Starting phenix.real_space_refine on Mon Feb 19 20:09:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mir_23862/02_2024/7mir_23862_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mir_23862/02_2024/7mir_23862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mir_23862/02_2024/7mir_23862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mir_23862/02_2024/7mir_23862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mir_23862/02_2024/7mir_23862_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mir_23862/02_2024/7mir_23862_trim_updated.pdb" } resolution = 2.5 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= 0.004 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 Mg 2 5.21 5 S 45 5.16 5 C 8207 2.51 5 N 2231 2.21 5 O 2507 1.98 5 H 12748 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 862": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25745 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 12193 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 31, 'TRANS': 718} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 3 Chain: "C" Number of atoms: 11500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 11500 Classifications: {'peptide': 724} Link IDs: {'PTRANS': 27, 'TRANS': 696} Chain breaks: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.58, per 1000 atoms: 0.45 Number of scatterers: 25745 At special positions: 0 Unit cell: (137.16, 123.12, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 S 45 16.00 P 4 15.00 Mg 2 11.99 O 2507 8.00 N 2231 7.00 C 8207 6.00 H 12748 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 5826 OH TYR A 452 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 8 sheets defined 53.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.31 Creating SS restraints... Processing helix chain 'A' and resid 136 through 157 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 165 through 181 Processing helix chain 'A' and resid 185 through 205 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.685A pdb=" N LYS A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.214A pdb=" N TYR A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.660A pdb=" N THR A 306 " --> pdb=" O HIS A 302 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 375 through 395 removed outlier: 5.548A pdb=" N ARG A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 425 through 431 removed outlier: 3.738A pdb=" N THR A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 460 through 480 Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.869A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 526 through 530' Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 594 through 621 removed outlier: 3.608A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 654 Processing helix chain 'A' and resid 658 through 668 removed outlier: 3.678A pdb=" N ARG A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 684 through 688 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.785A pdb=" N SER A 700 " --> pdb=" O MET A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 774 removed outlier: 3.555A pdb=" N GLN A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 Processing helix chain 'A' and resid 801 through 816 Processing helix chain 'A' and resid 827 through 847 Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 79 removed outlier: 4.048A pdb=" N ASP B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.667A pdb=" N HIS B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'C' and resid 238 through 250 Processing helix chain 'C' and resid 279 through 301 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 320 through 332 removed outlier: 4.062A pdb=" N PHE C 332 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 364 Processing helix chain 'C' and resid 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 377 through 388 Processing helix chain 'C' and resid 398 through 413 removed outlier: 4.108A pdb=" N LEU C 411 " --> pdb=" O HIS C 407 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ARG C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 435 through 451 removed outlier: 3.789A pdb=" N ARG C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 447 " --> pdb=" O GLY C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'C' and resid 523 through 526 No H-bonds generated for 'chain 'C' and resid 523 through 526' Processing helix chain 'C' and resid 545 through 552 Processing helix chain 'C' and resid 555 through 562 Processing helix chain 'C' and resid 564 through 586 Proline residue: C 582 - end of helix Processing helix chain 'C' and resid 600 through 614 removed outlier: 3.622A pdb=" N ALA C 604 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 633 through 642 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 654 through 667 removed outlier: 4.425A pdb=" N ASP C 661 " --> pdb=" O ILE C 657 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR C 662 " --> pdb=" O GLY C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 695 Processing helix chain 'C' and resid 701 through 713 Processing helix chain 'C' and resid 716 through 726 removed outlier: 4.365A pdb=" N ARG C 721 " --> pdb=" O TRP C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 755 Proline residue: C 746 - end of helix Processing helix chain 'C' and resid 772 through 788 removed outlier: 3.842A pdb=" N ASN C 788 " --> pdb=" O ALA C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 811 through 813 No H-bonds generated for 'chain 'C' and resid 811 through 813' Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 901 through 903 No H-bonds generated for 'chain 'C' and resid 901 through 903' Processing helix chain 'C' and resid 913 through 931 Processing helix chain 'C' and resid 1067 through 1074 Processing helix chain 'C' and resid 1079 through 1085 Processing helix chain 'C' and resid 1100 through 1117 Processing sheet with id= A, first strand: chain 'A' and resid 105 through 109 Processing sheet with id= B, first strand: chain 'A' and resid 121 through 123 Processing sheet with id= C, first strand: chain 'A' and resid 291 through 293 Processing sheet with id= D, first strand: chain 'A' and resid 403 through 411 removed outlier: 6.856A pdb=" N VAL A 442 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN A 407 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 440 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER A 409 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 438 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER A 357 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 346 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 265 through 267 Processing sheet with id= F, first strand: chain 'C' and resid 624 through 626 Processing sheet with id= G, first strand: chain 'C' and resid 763 through 768 removed outlier: 6.385A pdb=" N TYR C 891 " --> pdb=" O ILE C 837 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLU C 839 " --> pdb=" O TYR C 891 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 893 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU C 841 " --> pdb=" O PHE C 893 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE C 895 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 877 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL C 896 " --> pdb=" O PRO C 875 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 898 " --> pdb=" O LEU C 873 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU C 873 " --> pdb=" O VAL C 898 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 819 through 822 585 hydrogen bonds defined for protein. 1710 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: 12.10 Time building geometry restraints manager: 21.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12741 1.03 - 1.23: 8 1.23 - 1.42: 5591 1.42 - 1.61: 7583 1.61 - 1.81: 83 Bond restraints: 26006 Sorted by residual: bond pdb=" ND2 ASN A 733 " pdb="HD22 ASN A 733 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN A 733 " pdb="HD21 ASN A 733 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C4 AMP A 901 " pdb=" C5 AMP A 901 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C5 AMP A 901 " pdb=" C6 AMP A 901 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O5' ATP A 904 " pdb=" PA ATP A 904 " ideal model delta sigma weight residual 1.579 1.612 -0.033 1.10e-02 8.26e+03 8.77e+00 ... (remaining 26001 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.49: 334 106.49 - 113.36: 30433 113.36 - 120.23: 8685 120.23 - 127.10: 7350 127.10 - 133.97: 139 Bond angle restraints: 46941 Sorted by residual: angle pdb=" PB ATP A 904 " pdb=" O3B ATP A 904 " pdb=" PG ATP A 904 " ideal model delta sigma weight residual 139.87 132.08 7.79 1.00e+00 1.00e+00 6.06e+01 angle pdb=" PA ATP A 904 " pdb=" O3A ATP A 904 " pdb=" PB ATP A 904 " ideal model delta sigma weight residual 136.83 131.99 4.84 1.00e+00 1.00e+00 2.34e+01 angle pdb=" O2P AMP A 901 " pdb=" P AMP A 901 " pdb=" O3P AMP A 901 " ideal model delta sigma weight residual 119.90 107.62 12.28 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C LEU C 369 " pdb=" N ILE C 370 " pdb=" CA ILE C 370 " ideal model delta sigma weight residual 120.24 122.54 -2.30 6.30e-01 2.52e+00 1.34e+01 angle pdb=" C ILE C 370 " pdb=" CA ILE C 370 " pdb=" CB ILE C 370 " ideal model delta sigma weight residual 114.35 110.56 3.79 1.06e+00 8.90e-01 1.28e+01 ... (remaining 46936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 11111 17.53 - 35.07: 845 35.07 - 52.60: 207 52.60 - 70.14: 55 70.14 - 87.67: 20 Dihedral angle restraints: 12238 sinusoidal: 6686 harmonic: 5552 Sorted by residual: dihedral pdb=" CA SER C 259 " pdb=" C SER C 259 " pdb=" N VAL C 260 " pdb=" CA VAL C 260 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG ARG C 890 " pdb=" CD ARG C 890 " pdb=" NE ARG C 890 " pdb=" CZ ARG C 890 " ideal model delta sinusoidal sigma weight residual -180.00 -135.39 -44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 660 " pdb=" CD ARG A 660 " pdb=" NE ARG A 660 " pdb=" CZ ARG A 660 " ideal model delta sinusoidal sigma weight residual -90.00 -134.58 44.58 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 12235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1667 0.050 - 0.100: 243 0.100 - 0.150: 46 0.150 - 0.200: 1 0.200 - 0.250: 1 Chirality restraints: 1958 Sorted by residual: chirality pdb=" CA ASN A 733 " pdb=" N ASN A 733 " pdb=" C ASN A 733 " pdb=" CB ASN A 733 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE A 656 " pdb=" N ILE A 656 " pdb=" C ILE A 656 " pdb=" CB ILE A 656 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE A 134 " pdb=" N ILE A 134 " pdb=" C ILE A 134 " pdb=" CB ILE A 134 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1955 not shown) Planarity restraints: 3853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 733 " 0.064 2.00e-02 2.50e+03 6.45e-02 6.24e+01 pdb=" CG ASN A 733 " 0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 733 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 733 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 733 " -0.091 2.00e-02 2.50e+03 pdb="HD22 ASN A 733 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AMP A 901 " -0.062 2.00e-02 2.50e+03 2.74e-02 2.07e+01 pdb=" C2 AMP A 901 " 0.010 2.00e-02 2.50e+03 pdb=" C4 AMP A 901 " 0.019 2.00e-02 2.50e+03 pdb=" C5 AMP A 901 " 0.017 2.00e-02 2.50e+03 pdb=" C6 AMP A 901 " -0.002 2.00e-02 2.50e+03 pdb=" C8 AMP A 901 " 0.019 2.00e-02 2.50e+03 pdb=" N1 AMP A 901 " -0.003 2.00e-02 2.50e+03 pdb=" N3 AMP A 901 " 0.019 2.00e-02 2.50e+03 pdb=" N6 AMP A 901 " -0.048 2.00e-02 2.50e+03 pdb=" N7 AMP A 901 " 0.023 2.00e-02 2.50e+03 pdb=" N9 AMP A 901 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 680 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO C 681 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 681 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 681 " 0.021 5.00e-02 4.00e+02 ... (remaining 3850 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1159 2.19 - 2.79: 52083 2.79 - 3.39: 71614 3.39 - 4.00: 94051 4.00 - 4.60: 145543 Nonbonded interactions: 364450 Sorted by model distance: nonbonded pdb=" HD1 HIS C 281 " pdb=" OD2 ASP C 410 " model vdw 1.585 1.850 nonbonded pdb="HH22 ARG A 660 " pdb=" OE2 GLU B 15 " model vdw 1.595 1.850 nonbonded pdb=" HE2 HIS A 492 " pdb=" O3P AMP A 901 " model vdw 1.606 1.850 nonbonded pdb=" OE2 GLU C 352 " pdb="HH22 ARG C 355 " model vdw 1.613 1.850 nonbonded pdb=" H GLU A 221 " pdb=" OD2 ASP A 793 " model vdw 1.616 1.850 ... (remaining 364445 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: 10.940 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: 15.590 Check model and map are aligned: 0.150 Set scattering table: 0.240 Process input model: 85.960 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 13258 Z= 0.205 Angle : 0.485 12.277 17903 Z= 0.261 Chirality : 0.037 0.250 1958 Planarity : 0.003 0.045 2320 Dihedral : 14.430 87.670 5023 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.82 (0.22), residues: 1583 helix: 2.22 (0.18), residues: 868 sheet: 0.71 (0.52), residues: 94 loop : -0.13 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 845 HIS 0.011 0.001 HIS C 673 PHE 0.019 0.001 PHE C 719 TYR 0.009 0.001 TYR C 383 ARG 0.003 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 2.9571 time to fit residues: 539.5491 Evaluate side-chains 123 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.0070 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN A 726 HIS A 733 ASN B 50 GLN C 537 GLN ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13258 Z= 0.266 Angle : 0.501 6.401 17903 Z= 0.265 Chirality : 0.038 0.148 1958 Planarity : 0.004 0.043 2320 Dihedral : 5.709 79.746 1782 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.49 % Allowed : 6.97 % Favored : 92.54 % 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: 1.63 (0.21), residues: 1583 helix: 2.07 (0.18), residues: 873 sheet: 0.70 (0.52), residues: 94 loop : -0.27 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.004 0.001 HIS C 673 PHE 0.020 0.002 PHE A 475 TYR 0.014 0.002 TYR C 383 ARG 0.008 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7625 (ttm170) outliers start: 7 outliers final: 6 residues processed: 135 average time/residue: 2.8835 time to fit residues: 424.5523 Evaluate side-chains 131 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 600 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13258 Z= 0.377 Angle : 0.558 6.652 17903 Z= 0.301 Chirality : 0.041 0.151 1958 Planarity : 0.004 0.048 2320 Dihedral : 5.838 85.709 1782 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.06 % Allowed : 8.44 % Favored : 90.50 % 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: 1.27 (0.21), residues: 1583 helix: 1.74 (0.17), residues: 873 sheet: 0.63 (0.52), residues: 94 loop : -0.39 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 277 HIS 0.005 0.001 HIS C 673 PHE 0.024 0.002 PHE A 475 TYR 0.016 0.002 TYR C 383 ARG 0.010 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7597 (ttm170) REVERT: C 310 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7272 (mtmt) outliers start: 15 outliers final: 9 residues processed: 135 average time/residue: 2.8206 time to fit residues: 416.5820 Evaluate side-chains 126 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 698 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 2.1980 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13258 Z= 0.268 Angle : 0.503 6.499 17903 Z= 0.267 Chirality : 0.038 0.147 1958 Planarity : 0.004 0.046 2320 Dihedral : 5.580 81.857 1782 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.13 % Allowed : 9.78 % Favored : 89.09 % 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: 1.39 (0.21), residues: 1583 helix: 1.87 (0.18), residues: 874 sheet: 0.62 (0.52), residues: 94 loop : -0.38 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.006 0.001 HIS C 673 PHE 0.020 0.002 PHE C 719 TYR 0.013 0.002 TYR C 383 ARG 0.005 0.000 ARG C 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7560 (ttm170) REVERT: A 767 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: A 773 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 793 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: B 7 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5762 (tm-30) REVERT: B 78 LYS cc_start: 0.7136 (tppt) cc_final: 0.6881 (mptt) outliers start: 16 outliers final: 8 residues processed: 138 average time/residue: 2.9376 time to fit residues: 442.4856 Evaluate side-chains 132 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 698 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN C 611 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13258 Z= 0.180 Angle : 0.466 7.040 17903 Z= 0.245 Chirality : 0.036 0.147 1958 Planarity : 0.003 0.047 2320 Dihedral : 5.366 79.795 1782 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.84 % Allowed : 10.84 % Favored : 88.32 % 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: 1.65 (0.21), residues: 1583 helix: 2.11 (0.18), residues: 875 sheet: 0.77 (0.52), residues: 92 loop : -0.32 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS C 673 PHE 0.019 0.001 PHE C 719 TYR 0.012 0.001 TYR C 911 ARG 0.002 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7575 (ttm170) REVERT: A 773 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7830 (mp) REVERT: C 310 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7053 (mtmm) REVERT: C 920 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6928 (mp10) REVERT: C 1111 LYS cc_start: 0.7929 (tmtm) cc_final: 0.7465 (tmmt) outliers start: 12 outliers final: 5 residues processed: 134 average time/residue: 2.8853 time to fit residues: 421.5919 Evaluate side-chains 131 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 920 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13258 Z= 0.268 Angle : 0.505 7.016 17903 Z= 0.268 Chirality : 0.038 0.148 1958 Planarity : 0.004 0.047 2320 Dihedral : 5.556 83.841 1782 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.06 % Allowed : 11.33 % Favored : 87.61 % 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 (0.21), residues: 1583 helix: 2.00 (0.18), residues: 875 sheet: 0.61 (0.52), residues: 94 loop : -0.38 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.006 0.001 HIS C 673 PHE 0.020 0.002 PHE A 475 TYR 0.012 0.002 TYR C 383 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7550 (ttm170) REVERT: A 767 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: A 773 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7849 (mp) REVERT: C 310 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7067 (mtmm) REVERT: C 920 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: C 1111 LYS cc_start: 0.7931 (tmtm) cc_final: 0.7460 (tmmt) outliers start: 15 outliers final: 6 residues processed: 135 average time/residue: 2.8332 time to fit residues: 417.1857 Evaluate side-chains 131 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 920 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13258 Z= 0.262 Angle : 0.502 7.541 17903 Z= 0.266 Chirality : 0.038 0.146 1958 Planarity : 0.004 0.048 2320 Dihedral : 5.535 83.389 1782 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.13 % Allowed : 11.47 % Favored : 87.40 % 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: 1.51 (0.21), residues: 1583 helix: 2.00 (0.18), residues: 875 sheet: 0.63 (0.52), residues: 94 loop : -0.38 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.006 0.001 HIS C 673 PHE 0.020 0.002 PHE C 719 TYR 0.014 0.002 TYR C 911 ARG 0.003 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7573 (ttm170) REVERT: A 767 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6491 (mt-10) REVERT: A 773 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7881 (mp) REVERT: C 310 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7135 (mtmm) REVERT: C 920 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6940 (mp10) outliers start: 16 outliers final: 7 residues processed: 132 average time/residue: 2.8358 time to fit residues: 409.8546 Evaluate side-chains 130 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 920 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13258 Z= 0.177 Angle : 0.465 7.723 17903 Z= 0.243 Chirality : 0.036 0.146 1958 Planarity : 0.003 0.045 2320 Dihedral : 5.321 81.752 1782 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.06 % Allowed : 11.68 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.21), residues: 1583 helix: 2.22 (0.18), residues: 875 sheet: 0.77 (0.52), residues: 92 loop : -0.32 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.006 0.001 HIS C 673 PHE 0.019 0.001 PHE C 719 TYR 0.016 0.001 TYR C 911 ARG 0.002 0.000 ARG C 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7588 (ttm170) REVERT: A 767 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: A 773 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7886 (mp) REVERT: B 7 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5761 (tm-30) REVERT: C 310 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7041 (mtmm) REVERT: C 920 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6995 (mp10) outliers start: 15 outliers final: 6 residues processed: 130 average time/residue: 2.8144 time to fit residues: 401.1114 Evaluate side-chains 129 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 920 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13258 Z= 0.281 Angle : 0.511 7.702 17903 Z= 0.271 Chirality : 0.038 0.148 1958 Planarity : 0.004 0.048 2320 Dihedral : 5.566 84.449 1782 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.34 % Allowed : 11.19 % Favored : 87.47 % 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: 1.53 (0.21), residues: 1583 helix: 2.01 (0.18), residues: 875 sheet: 0.60 (0.52), residues: 94 loop : -0.36 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.007 0.001 HIS C 673 PHE 0.022 0.002 PHE A 475 TYR 0.014 0.002 TYR C 911 ARG 0.003 0.000 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7578 (ttm170) REVERT: A 773 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7914 (mp) REVERT: B 7 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5836 (tm-30) REVERT: C 310 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7128 (mtmm) REVERT: C 920 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6995 (mp10) outliers start: 19 outliers final: 9 residues processed: 133 average time/residue: 2.7924 time to fit residues: 406.2708 Evaluate side-chains 132 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 920 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13258 Z= 0.262 Angle : 0.502 8.631 17903 Z= 0.265 Chirality : 0.038 0.146 1958 Planarity : 0.004 0.047 2320 Dihedral : 5.526 83.588 1782 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.06 % Allowed : 11.47 % Favored : 87.47 % 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: 1.50 (0.21), residues: 1583 helix: 1.99 (0.18), residues: 875 sheet: 0.60 (0.52), residues: 94 loop : -0.38 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.007 0.001 HIS C 673 PHE 0.019 0.002 PHE C 719 TYR 0.015 0.002 TYR C 911 ARG 0.003 0.000 ARG A 505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7569 (ttm170) REVERT: A 773 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7898 (mp) REVERT: B 7 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5813 (tm-30) REVERT: C 310 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7122 (mtmm) REVERT: C 920 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.6993 (mp10) outliers start: 15 outliers final: 8 residues processed: 128 average time/residue: 2.9020 time to fit residues: 405.5962 Evaluate side-chains 130 residues out of total 1421 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 920 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A 733 ASN B 50 GLN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091106 restraints weight = 50902.792| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.76 r_work: 0.3030 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13258 Z= 0.257 Angle : 0.502 9.161 17903 Z= 0.265 Chirality : 0.038 0.147 1958 Planarity : 0.004 0.047 2320 Dihedral : 5.525 83.616 1782 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.06 % Allowed : 11.47 % Favored : 87.47 % 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: 1.49 (0.21), residues: 1583 helix: 1.98 (0.18), residues: 875 sheet: 0.62 (0.52), residues: 94 loop : -0.38 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.007 0.001 HIS C 673 PHE 0.020 0.002 PHE C 719 TYR 0.015 0.002 TYR C 911 ARG 0.003 0.000 ARG A 505 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8752.73 seconds wall clock time: 156 minutes 29.24 seconds (9389.24 seconds total)