Starting phenix.real_space_refine on Thu Jan 18 05:05:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln7_0926/01_2024/6ln7_0926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln7_0926/01_2024/6ln7_0926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln7_0926/01_2024/6ln7_0926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln7_0926/01_2024/6ln7_0926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln7_0926/01_2024/6ln7_0926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln7_0926/01_2024/6ln7_0926_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 4988 2.51 5 N 1311 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 878": "OD1" <-> "OD2" Residue "A TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 907": "OE1" <-> "OE2" Residue "A ASP 980": "OD1" <-> "OD2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7840 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7840 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'peptide': 1011, 'undetermined': 4} Link IDs: {'PTRANS': 46, 'TRANS': 964, None: 4} Not linked: pdbres="SER A1031 " pdbres="ACP A2001 " Not linked: pdbres="ACP A2001 " pdbres=" MG A2002 " Not linked: pdbres=" MG A2002 " pdbres=" CA A2003 " Not linked: pdbres=" CA A2003 " pdbres=" CA A2004 " Chain breaks: 1 Time building chain proxies: 4.69, per 1000 atoms: 0.60 Number of scatterers: 7840 At special positions: 0 Unit cell: (103.335, 80.925, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 57 16.00 P 3 15.00 Mg 1 11.99 O 1478 8.00 N 1311 7.00 C 4988 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: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 8 sheets defined 47.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.618A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 57 removed outlier: 3.966A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.897A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 89 through 117 removed outlier: 3.815A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 234 No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 248 through 274 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 288 through 306 Processing helix chain 'A' and resid 311 through 329 removed outlier: 3.816A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.672A pdb=" N VAL A 339 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.650A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.569A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.658A pdb=" N ARG A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 583 through 586 No H-bonds generated for 'chain 'A' and resid 583 through 586' Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 662 through 669 removed outlier: 3.806A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.679A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 710 No H-bonds generated for 'chain 'A' and resid 707 through 710' Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 739 through 780 removed outlier: 3.561A pdb=" N VAL A 746 " --> pdb=" O VAL A 743 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 752 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 761 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 763 " --> pdb=" O ILE A 760 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 764 " --> pdb=" O ARG A 761 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 765 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 766 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 768 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 772 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS A 773 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 776 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 777 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 780 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 798 Processing helix chain 'A' and resid 801 through 808 removed outlier: 4.135A pdb=" N LEU A 806 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.648A pdb=" N ALA A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.579A pdb=" N PHE A 890 " --> pdb=" O CYS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 914 removed outlier: 3.766A pdb=" N SER A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 948 Processing helix chain 'A' and resid 952 through 956 Processing helix chain 'A' and resid 963 through 991 Proline residue: A 975 - end of helix removed outlier: 3.797A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 3.621A pdb=" N LEU A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) Proline residue: A1024 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.321A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.748A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 331 through 333 Processing sheet with id= D, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.622A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 621 " --> pdb=" O SER A 350 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 424 through 428 Processing sheet with id= F, first strand: chain 'A' and resid 376 through 383 removed outlier: 5.527A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 362 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET A 366 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS A 595 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE A 368 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N VAL A 593 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 13.044A pdb=" N ASP A 370 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.948A pdb=" N THR A 591 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.999A pdb=" N LEU A 590 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE A 527 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N PHE A 592 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL A 529 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.436A pdb=" N CYS A 674 " --> pdb=" O PHE A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 339 hydrogen bonds defined for protein. 897 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: 2.65 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2578 1.35 - 1.48: 1791 1.48 - 1.61: 3522 1.61 - 1.73: 4 1.73 - 1.86: 90 Bond restraints: 7985 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.307 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C4' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.428 1.301 0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 1.335 1.449 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.494 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.28: 227 106.28 - 113.21: 4486 113.21 - 120.13: 2692 120.13 - 127.06: 3350 127.06 - 133.98: 89 Bond angle restraints: 10844 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 109.50 -15.75 3.00e+00 1.11e-01 2.76e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.64 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 108.35 10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 108.99 10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 108.65 10.30 3.00e+00 1.11e-01 1.18e+01 ... (remaining 10839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.02: 4714 26.02 - 52.04: 129 52.04 - 78.06: 12 78.06 - 104.08: 2 104.08 - 130.10: 1 Dihedral angle restraints: 4858 sinusoidal: 1938 harmonic: 2920 Sorted by residual: dihedral pdb=" O1A ACP A2001 " pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" PB ACP A2001 " ideal model delta sinusoidal sigma weight residual -48.75 81.35 -130.10 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CA VAL A 949 " pdb=" C VAL A 949 " pdb=" N GLU A 950 " pdb=" CA GLU A 950 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP A 370 " pdb=" CB ASP A 370 " pdb=" CG ASP A 370 " pdb=" OD1 ASP A 370 " ideal model delta sinusoidal sigma weight residual -30.00 -87.58 57.58 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1184 0.078 - 0.155: 88 0.155 - 0.233: 0 0.233 - 0.310: 0 0.310 - 0.388: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CG LEU A 806 " pdb=" CB LEU A 806 " pdb=" CD1 LEU A 806 " pdb=" CD2 LEU A 806 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1270 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A1017 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 975 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 194 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 195 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " 0.019 5.00e-02 4.00e+02 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 7429 3.22 - 3.78: 12046 3.78 - 4.34: 17839 4.34 - 4.90: 28400 Nonbonded interactions: 65839 Sorted by model distance: nonbonded pdb=" OD1 ASP A 351 " pdb="MG MG A2002 " model vdw 2.101 2.170 nonbonded pdb=" OE2 GLU A 309 " pdb=" OD1 ASN A 795 " model vdw 2.114 3.040 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.134 2.170 nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.138 2.170 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.150 3.040 ... (remaining 65834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 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: 1.380 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.770 Find NCS groups from input model: 0.180 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.005 0.228 7985 Z= 0.315 Angle : 0.647 15.750 10844 Z= 0.341 Chirality : 0.042 0.388 1273 Planarity : 0.004 0.041 1377 Dihedral : 12.197 130.104 2966 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -3.93 (0.20), residues: 1007 helix: -3.29 (0.13), residues: 501 sheet: -1.13 (0.46), residues: 113 loop : -1.80 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 793 HIS 0.005 0.001 HIS A 566 PHE 0.010 0.001 PHE A 367 TYR 0.009 0.001 TYR A 842 ARG 0.005 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.010 Fit side-chains REVERT: A 1 MET cc_start: 0.7214 (tpp) cc_final: 0.6660 (tpp) REVERT: A 33 LYS cc_start: 0.8417 (tmtt) cc_final: 0.7918 (ttmm) REVERT: A 254 ASP cc_start: 0.7702 (m-30) cc_final: 0.7412 (m-30) REVERT: A 365 ARG cc_start: 0.7824 (mtt90) cc_final: 0.7414 (mtt180) REVERT: A 381 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 494 MET cc_start: 0.8920 (ttt) cc_final: 0.8596 (ttm) REVERT: A 732 MET cc_start: 0.8595 (ttt) cc_final: 0.8393 (ttp) REVERT: A 824 LYS cc_start: 0.8486 (mttm) cc_final: 0.8238 (mptt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 1.4531 time to fit residues: 257.4422 Evaluate side-chains 113 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 HIS A 278 HIS A 469 ASN A 582 ASN A 868 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7985 Z= 0.196 Angle : 0.522 6.240 10844 Z= 0.267 Chirality : 0.041 0.129 1273 Planarity : 0.005 0.046 1377 Dihedral : 8.531 166.046 1103 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.20 % Allowed : 12.50 % Favored : 85.30 % 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: -1.35 (0.24), residues: 1007 helix: -0.51 (0.21), residues: 495 sheet: -0.90 (0.44), residues: 114 loop : -1.20 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.013 0.001 PHE A 367 TYR 0.012 0.002 TYR A 842 ARG 0.004 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.923 Fit side-chains REVERT: A 1 MET cc_start: 0.7206 (tpp) cc_final: 0.6892 (tpp) REVERT: A 33 LYS cc_start: 0.8439 (tmtt) cc_final: 0.7914 (ttmm) REVERT: A 135 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8100 (ttmm) REVERT: A 254 ASP cc_start: 0.7539 (m-30) cc_final: 0.7217 (m-30) REVERT: A 324 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7356 (ttp-110) REVERT: A 370 ASP cc_start: 0.7681 (t70) cc_final: 0.7438 (t70) REVERT: A 381 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8102 (mt-10) REVERT: A 466 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 494 MET cc_start: 0.8866 (ttt) cc_final: 0.8561 (ttm) REVERT: A 732 MET cc_start: 0.8553 (ttt) cc_final: 0.8301 (ttp) outliers start: 19 outliers final: 8 residues processed: 123 average time/residue: 1.3371 time to fit residues: 173.5961 Evaluate side-chains 119 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 579 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 GLN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7985 Z= 0.187 Angle : 0.500 5.853 10844 Z= 0.255 Chirality : 0.041 0.168 1273 Planarity : 0.004 0.046 1377 Dihedral : 8.536 167.353 1103 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.66 % Allowed : 13.89 % Favored : 83.45 % 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: -0.45 (0.25), residues: 1007 helix: 0.41 (0.23), residues: 498 sheet: -1.01 (0.43), residues: 109 loop : -0.85 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.011 0.001 PHE A 592 TYR 0.013 0.002 TYR A 842 ARG 0.005 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.855 Fit side-chains REVERT: A 33 LYS cc_start: 0.8436 (tmtt) cc_final: 0.7906 (ttmm) REVERT: A 51 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7119 (tp30) REVERT: A 117 GLU cc_start: 0.7642 (tp30) cc_final: 0.7421 (tp30) REVERT: A 135 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8181 (ttmm) REVERT: A 153 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8424 (pt) REVERT: A 172 THR cc_start: 0.8719 (t) cc_final: 0.8423 (p) REVERT: A 246 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6174 (ptm160) REVERT: A 254 ASP cc_start: 0.7608 (m-30) cc_final: 0.7243 (m-30) REVERT: A 324 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7415 (ttp-110) REVERT: A 381 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 452 MET cc_start: 0.8473 (ptm) cc_final: 0.8253 (ptp) REVERT: A 466 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7654 (mt-10) REVERT: A 494 MET cc_start: 0.8858 (ttt) cc_final: 0.8485 (ttm) REVERT: A 585 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8202 (mtmt) outliers start: 23 outliers final: 9 residues processed: 140 average time/residue: 1.2748 time to fit residues: 188.9279 Evaluate side-chains 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1023 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.0030 overall best weight: 1.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7985 Z= 0.216 Angle : 0.517 6.081 10844 Z= 0.260 Chirality : 0.042 0.178 1273 Planarity : 0.004 0.046 1377 Dihedral : 8.652 169.613 1103 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.20 % Allowed : 16.32 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1007 helix: 0.75 (0.24), residues: 498 sheet: -0.80 (0.42), residues: 119 loop : -0.75 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.014 0.001 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.005 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.867 Fit side-chains REVERT: A 33 LYS cc_start: 0.8484 (tmtt) cc_final: 0.7897 (ttmm) REVERT: A 51 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7169 (tp30) REVERT: A 117 GLU cc_start: 0.7687 (tp30) cc_final: 0.7457 (tp30) REVERT: A 135 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8208 (ttmm) REVERT: A 246 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6271 (ptm160) REVERT: A 254 ASP cc_start: 0.7640 (m-30) cc_final: 0.7345 (m-30) REVERT: A 324 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7410 (ttp-110) REVERT: A 366 MET cc_start: 0.8869 (ptt) cc_final: 0.8532 (ptt) REVERT: A 381 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 452 MET cc_start: 0.8427 (ptm) cc_final: 0.8212 (ptp) REVERT: A 466 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 494 MET cc_start: 0.8719 (ttt) cc_final: 0.8506 (ttm) REVERT: A 876 LYS cc_start: 0.6972 (mtmm) cc_final: 0.6259 (mtmm) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 1.3431 time to fit residues: 182.7039 Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1023 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 87 optimal weight: 0.0010 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7985 Z= 0.236 Angle : 0.524 6.404 10844 Z= 0.264 Chirality : 0.042 0.175 1273 Planarity : 0.004 0.046 1377 Dihedral : 8.907 179.530 1103 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.08 % Allowed : 17.36 % Favored : 80.56 % 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 (0.26), residues: 1007 helix: 0.81 (0.24), residues: 499 sheet: -0.81 (0.42), residues: 119 loop : -0.66 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.014 0.001 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.006 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.904 Fit side-chains REVERT: A 33 LYS cc_start: 0.8512 (tmtt) cc_final: 0.7898 (ttmm) REVERT: A 65 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8648 (mp) REVERT: A 117 GLU cc_start: 0.7642 (tp30) cc_final: 0.7438 (tp30) REVERT: A 135 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8236 (ttmm) REVERT: A 246 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6569 (ptm160) REVERT: A 254 ASP cc_start: 0.7643 (m-30) cc_final: 0.7395 (m-30) REVERT: A 324 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7412 (ttp-110) REVERT: A 381 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8086 (mt-10) REVERT: A 466 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 494 MET cc_start: 0.8708 (ttt) cc_final: 0.8424 (ttm) REVERT: A 571 ARG cc_start: 0.7367 (mpp80) cc_final: 0.7099 (mtt90) outliers start: 18 outliers final: 12 residues processed: 130 average time/residue: 1.2758 time to fit residues: 175.2546 Evaluate side-chains 133 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 992 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0570 chunk 19 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7985 Z= 0.145 Angle : 0.479 7.108 10844 Z= 0.244 Chirality : 0.040 0.164 1273 Planarity : 0.004 0.046 1377 Dihedral : 8.684 176.155 1103 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.27 % Allowed : 18.29 % Favored : 80.44 % 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: 0.38 (0.26), residues: 1007 helix: 1.14 (0.24), residues: 497 sheet: -0.80 (0.44), residues: 107 loop : -0.47 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.010 0.001 PHE A 592 TYR 0.011 0.001 TYR A 842 ARG 0.006 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.821 Fit side-chains REVERT: A 33 LYS cc_start: 0.8502 (tmtt) cc_final: 0.7891 (ttmm) REVERT: A 135 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8209 (ttmm) REVERT: A 158 LYS cc_start: 0.8886 (tttt) cc_final: 0.8669 (ttpt) REVERT: A 246 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6583 (ptm160) REVERT: A 254 ASP cc_start: 0.7545 (m-30) cc_final: 0.7256 (m-30) REVERT: A 324 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7373 (ttp-110) REVERT: A 366 MET cc_start: 0.8755 (ptt) cc_final: 0.8504 (ptt) REVERT: A 381 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 400 LYS cc_start: 0.7371 (mtpt) cc_final: 0.7078 (ptmm) REVERT: A 466 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7670 (mt-10) REVERT: A 479 MET cc_start: 0.8016 (mtt) cc_final: 0.7694 (mtt) outliers start: 11 outliers final: 4 residues processed: 131 average time/residue: 1.2907 time to fit residues: 178.6080 Evaluate side-chains 126 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 522 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 58 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 406 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7985 Z= 0.151 Angle : 0.486 8.656 10844 Z= 0.243 Chirality : 0.040 0.164 1273 Planarity : 0.004 0.045 1377 Dihedral : 8.673 176.308 1103 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.39 % Allowed : 18.52 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1007 helix: 1.35 (0.24), residues: 490 sheet: -0.71 (0.46), residues: 104 loop : -0.42 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 854 HIS 0.003 0.000 HIS A 566 PHE 0.010 0.001 PHE A 367 TYR 0.013 0.001 TYR A 842 ARG 0.006 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.693 Fit side-chains REVERT: A 33 LYS cc_start: 0.8503 (tmtt) cc_final: 0.7887 (ttmm) REVERT: A 135 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8146 (ttmm) REVERT: A 246 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6464 (ptm160) REVERT: A 254 ASP cc_start: 0.7539 (m-30) cc_final: 0.7207 (m-30) REVERT: A 324 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7368 (ttp-110) REVERT: A 366 MET cc_start: 0.8822 (ptt) cc_final: 0.8562 (ptt) REVERT: A 381 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8036 (mt-10) REVERT: A 403 ASN cc_start: 0.8241 (p0) cc_final: 0.8029 (p0) REVERT: A 466 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 479 MET cc_start: 0.8036 (mtt) cc_final: 0.7663 (mtt) REVERT: A 576 HIS cc_start: 0.7111 (m170) cc_final: 0.6828 (m-70) outliers start: 12 outliers final: 5 residues processed: 129 average time/residue: 1.2691 time to fit residues: 173.2893 Evaluate side-chains 124 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7985 Z= 0.193 Angle : 0.522 9.961 10844 Z= 0.259 Chirality : 0.041 0.169 1273 Planarity : 0.004 0.045 1377 Dihedral : 8.745 175.248 1103 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.39 % Allowed : 19.21 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1007 helix: 1.25 (0.24), residues: 498 sheet: -0.70 (0.45), residues: 107 loop : -0.44 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.013 0.001 PHE A 367 TYR 0.015 0.001 TYR A 842 ARG 0.006 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.912 Fit side-chains REVERT: A 33 LYS cc_start: 0.8611 (tmtt) cc_final: 0.7940 (ttmm) REVERT: A 135 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8205 (ttmm) REVERT: A 246 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6500 (ptm160) REVERT: A 254 ASP cc_start: 0.7573 (m-30) cc_final: 0.7274 (m-30) REVERT: A 324 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7388 (ttp-110) REVERT: A 366 MET cc_start: 0.8887 (ptt) cc_final: 0.8632 (ptt) REVERT: A 381 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 466 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 479 MET cc_start: 0.8044 (mtt) cc_final: 0.7703 (mtt) REVERT: A 576 HIS cc_start: 0.7256 (m170) cc_final: 0.6980 (m-70) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 1.3010 time to fit residues: 167.5698 Evaluate side-chains 123 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 992 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7985 Z= 0.165 Angle : 0.509 11.258 10844 Z= 0.251 Chirality : 0.041 0.168 1273 Planarity : 0.004 0.045 1377 Dihedral : 8.661 171.698 1103 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.16 % Allowed : 19.33 % Favored : 79.51 % 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: 0.67 (0.26), residues: 1007 helix: 1.41 (0.24), residues: 491 sheet: -0.62 (0.45), residues: 107 loop : -0.35 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.011 0.001 PHE A 367 TYR 0.013 0.001 TYR A 842 ARG 0.007 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.933 Fit side-chains REVERT: A 33 LYS cc_start: 0.8614 (tmtt) cc_final: 0.7933 (ttmm) REVERT: A 135 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8108 (ttmm) REVERT: A 246 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6471 (ptm160) REVERT: A 254 ASP cc_start: 0.7546 (m-30) cc_final: 0.7255 (m-30) REVERT: A 324 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7376 (ttp-110) REVERT: A 381 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8039 (mt-10) REVERT: A 466 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 479 MET cc_start: 0.8052 (mtt) cc_final: 0.7732 (mtt) REVERT: A 576 HIS cc_start: 0.7206 (m170) cc_final: 0.6956 (m-70) outliers start: 10 outliers final: 7 residues processed: 118 average time/residue: 1.3250 time to fit residues: 165.2956 Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 992 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 0.0050 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 0.0570 overall best weight: 0.3112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7985 Z= 0.129 Angle : 0.490 11.712 10844 Z= 0.242 Chirality : 0.039 0.166 1273 Planarity : 0.004 0.045 1377 Dihedral : 8.493 172.190 1103 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.39 % Allowed : 19.21 % Favored : 79.40 % 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 (0.27), residues: 1007 helix: 1.60 (0.24), residues: 490 sheet: -0.20 (0.46), residues: 117 loop : -0.32 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.002 0.000 HIS A 566 PHE 0.008 0.001 PHE A 592 TYR 0.011 0.001 TYR A 842 ARG 0.007 0.000 ARG A 572 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 0.934 Fit side-chains REVERT: A 33 LYS cc_start: 0.8604 (tmtt) cc_final: 0.7923 (ttmm) REVERT: A 135 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8145 (ttmm) REVERT: A 174 ARG cc_start: 0.7779 (mmm160) cc_final: 0.7530 (mtp85) REVERT: A 246 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6252 (ptm160) REVERT: A 254 ASP cc_start: 0.7444 (m-30) cc_final: 0.7129 (m-30) REVERT: A 278 HIS cc_start: 0.7776 (p90) cc_final: 0.7386 (p-80) REVERT: A 324 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7293 (ttp-110) REVERT: A 466 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7781 (mt-10) REVERT: A 479 MET cc_start: 0.7953 (mtt) cc_final: 0.7621 (mtt) REVERT: A 576 HIS cc_start: 0.7174 (m170) cc_final: 0.6970 (m-70) outliers start: 12 outliers final: 3 residues processed: 135 average time/residue: 1.2008 time to fit residues: 172.1416 Evaluate side-chains 122 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 599 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN A 643 GLN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.096103 restraints weight = 8748.528| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.74 r_work: 0.2809 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7985 Z= 0.209 Angle : 0.541 12.817 10844 Z= 0.265 Chirality : 0.042 0.171 1273 Planarity : 0.004 0.044 1377 Dihedral : 8.689 171.293 1103 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.04 % Allowed : 20.49 % Favored : 78.47 % 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: 0.76 (0.26), residues: 1007 helix: 1.47 (0.24), residues: 492 sheet: -0.32 (0.47), residues: 109 loop : -0.38 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.013 0.001 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.007 0.000 ARG A 572 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.39 seconds wall clock time: 62 minutes 11.47 seconds (3731.47 seconds total)