Starting phenix.real_space_refine on Mon Mar 11 09:24:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/03_2024/6ln6_0925_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/03_2024/6ln6_0925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/03_2024/6ln6_0925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/03_2024/6ln6_0925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/03_2024/6ln6_0925_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln6_0925/03_2024/6ln6_0925_updated.pdb" } resolution = 2.9 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= 0.013 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 4986 2.51 5 N 1310 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A ASP 658": "OD1" <-> "OD2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A GLU 907": "OE1" <-> "OE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7836 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7836 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'peptide': 1010, 'undetermined': 4} Link IDs: {'PTRANS': 46, 'TRANS': 963, 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: 4.61, per 1000 atoms: 0.59 Number of scatterers: 7836 At special positions: 0 Unit cell: (103.335, 79.68, 140.685, 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 1477 8.00 N 1310 7.00 C 4986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.02 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 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: 40 helices and 8 sheets defined 47.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 4.101A 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 56 removed outlier: 3.773A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 removed outlier: 3.740A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 119 removed outlier: 3.913A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.728A 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 248 through 274 Processing helix chain 'A' and resid 277 through 280 removed outlier: 3.826A pdb=" N ASN A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 288 through 306 Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.809A pdb=" N VAL A 339 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.686A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.539A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.615A pdb=" N ARG A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.561A pdb=" N VAL A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.944A pdb=" N ILE A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.518A pdb=" N SER A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) 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 671 removed outlier: 3.593A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 693 removed outlier: 3.648A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Proline residue: A 708 - end of helix removed outlier: 3.525A pdb=" N LYS A 711 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 739 through 780 removed outlier: 3.507A pdb=" N VAL A 743 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 747 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 748 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 752 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 761 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 763 " --> pdb=" O ILE A 760 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 764 " --> pdb=" O ARG A 761 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 765 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 767 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 768 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 772 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS A 773 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 776 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 777 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 780 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 798 removed outlier: 3.557A pdb=" N ASN A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 806 removed outlier: 4.344A pdb=" N LEU A 806 " --> pdb=" O PRO A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 831 through 856 removed outlier: 3.546A pdb=" N TYR A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 854 " --> pdb=" O ALA A 850 " (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 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 893 through 911 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 950 through 956 removed outlier: 4.631A pdb=" N LEU A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 989 Proline residue: A 975 - end of helix removed outlier: 3.730A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 3.529A 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 126 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.916A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.657A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 621 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 424 through 428 Processing sheet with id= E, first strand: chain 'A' and resid 378 through 383 removed outlier: 5.242A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N MET A 366 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS A 595 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 368 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N VAL A 593 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 12.874A pdb=" N ASP A 370 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 16.197A pdb=" N THR A 591 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.905A pdb=" N LEU A 590 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE A 527 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE A 592 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL A 529 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.429A pdb=" N CYS A 674 " --> pdb=" O PHE A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 174 through 176 removed outlier: 3.538A pdb=" N ALA A 216 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 864 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: 2.61 Time building geometry restraints manager: 3.55 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: 2572 1.35 - 1.48: 1792 1.48 - 1.61: 3523 1.61 - 1.73: 4 1.73 - 1.86: 90 Bond restraints: 7981 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.616 -0.226 2.00e-02 2.50e+03 1.27e+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 1.299 0.129 2.00e-02 2.50e+03 4.15e+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 2.15e+01 ... (remaining 7976 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.30: 231 106.30 - 113.23: 4504 113.23 - 120.16: 2682 120.16 - 127.09: 3333 127.09 - 134.02: 89 Bond angle restraints: 10839 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 109.88 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.22 -12.17 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 108.30 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 108.87 10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 109.05 9.90 3.00e+00 1.11e-01 1.09e+01 ... (remaining 10834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.54: 4698 25.54 - 51.08: 144 51.08 - 76.62: 14 76.62 - 102.16: 3 102.16 - 127.70: 1 Dihedral angle restraints: 4860 sinusoidal: 1941 harmonic: 2919 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 78.95 -127.70 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA CYS A 887 " pdb=" C CYS A 887 " pdb=" N ALA A 888 " pdb=" CA ALA A 888 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N ASP A 422 " pdb=" CA ASP A 422 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1177 0.076 - 0.151: 95 0.151 - 0.227: 0 0.227 - 0.303: 0 0.303 - 0.378: 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 -2.37 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PRO A 248 " pdb=" N PRO A 248 " pdb=" C PRO A 248 " pdb=" CB PRO A 248 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA VAL A 194 " pdb=" N VAL A 194 " pdb=" C VAL A 194 " pdb=" CB VAL A 194 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1270 not shown) Planarity restraints: 1376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A1017 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 502 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO A 503 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 975 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.020 5.00e-02 4.00e+02 ... (remaining 1373 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 87 2.61 - 3.18: 6702 3.18 - 3.75: 12048 3.75 - 4.33: 17946 4.33 - 4.90: 28887 Nonbonded interactions: 65670 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.035 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.125 2.170 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.137 3.040 nonbonded pdb=" OE2 GLU A 309 " pdb=" OD1 ASN A 795 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP A 351 " pdb="MG MG A2002 " model vdw 2.191 2.170 ... (remaining 65665 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: 0.230 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: 0.000 Extract box with map and model: 1.450 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.720 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 0.226 7981 Z= 0.360 Angle : 0.642 16.126 10839 Z= 0.341 Chirality : 0.041 0.378 1273 Planarity : 0.004 0.045 1376 Dihedral : 12.490 127.700 2965 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -3.94 (0.20), residues: 1006 helix: -3.34 (0.14), residues: 484 sheet: -1.64 (0.37), residues: 124 loop : -1.65 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 793 HIS 0.007 0.001 HIS A 566 PHE 0.011 0.001 PHE A 367 TYR 0.006 0.001 TYR A 842 ARG 0.002 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8025 (mttp) cc_final: 0.7802 (mtmt) REVERT: A 33 LYS cc_start: 0.8070 (tttt) cc_final: 0.7563 (ttpt) REVERT: A 83 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6276 (mp0) REVERT: A 135 LYS cc_start: 0.8128 (mppt) cc_final: 0.7713 (tptt) REVERT: A 172 THR cc_start: 0.8481 (m) cc_final: 0.8265 (t) REVERT: A 179 ILE cc_start: 0.7648 (mp) cc_final: 0.7405 (tt) REVERT: A 231 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 235 ILE cc_start: 0.7476 (pt) cc_final: 0.7203 (pp) REVERT: A 290 ARG cc_start: 0.7343 (tpp80) cc_final: 0.7083 (mtp85) REVERT: A 297 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7733 (mttt) REVERT: A 494 MET cc_start: 0.8607 (ttt) cc_final: 0.7843 (tmm) REVERT: A 542 GLN cc_start: 0.7434 (mp10) cc_final: 0.7079 (mp-120) REVERT: A 575 MET cc_start: 0.7900 (mtt) cc_final: 0.7682 (mtm) REVERT: A 615 GLN cc_start: 0.7812 (tt0) cc_final: 0.7236 (mt0) REVERT: A 693 PHE cc_start: 0.8075 (m-10) cc_final: 0.7667 (m-10) REVERT: A 883 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6822 (mm-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 1.1158 time to fit residues: 207.5490 Evaluate side-chains 136 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 19 ASN A 190 HIS A 421 ASN A 453 ASN A 501 ASN A 568 ASN A 582 ASN A 817 ASN A 868 GLN A 913 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7981 Z= 0.163 Angle : 0.493 5.550 10839 Z= 0.258 Chirality : 0.041 0.135 1273 Planarity : 0.005 0.049 1376 Dihedral : 8.359 157.041 1102 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.74 % Allowed : 10.53 % Favored : 87.73 % 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: -1.51 (0.24), residues: 1006 helix: -0.87 (0.22), residues: 486 sheet: -1.00 (0.42), residues: 119 loop : -0.93 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 PHE 0.009 0.001 PHE A 367 TYR 0.008 0.001 TYR A 842 ARG 0.007 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8029 (tttt) cc_final: 0.7554 (ttpt) REVERT: A 83 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6313 (mp0) REVERT: A 135 LYS cc_start: 0.8178 (mppt) cc_final: 0.7750 (tptt) REVERT: A 231 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 235 ILE cc_start: 0.7490 (pt) cc_final: 0.7169 (pp) REVERT: A 297 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7883 (mtpp) REVERT: A 340 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6744 (tp30) REVERT: A 494 MET cc_start: 0.8657 (ttt) cc_final: 0.7900 (tmm) REVERT: A 542 GLN cc_start: 0.7218 (mp10) cc_final: 0.6952 (mp-120) REVERT: A 561 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8254 (tp) REVERT: A 575 MET cc_start: 0.7989 (mtt) cc_final: 0.7651 (mtm) REVERT: A 576 HIS cc_start: 0.8035 (m170) cc_final: 0.7757 (m90) REVERT: A 615 GLN cc_start: 0.7707 (tt0) cc_final: 0.7157 (mt0) REVERT: A 689 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 693 PHE cc_start: 0.8049 (m-10) cc_final: 0.7706 (m-10) REVERT: A 816 MET cc_start: 0.8294 (mmm) cc_final: 0.8057 (mmm) REVERT: A 883 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6771 (mm-30) outliers start: 15 outliers final: 6 residues processed: 140 average time/residue: 1.1212 time to fit residues: 167.3591 Evaluate side-chains 134 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 275 ASN A 453 ASN A 568 ASN A 582 ASN A 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7981 Z= 0.200 Angle : 0.498 5.521 10839 Z= 0.255 Chirality : 0.042 0.134 1273 Planarity : 0.004 0.048 1376 Dihedral : 8.665 170.441 1102 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 12.62 % 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: -0.61 (0.26), residues: 1006 helix: 0.07 (0.24), residues: 487 sheet: -0.83 (0.43), residues: 119 loop : -0.68 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 PHE 0.012 0.001 PHE A 367 TYR 0.011 0.001 TYR A 842 ARG 0.008 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.990 Fit side-chains REVERT: A 33 LYS cc_start: 0.8020 (tttt) cc_final: 0.7540 (ttpt) REVERT: A 55 GLU cc_start: 0.7883 (pt0) cc_final: 0.7655 (tt0) REVERT: A 135 LYS cc_start: 0.8296 (mppt) cc_final: 0.7779 (tptt) REVERT: A 139 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7294 (mtp85) REVERT: A 231 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 235 ILE cc_start: 0.7522 (pt) cc_final: 0.7198 (pp) REVERT: A 340 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6768 (tp30) REVERT: A 561 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 576 HIS cc_start: 0.8050 (m170) cc_final: 0.7763 (m90) REVERT: A 615 GLN cc_start: 0.7732 (tt0) cc_final: 0.7183 (mt0) REVERT: A 685 LYS cc_start: 0.7738 (ttpp) cc_final: 0.7458 (mtpt) REVERT: A 689 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: A 816 MET cc_start: 0.8344 (mmm) cc_final: 0.8037 (mmm) REVERT: A 883 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6880 (mm-30) REVERT: A 1023 MET cc_start: 0.6008 (tpt) cc_final: 0.5731 (tpp) outliers start: 18 outliers final: 9 residues processed: 137 average time/residue: 1.2051 time to fit residues: 175.7607 Evaluate side-chains 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7981 Z= 0.177 Angle : 0.477 5.479 10839 Z= 0.246 Chirality : 0.041 0.128 1273 Planarity : 0.004 0.049 1376 Dihedral : 8.693 173.268 1102 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.89 % Allowed : 12.73 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1006 helix: 0.51 (0.24), residues: 488 sheet: -0.62 (0.43), residues: 119 loop : -0.48 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 PHE 0.010 0.001 PHE A 367 TYR 0.010 0.001 TYR A 842 ARG 0.009 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.043 Fit side-chains REVERT: A 33 LYS cc_start: 0.8008 (tttt) cc_final: 0.7527 (ttpt) REVERT: A 83 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6864 (mt-10) REVERT: A 139 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6976 (mtp85) REVERT: A 231 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 235 ILE cc_start: 0.7540 (pt) cc_final: 0.7189 (pp) REVERT: A 561 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8363 (tp) REVERT: A 615 GLN cc_start: 0.7719 (tt0) cc_final: 0.7216 (mt0) REVERT: A 685 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7457 (mtpt) REVERT: A 689 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: A 816 MET cc_start: 0.8340 (mmm) cc_final: 0.8016 (mmm) REVERT: A 1023 MET cc_start: 0.6145 (tpt) cc_final: 0.5853 (tpp) outliers start: 25 outliers final: 9 residues processed: 133 average time/residue: 1.1712 time to fit residues: 165.5394 Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 916 SER 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: 0.0010 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 7981 Z= 0.448 Angle : 0.654 6.480 10839 Z= 0.332 Chirality : 0.049 0.184 1273 Planarity : 0.005 0.047 1376 Dihedral : 9.073 161.662 1102 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.24 % Allowed : 13.66 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1006 helix: 0.09 (0.24), residues: 489 sheet: -1.09 (0.43), residues: 108 loop : -0.64 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 107 HIS 0.008 0.001 HIS A 566 PHE 0.024 0.002 PHE A 367 TYR 0.015 0.002 TYR A 295 ARG 0.010 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.901 Fit side-chains REVERT: A 33 LYS cc_start: 0.8010 (tttt) cc_final: 0.7472 (ttpt) REVERT: A 139 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7262 (mtp85) REVERT: A 180 LEU cc_start: 0.8619 (tp) cc_final: 0.8374 (tt) REVERT: A 188 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 231 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 235 ILE cc_start: 0.7719 (pt) cc_final: 0.7322 (pp) REVERT: A 406 GLN cc_start: 0.7003 (mp10) cc_final: 0.6456 (mp10) REVERT: A 494 MET cc_start: 0.8679 (ttt) cc_final: 0.7855 (tmm) REVERT: A 550 GLU cc_start: 0.7315 (tt0) cc_final: 0.7014 (mt-10) REVERT: A 561 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 615 GLN cc_start: 0.7679 (tt0) cc_final: 0.7106 (mt0) REVERT: A 685 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7559 (mtpt) REVERT: A 689 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: A 816 MET cc_start: 0.8337 (mmm) cc_final: 0.8062 (mmm) REVERT: A 883 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7177 (mp0) REVERT: A 1023 MET cc_start: 0.6181 (tpt) cc_final: 0.5929 (mmt) outliers start: 28 outliers final: 15 residues processed: 132 average time/residue: 1.1948 time to fit residues: 167.2584 Evaluate side-chains 134 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 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 568 ASN A 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7981 Z= 0.185 Angle : 0.495 5.506 10839 Z= 0.255 Chirality : 0.042 0.130 1273 Planarity : 0.005 0.051 1376 Dihedral : 8.849 164.954 1102 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.01 % Allowed : 14.70 % Favored : 82.29 % 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: 1006 helix: 0.49 (0.24), residues: 495 sheet: -0.70 (0.45), residues: 106 loop : -0.39 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.009 0.001 PHE A 367 TYR 0.009 0.001 TYR A 842 ARG 0.011 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.951 Fit side-chains REVERT: A 33 LYS cc_start: 0.8007 (tttt) cc_final: 0.7473 (ttpt) REVERT: A 139 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7047 (mtp85) REVERT: A 180 LEU cc_start: 0.8540 (tp) cc_final: 0.8281 (tt) REVERT: A 231 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7739 (mm-30) REVERT: A 235 ILE cc_start: 0.7620 (pt) cc_final: 0.7208 (pp) REVERT: A 406 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6436 (mp10) REVERT: A 494 MET cc_start: 0.8655 (ttt) cc_final: 0.7845 (tmm) REVERT: A 550 GLU cc_start: 0.7240 (tt0) cc_final: 0.6915 (mt-10) REVERT: A 561 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8356 (tp) REVERT: A 615 GLN cc_start: 0.7664 (tt0) cc_final: 0.7202 (mt0) REVERT: A 685 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7499 (mtpt) REVERT: A 689 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: A 816 MET cc_start: 0.8326 (mmm) cc_final: 0.8035 (mmm) REVERT: A 1023 MET cc_start: 0.6106 (tpt) cc_final: 0.5849 (mmm) outliers start: 26 outliers final: 11 residues processed: 131 average time/residue: 1.1793 time to fit residues: 164.1028 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 847 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7981 Z= 0.206 Angle : 0.502 5.484 10839 Z= 0.258 Chirality : 0.042 0.131 1273 Planarity : 0.005 0.050 1376 Dihedral : 8.841 163.973 1102 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.01 % Allowed : 15.39 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1006 helix: 0.63 (0.24), residues: 495 sheet: -0.68 (0.44), residues: 121 loop : -0.26 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.011 0.001 PHE A 367 TYR 0.010 0.001 TYR A 842 ARG 0.012 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.811 Fit side-chains REVERT: A 33 LYS cc_start: 0.8056 (tttt) cc_final: 0.7532 (ttpt) REVERT: A 139 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7019 (mtp85) REVERT: A 180 LEU cc_start: 0.8564 (tp) cc_final: 0.8325 (tt) REVERT: A 231 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 235 ILE cc_start: 0.7594 (pt) cc_final: 0.7216 (pp) REVERT: A 435 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: A 494 MET cc_start: 0.8648 (ttt) cc_final: 0.7856 (tmm) REVERT: A 561 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 615 GLN cc_start: 0.7668 (tt0) cc_final: 0.7171 (mt0) REVERT: A 685 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7495 (mtpt) REVERT: A 689 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: A 816 MET cc_start: 0.8343 (mmm) cc_final: 0.8031 (mmm) REVERT: A 883 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7314 (mp0) outliers start: 26 outliers final: 15 residues processed: 131 average time/residue: 1.1412 time to fit residues: 158.5595 Evaluate side-chains 130 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.0470 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7981 Z= 0.134 Angle : 0.459 5.433 10839 Z= 0.238 Chirality : 0.040 0.124 1273 Planarity : 0.004 0.051 1376 Dihedral : 8.690 165.266 1102 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.55 % Allowed : 15.62 % Favored : 81.83 % 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: 0.42 (0.27), residues: 1006 helix: 0.89 (0.25), residues: 495 sheet: -0.52 (0.46), residues: 110 loop : -0.10 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 854 HIS 0.003 0.000 HIS A 566 PHE 0.006 0.001 PHE A 985 TYR 0.010 0.001 TYR A 842 ARG 0.014 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.015 Fit side-chains REVERT: A 33 LYS cc_start: 0.7984 (tttt) cc_final: 0.7502 (ttpt) REVERT: A 139 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7250 (mtp85) REVERT: A 180 LEU cc_start: 0.8521 (tp) cc_final: 0.8300 (tt) REVERT: A 231 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 235 ILE cc_start: 0.7548 (pt) cc_final: 0.7185 (pp) REVERT: A 406 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6385 (mp10) REVERT: A 435 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: A 615 GLN cc_start: 0.7676 (tt0) cc_final: 0.7246 (mt0) REVERT: A 685 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7474 (mtpt) REVERT: A 689 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: A 816 MET cc_start: 0.8325 (mmm) cc_final: 0.8071 (mmm) outliers start: 22 outliers final: 11 residues processed: 125 average time/residue: 1.2521 time to fit residues: 166.0349 Evaluate side-chains 124 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 847 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 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 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7981 Z= 0.185 Angle : 0.485 5.472 10839 Z= 0.249 Chirality : 0.042 0.128 1273 Planarity : 0.004 0.053 1376 Dihedral : 8.749 164.083 1102 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.20 % Allowed : 15.97 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1006 helix: 0.88 (0.24), residues: 495 sheet: -0.48 (0.45), residues: 122 loop : -0.12 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 PHE 0.010 0.001 PHE A 367 TYR 0.011 0.001 TYR A 842 ARG 0.014 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.188 Fit side-chains REVERT: A 33 LYS cc_start: 0.7939 (tttt) cc_final: 0.7454 (ttpt) REVERT: A 139 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6980 (mtp85) REVERT: A 180 LEU cc_start: 0.8540 (tp) cc_final: 0.8274 (tt) REVERT: A 231 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 235 ILE cc_start: 0.7542 (pt) cc_final: 0.7161 (pp) REVERT: A 371 ARG cc_start: 0.7178 (mtm110) cc_final: 0.6479 (mtt-85) REVERT: A 406 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6413 (mp10) REVERT: A 433 VAL cc_start: 0.8036 (m) cc_final: 0.7751 (p) REVERT: A 435 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: A 561 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 615 GLN cc_start: 0.7671 (tt0) cc_final: 0.7171 (mt0) REVERT: A 685 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7468 (mtpt) REVERT: A 689 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: A 816 MET cc_start: 0.8358 (mmm) cc_final: 0.8065 (mmm) REVERT: A 883 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7144 (mp0) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 1.2153 time to fit residues: 163.6843 Evaluate side-chains 130 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 916 SER 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: 0.1980 chunk 100 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 0.2980 chunk 49 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7981 Z= 0.139 Angle : 0.454 5.427 10839 Z= 0.235 Chirality : 0.040 0.124 1273 Planarity : 0.004 0.054 1376 Dihedral : 8.636 165.670 1102 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.20 % Allowed : 15.86 % Favored : 81.94 % 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: 0.65 (0.27), residues: 1006 helix: 1.06 (0.25), residues: 495 sheet: -0.39 (0.47), residues: 110 loop : 0.04 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 854 HIS 0.003 0.000 HIS A 566 PHE 0.006 0.001 PHE A 985 TYR 0.010 0.001 TYR A 842 ARG 0.013 0.000 ARG A 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.877 Fit side-chains REVERT: A 33 LYS cc_start: 0.7884 (tttt) cc_final: 0.7410 (ttpt) REVERT: A 139 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7301 (mtp85) REVERT: A 180 LEU cc_start: 0.8512 (tp) cc_final: 0.8310 (tt) REVERT: A 231 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7695 (mm-30) REVERT: A 235 ILE cc_start: 0.7515 (pt) cc_final: 0.7140 (pp) REVERT: A 371 ARG cc_start: 0.7114 (mtm110) cc_final: 0.6525 (mtt-85) REVERT: A 406 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6256 (mp10) REVERT: A 433 VAL cc_start: 0.8009 (m) cc_final: 0.7722 (p) REVERT: A 435 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: A 494 MET cc_start: 0.8597 (ttt) cc_final: 0.7833 (tmm) REVERT: A 561 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 615 GLN cc_start: 0.7691 (tt0) cc_final: 0.7263 (mt0) REVERT: A 685 LYS cc_start: 0.7706 (ttpp) cc_final: 0.7464 (mtpt) REVERT: A 689 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: A 693 PHE cc_start: 0.7985 (m-10) cc_final: 0.7542 (m-10) REVERT: A 816 MET cc_start: 0.8334 (mmm) cc_final: 0.8063 (mmm) REVERT: A 883 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7096 (mp0) outliers start: 19 outliers final: 11 residues processed: 127 average time/residue: 1.2041 time to fit residues: 162.2062 Evaluate side-chains 129 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 847 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108962 restraints weight = 8352.910| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.67 r_work: 0.3006 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7981 Z= 0.338 Angle : 0.575 5.564 10839 Z= 0.293 Chirality : 0.045 0.143 1273 Planarity : 0.005 0.051 1376 Dihedral : 8.939 163.950 1102 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.97 % Allowed : 16.78 % Favored : 81.25 % 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: 0.12 (0.26), residues: 1006 helix: 0.61 (0.24), residues: 496 sheet: -0.68 (0.47), residues: 107 loop : -0.19 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.007 0.001 HIS A 566 PHE 0.018 0.002 PHE A 367 TYR 0.012 0.002 TYR A 295 ARG 0.013 0.001 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3362.89 seconds wall clock time: 60 minutes 21.79 seconds (3621.79 seconds total)