Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 04:42:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pty_13643/08_2023/7pty_13643.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pty_13643/08_2023/7pty_13643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pty_13643/08_2023/7pty_13643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pty_13643/08_2023/7pty_13643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pty_13643/08_2023/7pty_13643.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pty_13643/08_2023/7pty_13643.pdb" } resolution = 4.63 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 ------------------------------------------------------------------------------- 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= 0.000 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 8522 2.51 5 N 2267 2.21 5 O 2611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 704": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 13433 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6663 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 824} Chain breaks: 4 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 6770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 6770 Classifications: {'peptide': 865} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 838} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 7.05, per 1000 atoms: 0.52 Number of scatterers: 13433 At special positions: 0 Unit cell: (142.2, 102.6, 137.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 2611 8.00 N 2267 7.00 C 8522 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: 6.00 Conformation dependent library (CDL) restraints added in 1.9 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 2 sheets defined 64.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.709A pdb=" N ILE A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 131 through 160 removed outlier: 3.679A pdb=" N THR A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 190 removed outlier: 3.615A pdb=" N LYS A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 215 removed outlier: 3.903A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 236 Processing helix chain 'A' and resid 247 through 281 removed outlier: 3.905A pdb=" N GLN A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 307 Processing helix chain 'A' and resid 312 through 326 removed outlier: 3.722A pdb=" N ASN A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 353 removed outlier: 4.082A pdb=" N LYS A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 432 removed outlier: 3.956A pdb=" N VAL A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP A 432 " --> pdb=" O VAL A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 428 through 432' Processing helix chain 'A' and resid 461 through 475 removed outlier: 4.588A pdb=" N ILE A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.606A pdb=" N ILE A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.992A pdb=" N VAL A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 523 removed outlier: 4.094A pdb=" N LEU A 519 " --> pdb=" O ASN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.550A pdb=" N ILE A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 558 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 583 through 593 removed outlier: 3.526A pdb=" N VAL A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 593 " --> pdb=" O ASN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.503A pdb=" N THR A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.955A pdb=" N LEU A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.590A pdb=" N PHE A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 removed outlier: 3.600A pdb=" N LYS A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 718 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 776 through 783 removed outlier: 3.839A pdb=" N ILE A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET A 783 " --> pdb=" O HIS A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 797 Processing helix chain 'A' and resid 809 through 818 removed outlier: 3.519A pdb=" N GLY A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 829 removed outlier: 3.620A pdb=" N VAL A 823 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 851 Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 875 through 883 Processing helix chain 'A' and resid 885 through 894 removed outlier: 3.552A pdb=" N VAL A 889 " --> pdb=" O ASP A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 907 Processing helix chain 'A' and resid 908 through 916 Processing helix chain 'A' and resid 922 through 927 removed outlier: 4.118A pdb=" N PHE A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 removed outlier: 3.542A pdb=" N GLY B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 89 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.786A pdb=" N ILE B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 159 removed outlier: 4.001A pdb=" N THR B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.949A pdb=" N ILE B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 213 removed outlier: 4.237A pdb=" N GLU B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 236 removed outlier: 4.036A pdb=" N ASP B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 281 removed outlier: 4.108A pdb=" N TYR B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 253 " --> pdb=" O GLN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 327 removed outlier: 4.076A pdb=" N ASN B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 Processing helix chain 'B' and resid 352 through 355 removed outlier: 4.315A pdb=" N ILE B 355 " --> pdb=" O LYS B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 428 through 432 removed outlier: 3.628A pdb=" N VAL B 431 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 477 through 490 Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.516A pdb=" N HIS B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 522 Processing helix chain 'B' and resid 525 through 532 removed outlier: 3.712A pdb=" N LEU B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 4.240A pdb=" N GLU B 546 " --> pdb=" O HIS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 4.053A pdb=" N HIS B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 580 removed outlier: 4.317A pdb=" N ARG B 580 " --> pdb=" O HIS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 593 removed outlier: 3.819A pdb=" N ARG B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASN B 589 " --> pdb=" O LYS B 585 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU B 590 " --> pdb=" O THR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 617 through 626 removed outlier: 3.935A pdb=" N ASP B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 625 " --> pdb=" O ASP B 621 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 649 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 673 through 682 removed outlier: 4.268A pdb=" N PHE B 677 " --> pdb=" O ALA B 673 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 678 " --> pdb=" O PRO B 674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 679 " --> pdb=" O ILE B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 694 removed outlier: 3.772A pdb=" N LYS B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.935A pdb=" N ILE B 699 " --> pdb=" O LYS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 717 removed outlier: 3.772A pdb=" N PHE B 713 " --> pdb=" O THR B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 743 through 752 Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 776 through 784 Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.935A pdb=" N VAL B 791 " --> pdb=" O PRO B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 818 Processing helix chain 'B' and resid 819 through 829 Processing helix chain 'B' and resid 842 through 851 removed outlier: 3.543A pdb=" N LEU B 846 " --> pdb=" O THR B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 862 Processing helix chain 'B' and resid 875 through 884 Processing helix chain 'B' and resid 885 through 895 removed outlier: 4.160A pdb=" N GLU B 894 " --> pdb=" O ARG B 890 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 895 " --> pdb=" O LEU B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 906 No H-bonds generated for 'chain 'B' and resid 904 through 906' Processing helix chain 'B' and resid 907 through 916 removed outlier: 3.647A pdb=" N ILE B 911 " --> pdb=" O GLY B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 927 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 401 Processing sheet with id=AA2, first strand: chain 'B' and resid 406 through 408 removed outlier: 3.954A pdb=" N ARG B 438 " --> pdb=" O MET B 455 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 455 " --> pdb=" O ARG B 438 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 2052 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: 4.11 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4459 1.34 - 1.46: 2794 1.46 - 1.58: 6331 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 13647 Sorted by residual: bond pdb=" CA ARG A 215 " pdb=" C ARG A 215 " ideal model delta sigma weight residual 1.523 1.569 -0.045 1.34e-02 5.57e+03 1.15e+01 bond pdb=" C CYS B 424 " pdb=" N PRO B 425 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.12e+00 bond pdb=" CD GLU B 828 " pdb=" OE1 GLU B 828 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.88e+00 bond pdb=" CG GLU B 828 " pdb=" CD GLU B 828 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.33e+00 bond pdb=" C VAL A 214 " pdb=" N ARG A 215 " ideal model delta sigma weight residual 1.332 1.317 0.015 1.40e-02 5.10e+03 1.16e+00 ... (remaining 13642 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.07: 177 105.07 - 112.30: 7062 112.30 - 119.53: 4621 119.53 - 126.76: 6479 126.76 - 133.99: 108 Bond angle restraints: 18447 Sorted by residual: angle pdb=" N GLY B 191 " pdb=" CA GLY B 191 " pdb=" C GLY B 191 " ideal model delta sigma weight residual 112.50 117.59 -5.09 1.16e+00 7.43e-01 1.93e+01 angle pdb=" N GLU B 828 " pdb=" CA GLU B 828 " pdb=" CB GLU B 828 " ideal model delta sigma weight residual 110.28 116.53 -6.25 1.55e+00 4.16e-01 1.63e+01 angle pdb=" C LEU B 827 " pdb=" N GLU B 828 " pdb=" CA GLU B 828 " ideal model delta sigma weight residual 120.31 114.88 5.43 1.52e+00 4.33e-01 1.28e+01 angle pdb=" N VAL A 77 " pdb=" CA VAL A 77 " pdb=" C VAL A 77 " ideal model delta sigma weight residual 112.96 109.51 3.45 1.00e+00 1.00e+00 1.19e+01 angle pdb=" C LEU A 469 " pdb=" N TYR A 470 " pdb=" CA TYR A 470 " ideal model delta sigma weight residual 120.31 115.39 4.92 1.52e+00 4.33e-01 1.05e+01 ... (remaining 18442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7559 17.96 - 35.91: 683 35.91 - 53.87: 84 53.87 - 71.83: 11 71.83 - 89.78: 10 Dihedral angle restraints: 8347 sinusoidal: 3333 harmonic: 5014 Sorted by residual: dihedral pdb=" CA GLU A 164 " pdb=" C GLU A 164 " pdb=" N SER A 165 " pdb=" CA SER A 165 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA PHE A 444 " pdb=" C PHE A 444 " pdb=" N ASN A 445 " pdb=" CA ASN A 445 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA PHE B 156 " pdb=" C PHE B 156 " pdb=" N LYS B 157 " pdb=" CA LYS B 157 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1577 0.043 - 0.086: 480 0.086 - 0.129: 78 0.129 - 0.172: 8 0.172 - 0.216: 2 Chirality restraints: 2145 Sorted by residual: chirality pdb=" CB ILE B 366 " pdb=" CA ILE B 366 " pdb=" CG1 ILE B 366 " pdb=" CG2 ILE B 366 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU A 254 " pdb=" CB LEU A 254 " pdb=" CD1 LEU A 254 " pdb=" CD2 LEU A 254 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CA GLU B 114 " pdb=" N GLU B 114 " pdb=" C GLU B 114 " pdb=" CB GLU B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 2142 not shown) Planarity restraints: 2382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 448 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO B 449 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 216 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 217 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 415 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 416 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " -0.030 5.00e-02 4.00e+02 ... (remaining 2379 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1407 2.74 - 3.28: 16436 3.28 - 3.82: 23587 3.82 - 4.36: 28241 4.36 - 4.90: 42335 Nonbonded interactions: 112006 Sorted by model distance: nonbonded pdb=" O TYR B 511 " pdb=" NE2 GLN B 549 " model vdw 2.199 2.520 nonbonded pdb=" O GLU B 725 " pdb=" NE2 GLN B 729 " model vdw 2.202 2.520 nonbonded pdb=" O PHE B 462 " pdb=" ND1 HIS B 466 " model vdw 2.206 2.520 nonbonded pdb=" OG SER B 135 " pdb=" OG SER B 273 " model vdw 2.215 2.440 nonbonded pdb=" NE2 HIS B 779 " pdb=" O LEU B 808 " model vdw 2.219 2.520 ... (remaining 112001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 50 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 197 through 578 or (resid 579 and (name N o \ r name CA or name C or name O or name CB )) or resid 580 through 616 or (resid 6 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 618 through \ 928)) selection = (chain 'B' and (resid 50 through 90 or resid 93 through 98 or resid 106 through \ 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or re \ sid 216 through 219 or (resid 220 and (name N or name CA or name C or name O or \ name CB )) or resid 221 through 236 or resid 246 through 355 or resid 367 throug \ h 928)) } 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: 2.420 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: 10.600 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.730 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.003 0.045 13647 Z= 0.215 Angle : 0.681 8.072 18447 Z= 0.376 Chirality : 0.041 0.216 2145 Planarity : 0.005 0.060 2382 Dihedral : 13.762 89.785 5087 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer Outliers : 0.00 % 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: -1.41 (0.20), residues: 1699 helix: 0.31 (0.17), residues: 971 sheet: -3.98 (0.58), residues: 54 loop : -2.57 (0.23), residues: 674 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2360 time to fit residues: 25.2412 Evaluate side-chains 54 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 134 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 chunk 155 optimal weight: 20.0000 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 13647 Z= 0.157 Angle : 0.575 6.461 18447 Z= 0.310 Chirality : 0.039 0.226 2145 Planarity : 0.004 0.056 2382 Dihedral : 5.772 27.432 1804 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer Outliers : 0.20 % 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: -1.18 (0.20), residues: 1699 helix: 0.49 (0.16), residues: 1000 sheet: -3.81 (0.60), residues: 54 loop : -2.60 (0.23), residues: 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.592 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 68 average time/residue: 0.2176 time to fit residues: 24.8420 Evaluate side-chains 53 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13647 Z= 0.255 Angle : 0.647 6.649 18447 Z= 0.353 Chirality : 0.041 0.198 2145 Planarity : 0.005 0.079 2382 Dihedral : 5.985 27.491 1804 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer Outliers : 0.07 % 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 (0.20), residues: 1699 helix: 0.37 (0.16), residues: 982 sheet: -4.18 (0.56), residues: 55 loop : -2.57 (0.23), residues: 662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.783 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2196 time to fit residues: 24.2302 Evaluate side-chains 53 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.9980 chunk 116 optimal weight: 0.0570 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN A 526 GLN ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13647 Z= 0.185 Angle : 0.598 6.143 18447 Z= 0.323 Chirality : 0.040 0.224 2145 Planarity : 0.005 0.075 2382 Dihedral : 5.861 27.525 1804 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 0.07 % 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: -1.24 (0.20), residues: 1699 helix: 0.46 (0.16), residues: 991 sheet: -4.16 (0.63), residues: 48 loop : -2.61 (0.23), residues: 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2413 time to fit residues: 26.9004 Evaluate side-chains 53 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.0870 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 41 optimal weight: 0.0270 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 13647 Z= 0.151 Angle : 0.583 8.575 18447 Z= 0.308 Chirality : 0.039 0.267 2145 Planarity : 0.004 0.060 2382 Dihedral : 5.525 26.846 1804 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer Outliers : 0.14 % 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: -1.05 (0.20), residues: 1699 helix: 0.65 (0.16), residues: 998 sheet: -3.67 (0.65), residues: 48 loop : -2.69 (0.22), residues: 653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.2334 time to fit residues: 27.8407 Evaluate side-chains 54 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1679 time to fit residues: 2.6633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 165 optimal weight: 0.2980 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13647 Z= 0.179 Angle : 0.599 8.225 18447 Z= 0.320 Chirality : 0.039 0.219 2145 Planarity : 0.004 0.062 2382 Dihedral : 5.529 25.819 1804 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer Outliers : 0.00 % 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: -0.97 (0.20), residues: 1699 helix: 0.72 (0.17), residues: 983 sheet: -3.71 (0.64), residues: 48 loop : -2.57 (0.22), residues: 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2333 time to fit residues: 26.3650 Evaluate side-chains 51 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.808 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 93 optimal weight: 0.3980 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13647 Z= 0.156 Angle : 0.588 7.416 18447 Z= 0.313 Chirality : 0.039 0.217 2145 Planarity : 0.004 0.056 2382 Dihedral : 5.446 26.268 1804 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 0.00 % 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: -0.88 (0.20), residues: 1699 helix: 0.81 (0.16), residues: 984 sheet: -3.71 (0.64), residues: 48 loop : -2.56 (0.22), residues: 667 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2452 time to fit residues: 27.5761 Evaluate side-chains 51 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 13647 Z= 0.235 Angle : 0.640 7.208 18447 Z= 0.348 Chirality : 0.041 0.210 2145 Planarity : 0.005 0.058 2382 Dihedral : 5.679 26.217 1804 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer Outliers : 0.00 % 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: -1.06 (0.20), residues: 1699 helix: 0.62 (0.17), residues: 982 sheet: -3.83 (0.63), residues: 48 loop : -2.55 (0.22), residues: 669 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2352 time to fit residues: 25.4045 Evaluate side-chains 49 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 138 optimal weight: 0.0020 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13647 Z= 0.188 Angle : 0.616 7.288 18447 Z= 0.330 Chirality : 0.040 0.217 2145 Planarity : 0.004 0.056 2382 Dihedral : 5.639 26.422 1804 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer Outliers : 0.00 % 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: -1.03 (0.20), residues: 1699 helix: 0.65 (0.16), residues: 985 sheet: -3.77 (0.64), residues: 48 loop : -2.55 (0.22), residues: 666 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2271 time to fit residues: 23.7526 Evaluate side-chains 48 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 170 optimal weight: 0.0980 chunk 156 optimal weight: 10.0000 chunk 135 optimal weight: 0.0010 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 13647 Z= 0.156 Angle : 0.608 7.767 18447 Z= 0.320 Chirality : 0.040 0.227 2145 Planarity : 0.004 0.054 2382 Dihedral : 5.430 26.263 1804 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 0.00 % 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: -0.91 (0.20), residues: 1699 helix: 0.76 (0.17), residues: 984 sheet: -3.66 (0.65), residues: 48 loop : -2.53 (0.23), residues: 667 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2425 time to fit residues: 25.2103 Evaluate side-chains 48 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.9990 chunk 41 optimal weight: 0.0270 chunk 125 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 0.0870 chunk 135 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.046632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.038140 restraints weight = 167362.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.039011 restraints weight = 124840.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.039651 restraints weight = 99724.506| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 13647 Z= 0.151 Angle : 0.597 7.375 18447 Z= 0.313 Chirality : 0.040 0.236 2145 Planarity : 0.004 0.053 2382 Dihedral : 5.178 26.597 1804 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1699 helix: 0.86 (0.17), residues: 983 sheet: -3.65 (0.64), residues: 48 loop : -2.50 (0.23), residues: 668 =============================================================================== Job complete usr+sys time: 2077.76 seconds wall clock time: 40 minutes 31.75 seconds (2431.75 seconds total)