier: 3.556A pdb=" N PHE A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.612A pdb=" N CYS A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 252 removed outlier: 3.888A pdb=" N CYS A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.888A pdb=" N THR A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.538A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 4.133A pdb=" N LYS A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 334 removed outlier: 3.898A pdb=" N GLN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 321 " --> pdb=" O MET A 317 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N MET A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 382 removed outlier: 3.666A pdb=" N TRP A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 369 " --> pdb=" O HIS A 365 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 464 removed outlier: 3.738A pdb=" N ALA A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 463 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 3.560A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 479 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.562A pdb=" N LYS A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 515 through 520 removed outlier: 4.058A pdb=" N ILE A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 520 " --> pdb=" O MET A 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 520' Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.894A pdb=" N GLU A 568 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 571 " --> pdb=" O CYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.750A pdb=" N TRP A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 629 through 634 removed outlier: 4.152A pdb=" N TYR A 632 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 633 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 654 removed outlier: 3.639A pdb=" N PHE A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 644 " --> pdb=" O TYR A 640 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 649 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 671 removed outlier: 3.778A pdb=" N TYR A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 683 removed outlier: 3.774A pdb=" N SER A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.837A pdb=" N ALA A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 702 removed outlier: 3.566A pdb=" N ASP A 701 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 765 removed outlier: 3.519A pdb=" N THR A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 749 " --> pdb=" O THR A 745 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 752 " --> pdb=" O ARG A 748 " (cutoff:3.500A) Proline residue: A 755 - end of helix removed outlier: 3.611A pdb=" N ASN A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA A 759 " --> pdb=" O PRO A 755 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 774 removed outlier: 4.052A pdb=" N ILE A 773 " --> pdb=" O PRO A 769 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 774 " --> pdb=" O PRO A 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 769 through 774' Processing helix chain 'A' and resid 780 through 787 removed outlier: 4.047A pdb=" N LEU A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 removed outlier: 3.512A pdb=" N ASN A 799 " --> pdb=" O ASP A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 821 removed outlier: 3.604A pdb=" N TRP A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 818 " --> pdb=" O GLN A 814 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 819 " --> pdb=" O TRP A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 837 removed outlier: 3.728A pdb=" N ARG A 828 " --> pdb=" O THR A 824 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 849 removed outlier: 3.916A pdb=" N ALA A 847 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 904 removed outlier: 4.772A pdb=" N LEU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 713 removed outlier: 3.587A pdb=" N VAL A 721 " --> pdb=" O VAL A 710 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 801 through 802 removed outlier: 6.684A pdb=" N GLU A 801 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ALA A 862 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR A 859 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LEU A 882 " --> pdb=" O THR A 859 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 861 " --> pdb=" O LEU A 882 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 10.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6645 1.03 - 1.22: 23 1.22 - 1.42: 2892 1.42 - 1.61: 3930 1.61 - 1.81: 76 Bond restraints: 13566 Sorted by residual: bond pdb=" CB VAL A 324 " pdb=" CG1 VAL A 324 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.40e+00 bond pdb=" CA ASP A 621 " pdb=" C ASP A 621 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.41e-02 5.03e+03 6.55e+00 bond pdb=" CG LEU A 320 " pdb=" CD1 LEU A 320 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CG LEU A 321 " pdb=" CD2 LEU A 321 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.80e+00 bond pdb=" CA PHE A 524 " pdb=" CB PHE A 524 " ideal model delta sigma weight residual 1.534 1.500 0.034 1.45e-02 4.76e+03 5.35e+00 ... (remaining 13561 not shown) Histogram of bond angle deviations from ideal: 97.44 - 104.80: 136 104.80 - 112.17: 15376 112.17 - 119.53: 3645 119.53 - 126.90: 5239 126.90 - 134.26: 101 Bond angle restraints: 24497 Sorted by residual: angle pdb=" N LEU A 535 " pdb=" CA LEU A 535 " pdb=" C LEU A 535 " ideal model delta sigma weight residual 113.18 107.77 5.41 1.33e+00 5.65e-01 1.65e+01 angle pdb=" N LYS A 350 " pdb=" CA LYS A 350 " pdb=" CB LYS A 350 " ideal model delta sigma weight residual 114.17 109.88 4.29 1.14e+00 7.69e-01 1.41e+01 angle pdb=" N THR A 623 " pdb=" CA THR A 623 " pdb=" C THR A 623 " ideal model delta sigma weight residual 113.55 109.34 4.21 1.26e+00 6.30e-01 1.11e+01 angle pdb=" N ASP A 541 " pdb=" CA ASP A 541 " pdb=" C ASP A 541 " ideal model delta sigma weight residual 111.55 107.72 3.83 1.37e+00 5.33e-01 7.82e+00 angle pdb=" N ILE A 498 " pdb=" CA ILE A 498 " pdb=" CB ILE A 498 " ideal model delta sigma weight residual 111.23 106.85 4.38 1.65e+00 3.67e-01 7.06e+00 ... (remaining 24492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.63: 5719 14.63 - 29.27: 489 29.27 - 43.90: 139 43.90 - 58.53: 57 58.53 - 73.16: 5 Dihedral angle restraints: 6409 sinusoidal: 3493 harmonic: 2916 Sorted by residual: dihedral pdb=" CA HIS A 534 " pdb=" C HIS A 534 " pdb=" N LEU A 535 " pdb=" CA LEU A 535 " ideal model delta harmonic sigma weight residual 180.00 144.57 35.43 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA LEU A 706 " pdb=" C LEU A 706 " pdb=" N THR A 707 " pdb=" CA THR A 707 " ideal model delta harmonic sigma weight residual -180.00 -148.92 -31.08 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA PRO A 540 " pdb=" C PRO A 540 " pdb=" N ASP A 541 " pdb=" CA ASP A 541 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 6406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 603 0.036 - 0.071: 295 0.071 - 0.107: 100 0.107 - 0.143: 40 0.143 - 0.179: 6 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CB VAL A 455 " pdb=" CA VAL A 455 " pdb=" CG1 VAL A 455 " pdb=" CG2 VAL A 455 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CG LEU A 321 " pdb=" CB LEU A 321 " pdb=" CD1 LEU A 321 " pdb=" CD2 LEU A 321 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA PRO A 540 " pdb=" N PRO A 540 " pdb=" C PRO A 540 " pdb=" CB PRO A 540 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1041 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 459 " -0.022 2.00e-02 2.50e+03 1.57e-02 7.37e+00 pdb=" CG PHE A 459 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 459 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 459 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 459 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 459 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 459 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 459 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 459 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 459 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 459 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 459 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 534 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C HIS A 534 " -0.045 2.00e-02 2.50e+03 pdb=" O HIS A 534 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 535 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 547 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 548 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 548 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 548 " -0.031 5.00e-02 4.00e+02 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1587 2.25 - 2.84: 30500 2.84 - 3.43: 32464 3.43 - 4.01: 42752 4.01 - 4.60: 67443 Nonbonded interactions: 174746 Sorted by model distance: nonbonded pdb=" O PRO A 335 " pdb=" H ASP A 343 " model vdw 1.663 1.850 nonbonded pdb=" O ILE A 753 " pdb=" H GLN A 756 " model vdw 1.668 1.850 nonbonded pdb=" O PHE A 708 " pdb=" H LEU A 723 " model vdw 1.688 1.850 nonbonded pdb=" O HIS A 534 " pdb="HE21 GLN A 539 " model vdw 1.690 1.850 nonbonded pdb=" HG SER A 619 " pdb=" OG1 THR A 624 " model vdw 1.691 1.850 ... (remaining 174741 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: 0.660 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: 0.190 Extract box with map and model: 4.160 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 43.480 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.090 6899 Z= 0.690 Angle : 0.894 8.290 9356 Z= 0.508 Chirality : 0.050 0.179 1044 Planarity : 0.006 0.056 1219 Dihedral : 9.886 73.163 2558 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.57 (0.25), residues: 846 helix: -3.12 (0.18), residues: 378 sheet: -2.02 (1.01), residues: 19 loop : -1.61 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A 796 HIS 0.014 0.003 HIS A 654 PHE 0.046 0.004 PHE A 459 TYR 0.028 0.003 TYR A 667 ARG 0.009 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8846 (mtp) cc_final: 0.8589 (mmm) REVERT: A 524 PHE cc_start: 0.7147 (m-80) cc_final: 0.6905 (m-10) REVERT: A 751 ARG cc_start: 0.7671 (tpt90) cc_final: 0.7033 (tpm170) REVERT: A 822 ASP cc_start: 0.7983 (m-30) cc_final: 0.7780 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.5203 time to fit residues: 74.0291 Evaluate side-chains 74 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 141 ASN A 257 GLN A 669 HIS A 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6899 Z= 0.174 Angle : 0.608 5.975 9356 Z= 0.324 Chirality : 0.037 0.136 1044 Planarity : 0.005 0.050 1219 Dihedral : 6.068 28.331 917 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.53 % Allowed : 5.03 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.25), residues: 846 helix: -1.67 (0.20), residues: 442 sheet: -1.66 (1.04), residues: 19 loop : -1.71 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 600 HIS 0.006 0.001 HIS A 669 PHE 0.012 0.001 PHE A 327 TYR 0.017 0.001 TYR A 313 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 HIS cc_start: 0.8886 (m90) cc_final: 0.8565 (m90) REVERT: A 137 TRP cc_start: 0.8555 (t-100) cc_final: 0.7781 (t-100) outliers start: 4 outliers final: 2 residues processed: 92 average time/residue: 0.3955 time to fit residues: 48.5603 Evaluate side-chains 70 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 677 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 129 ASN A 252 HIS A 381 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6899 Z= 0.245 Angle : 0.579 4.922 9356 Z= 0.313 Chirality : 0.038 0.134 1044 Planarity : 0.005 0.065 1219 Dihedral : 5.639 24.931 917 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.66 % Allowed : 7.15 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.27), residues: 846 helix: -1.01 (0.22), residues: 444 sheet: -1.35 (0.94), residues: 29 loop : -1.75 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 817 HIS 0.006 0.001 HIS A 517 PHE 0.015 0.002 PHE A 531 TYR 0.010 0.001 TYR A 241 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.9146 (tt) cc_final: 0.8890 (tt) REVERT: A 742 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8520 (tp-100) REVERT: A 879 MET cc_start: 0.8409 (ttt) cc_final: 0.8048 (tpp) outliers start: 5 outliers final: 3 residues processed: 81 average time/residue: 0.4287 time to fit residues: 46.4701 Evaluate side-chains 69 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 677 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6899 Z= 0.151 Angle : 0.513 5.883 9356 Z= 0.272 Chirality : 0.036 0.133 1044 Planarity : 0.004 0.048 1219 Dihedral : 5.160 24.518 917 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.06 % Allowed : 7.42 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.28), residues: 846 helix: -0.28 (0.24), residues: 439 sheet: -1.05 (0.95), residues: 29 loop : -1.56 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 600 HIS 0.005 0.001 HIS A 43 PHE 0.011 0.001 PHE A 524 TYR 0.015 0.001 TYR A 120 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TRP cc_start: 0.8733 (t-100) cc_final: 0.8137 (t-100) REVERT: A 742 GLN cc_start: 0.8887 (tp-100) cc_final: 0.8553 (tp-100) REVERT: A 879 MET cc_start: 0.8397 (ttt) cc_final: 0.7884 (tpp) REVERT: A 882 LEU cc_start: 0.8242 (mp) cc_final: 0.7503 (tt) outliers start: 8 outliers final: 4 residues processed: 76 average time/residue: 0.4083 time to fit residues: 41.8617 Evaluate side-chains 66 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 777 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN A 754 GLN A 758 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6899 Z= 0.180 Angle : 0.513 4.947 9356 Z= 0.270 Chirality : 0.036 0.129 1044 Planarity : 0.004 0.048 1219 Dihedral : 4.949 22.482 917 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.66 % Allowed : 7.55 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.29), residues: 846 helix: 0.09 (0.24), residues: 442 sheet: -0.94 (0.92), residues: 29 loop : -1.50 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 796 HIS 0.005 0.001 HIS A 558 PHE 0.011 0.001 PHE A 531 TYR 0.015 0.001 TYR A 120 ARG 0.001 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8522 (tp-100) REVERT: A 879 MET cc_start: 0.8389 (ttt) cc_final: 0.8033 (tpp) REVERT: A 882 LEU cc_start: 0.8287 (mp) cc_final: 0.7583 (tt) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.3840 time to fit residues: 34.2811 Evaluate side-chains 64 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 777 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 79 optimal weight: 0.6980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6899 Z= 0.125 Angle : 0.479 4.631 9356 Z= 0.247 Chirality : 0.036 0.127 1044 Planarity : 0.004 0.047 1219 Dihedral : 4.634 22.288 917 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.66 % Allowed : 7.81 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.29), residues: 846 helix: 0.48 (0.25), residues: 451 sheet: -0.54 (1.20), residues: 19 loop : -1.29 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 817 HIS 0.003 0.001 HIS A 43 PHE 0.008 0.001 PHE A 816 TYR 0.009 0.001 TYR A 120 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8476 (tp-100) REVERT: A 777 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7644 (t0) REVERT: A 879 MET cc_start: 0.8361 (ttt) cc_final: 0.8027 (tpp) REVERT: A 882 LEU cc_start: 0.8376 (mp) cc_final: 0.7638 (tt) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.3565 time to fit residues: 33.7130 Evaluate side-chains 65 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain A residue 777 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6899 Z= 0.136 Angle : 0.476 4.312 9356 Z= 0.247 Chirality : 0.035 0.123 1044 Planarity : 0.004 0.047 1219 Dihedral : 4.490 20.863 917 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.79 % Allowed : 7.81 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.29), residues: 846 helix: 0.73 (0.25), residues: 446 sheet: -0.61 (1.19), residues: 19 loop : -1.23 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 817 HIS 0.003 0.001 HIS A 654 PHE 0.009 0.001 PHE A 531 TYR 0.010 0.001 TYR A 120 ARG 0.001 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8471 (tp-100) REVERT: A 751 ARG cc_start: 0.7367 (tpt90) cc_final: 0.6630 (tpm170) REVERT: A 777 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7667 (t0) REVERT: A 879 MET cc_start: 0.8341 (ttt) cc_final: 0.8055 (tpp) REVERT: A 882 LEU cc_start: 0.8354 (mp) cc_final: 0.7685 (tt) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.3680 time to fit residues: 35.3644 Evaluate side-chains 69 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain A residue 777 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 0.0170 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6899 Z= 0.135 Angle : 0.476 6.810 9356 Z= 0.245 Chirality : 0.035 0.122 1044 Planarity : 0.004 0.047 1219 Dihedral : 4.391 20.932 917 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.53 % Allowed : 8.21 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.30), residues: 846 helix: 0.93 (0.25), residues: 445 sheet: -0.66 (1.21), residues: 19 loop : -1.13 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 796 HIS 0.003 0.001 HIS A 43 PHE 0.008 0.001 PHE A 531 TYR 0.007 0.001 TYR A 120 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8457 (tp-100) REVERT: A 751 ARG cc_start: 0.7369 (tpt90) cc_final: 0.6642 (tpm170) REVERT: A 777 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7624 (t0) REVERT: A 879 MET cc_start: 0.8287 (ttt) cc_final: 0.7982 (tpp) REVERT: A 882 LEU cc_start: 0.8379 (mp) cc_final: 0.7739 (tt) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.4185 time to fit residues: 37.5801 Evaluate side-chains 69 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 777 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6899 Z= 0.217 Angle : 0.519 4.469 9356 Z= 0.273 Chirality : 0.037 0.139 1044 Planarity : 0.004 0.047 1219 Dihedral : 4.584 20.745 917 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.66 % Allowed : 8.34 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.29), residues: 846 helix: 0.74 (0.25), residues: 444 sheet: -0.46 (1.00), residues: 29 loop : -1.22 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 796 HIS 0.005 0.001 HIS A 654 PHE 0.015 0.001 PHE A 531 TYR 0.010 0.001 TYR A 885 ARG 0.002 0.000 ARG A 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 GLN cc_start: 0.7460 (tt0) cc_final: 0.7057 (pt0) REVERT: A 742 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8432 (tp-100) REVERT: A 751 ARG cc_start: 0.7420 (tpt90) cc_final: 0.6692 (tpm170) REVERT: A 879 MET cc_start: 0.8400 (ttt) cc_final: 0.8027 (tpp) REVERT: A 882 LEU cc_start: 0.8275 (mp) cc_final: 0.7766 (tp) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.4194 time to fit residues: 38.8469 Evaluate side-chains 68 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 777 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6899 Z= 0.135 Angle : 0.481 6.879 9356 Z= 0.247 Chirality : 0.035 0.125 1044 Planarity : 0.004 0.046 1219 Dihedral : 4.399 21.507 917 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.53 % Allowed : 9.01 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 846 helix: 0.93 (0.25), residues: 450 sheet: -0.56 (0.96), residues: 29 loop : -1.12 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 817 HIS 0.003 0.001 HIS A 637 PHE 0.009 0.001 PHE A 816 TYR 0.015 0.001 TYR A 661 ARG 0.002 0.000 ARG A 840 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 GLN cc_start: 0.7460 (tt0) cc_final: 0.7041 (pt0) REVERT: A 742 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8435 (tp-100) REVERT: A 777 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7615 (t0) REVERT: A 879 MET cc_start: 0.8325 (ttt) cc_final: 0.7979 (tpp) REVERT: A 882 LEU cc_start: 0.8314 (mp) cc_final: 0.7826 (tp) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.4014 time to fit residues: 37.3690 Evaluate side-chains 71 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.119354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.092027 restraints weight = 62039.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.094280 restraints weight = 28145.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.095454 restraints weight = 19890.155| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6899 Z= 0.126 Angle : 0.466 5.664 9356 Z= 0.238 Chirality : 0.035 0.123 1044 Planarity : 0.003 0.047 1219 Dihedral : 4.248 20.160 917 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.53 % Allowed : 8.87 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.30), residues: 846 helix: 1.22 (0.25), residues: 444 sheet: -0.54 (0.95), residues: 29 loop : -1.08 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 137 HIS 0.003 0.001 HIS A 637 PHE 0.008 0.001 PHE A 816 TYR 0.010 0.001 TYR A 885 ARG 0.002 0.000 ARG A 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.56 seconds wall clock time: 52 minutes 6.92 seconds (3126.92 seconds total)