Starting phenix.real_space_refine on Sun Apr 7 06:03:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox4_17256/04_2024/8ox4_17256_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox4_17256/04_2024/8ox4_17256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox4_17256/04_2024/8ox4_17256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox4_17256/04_2024/8ox4_17256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox4_17256/04_2024/8ox4_17256_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox4_17256/04_2024/8ox4_17256_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 6310 2.51 5 N 1610 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 277": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9757 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 7015 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 20, 'TRANS': 849} Chain breaks: 4 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.59 Number of scatterers: 9757 At special positions: 0 Unit cell: (87.992, 95.756, 170.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1786 8.00 N 1610 7.00 C 6310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 1.8 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 7 sheets defined 49.5% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.678A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.601A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 173 removed outlier: 3.723A pdb=" N LEU A 145 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.140A pdb=" N VAL A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 154 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 155 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 161 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 164 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 365 removed outlier: 3.510A pdb=" N VAL A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.840A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 4.351A pdb=" N THR A 398 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 421 removed outlier: 4.250A pdb=" N TYR A 405 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 406 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A 408 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 413 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 414 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP A 421 " --> pdb=" O PHE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.750A pdb=" N ASN A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.980A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 removed outlier: 4.145A pdb=" N GLU A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 676 removed outlier: 4.452A pdb=" N GLU A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.931A pdb=" N ARG A 683 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 removed outlier: 3.608A pdb=" N ILE A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.580A pdb=" N ALA A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 758 through 772 Processing helix chain 'A' and resid 803 through 810 removed outlier: 3.576A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 857 Processing helix chain 'A' and resid 870 through 884 removed outlier: 3.674A pdb=" N VAL A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 4.373A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 902 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 937 removed outlier: 3.716A pdb=" N LEU A 935 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 936 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 937 " --> pdb=" O ARG A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 959 removed outlier: 4.033A pdb=" N TYR A 956 " --> pdb=" O ARG A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 968 removed outlier: 3.760A pdb=" N TYR A 968 " --> pdb=" O HIS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.982A pdb=" N THR A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 987 " --> pdb=" O TRP A 983 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'A' and resid 1009 through 1013 Processing helix chain 'A' and resid 1016 through 1023 Processing helix chain 'A' and resid 1033 through 1056 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1091 removed outlier: 3.795A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1118 removed outlier: 3.732A pdb=" N PHE A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1125 removed outlier: 3.892A pdb=" N VAL A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A1125 " --> pdb=" O GLY A1121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1120 through 1125' Processing helix chain 'A' and resid 1136 through 1139 No H-bonds generated for 'chain 'A' and resid 1136 through 1139' Processing helix chain 'A' and resid 1143 through 1170 removed outlier: 3.659A pdb=" N CYS A1156 " --> pdb=" O THR A1152 " (cutoff:3.500A) Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1174 through 1180 Processing helix chain 'B' and resid 47 through 74 removed outlier: 3.772A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.557A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 147 through 150 No H-bonds generated for 'chain 'B' and resid 147 through 150' Processing helix chain 'B' and resid 155 through 160 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 323 through 350 Processing sheet with id= A, first strand: chain 'A' and resid 906 through 909 removed outlier: 6.582A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS A 727 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER A 453 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP A 729 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 863 " --> pdb=" O VAL A 730 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.539A pdb=" N THR A 465 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.546A pdb=" N MET A 538 " --> pdb=" O GLN A 549 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 567 through 569 Processing sheet with id= E, first strand: chain 'A' and resid 655 through 660 removed outlier: 3.579A pdb=" N ALA A 592 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 77 through 81 removed outlier: 5.804A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 103 through 109 removed outlier: 4.108A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1014 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: 2.97 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3070 1.35 - 1.48: 2608 1.48 - 1.60: 4232 1.60 - 1.73: 4 1.73 - 1.86: 76 Bond restraints: 9990 Sorted by residual: bond pdb=" C1' ACP A1201 " pdb=" O4' ACP A1201 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ACP A1201 " pdb=" C2' ACP A1201 " ideal model delta sigma weight residual 1.527 1.315 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C4' ACP A1201 " pdb=" O4' ACP A1201 " ideal model delta sigma weight residual 1.428 1.305 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 1.335 1.452 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C2' ACP A1201 " pdb=" O2' ACP A1201 " ideal model delta sigma weight residual 1.401 1.493 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 9985 not shown) Histogram of bond angle deviations from ideal: 99.94 - 107.04: 260 107.04 - 114.15: 5738 114.15 - 121.25: 5180 121.25 - 128.36: 2284 128.36 - 135.47: 95 Bond angle restraints: 13557 Sorted by residual: angle pdb=" O3A ACP A1201 " pdb=" PA ACP A1201 " pdb=" O5' ACP A1201 " ideal model delta sigma weight residual 93.75 108.98 -15.23 3.00e+00 1.11e-01 2.58e+01 angle pdb=" N1 ACP A1201 " pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 119.32 104.55 14.77 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C5 ACP A1201 " pdb=" C6 ACP A1201 " pdb=" N6 ACP A1201 " ideal model delta sigma weight residual 122.65 135.47 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C3B ACP A1201 " pdb=" PB ACP A1201 " pdb=" O3A ACP A1201 " ideal model delta sigma weight residual 98.05 109.44 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O1B ACP A1201 " pdb=" PB ACP A1201 " pdb=" O2B ACP A1201 " ideal model delta sigma weight residual 119.60 109.44 10.16 3.00e+00 1.11e-01 1.15e+01 ... (remaining 13552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.56: 5817 33.56 - 67.12: 150 67.12 - 100.68: 16 100.68 - 134.24: 4 134.24 - 167.80: 1 Dihedral angle restraints: 5988 sinusoidal: 2480 harmonic: 3508 Sorted by residual: dihedral pdb=" O1A ACP A1201 " pdb=" O3A ACP A1201 " pdb=" PA ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sinusoidal sigma weight residual 311.25 143.45 167.80 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA PRO B 90 " pdb=" C PRO B 90 " pdb=" N CYS B 91 " pdb=" CA CYS B 91 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ILE A 463 " pdb=" C ILE A 463 " pdb=" N MET A 464 " pdb=" CA MET A 464 " ideal model delta harmonic sigma weight residual -180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1392 0.066 - 0.132: 125 0.132 - 0.198: 8 0.198 - 0.264: 1 0.264 - 0.330: 1 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C2' ACP A1201 " pdb=" C1' ACP A1201 " pdb=" C3' ACP A1201 " pdb=" O2' ACP A1201 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 864 " pdb=" N ILE A 864 " pdb=" C ILE A 864 " pdb=" CB ILE A 864 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1524 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1131 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C GLN A1131 " 0.038 2.00e-02 2.50e+03 pdb=" O GLN A1131 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A1132 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO B 170 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 195 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 196 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.024 5.00e-02 4.00e+02 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 68 2.50 - 3.10: 7451 3.10 - 3.70: 14804 3.70 - 4.30: 22683 4.30 - 4.90: 37217 Nonbonded interactions: 82223 Sorted by model distance: nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.898 2.440 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1202 " model vdw 1.947 2.170 nonbonded pdb=" O THR A 978 " pdb=" OH TYR A1069 " model vdw 1.988 2.440 nonbonded pdb=" O VAL A 990 " pdb=" OG SER A 994 " model vdw 2.046 2.440 nonbonded pdb=" O THR A 635 " pdb=" OG1 THR A 639 " model vdw 2.057 2.440 ... (remaining 82218 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=0.00 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: 0.680 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: 2.500 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 30.350 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 9990 Z= 0.303 Angle : 0.611 15.233 13557 Z= 0.287 Chirality : 0.040 0.330 1527 Planarity : 0.004 0.047 1698 Dihedral : 15.727 167.799 3721 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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 (0.25), residues: 1186 helix: -0.18 (0.22), residues: 565 sheet: 0.35 (0.47), residues: 131 loop : -0.80 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1171 HIS 0.003 0.001 HIS A 535 PHE 0.011 0.001 PHE A1132 TYR 0.012 0.001 TYR A 427 ARG 0.003 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 CYS cc_start: 0.7910 (t) cc_final: 0.6926 (t) REVERT: A 535 HIS cc_start: 0.8220 (p-80) cc_final: 0.7454 (p-80) REVERT: A 654 LEU cc_start: 0.6891 (mp) cc_final: 0.6538 (mp) REVERT: A 799 LEU cc_start: 0.8033 (mp) cc_final: 0.7535 (tt) REVERT: A 864 ILE cc_start: 0.7763 (mm) cc_final: 0.7477 (mm) REVERT: B 29 ASP cc_start: 0.6342 (t0) cc_final: 0.6072 (t70) REVERT: B 45 LEU cc_start: 0.7526 (mt) cc_final: 0.7264 (mt) REVERT: B 79 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7143 (mt-10) REVERT: B 277 GLU cc_start: 0.5944 (mt-10) cc_final: 0.5718 (mt-10) REVERT: B 310 MET cc_start: 0.8072 (tmm) cc_final: 0.7774 (tmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2448 time to fit residues: 46.0342 Evaluate side-chains 114 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS A 526 GLN A 741 ASN A1138 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9990 Z= 0.275 Angle : 0.582 9.149 13557 Z= 0.298 Chirality : 0.043 0.240 1527 Planarity : 0.004 0.041 1698 Dihedral : 10.499 178.147 1442 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.76 % Allowed : 7.72 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1186 helix: 0.07 (0.21), residues: 577 sheet: 0.28 (0.46), residues: 146 loop : -0.89 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1171 HIS 0.004 0.001 HIS A 359 PHE 0.031 0.002 PHE A 113 TYR 0.011 0.001 TYR B 121 ARG 0.003 0.000 ARG A 867 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.5546 (tpp) cc_final: 0.5308 (tpp) REVERT: A 135 GLN cc_start: 0.7767 (mp10) cc_final: 0.7441 (mp10) REVERT: A 535 HIS cc_start: 0.8161 (p-80) cc_final: 0.7531 (p-80) REVERT: A 692 GLU cc_start: 0.7278 (mp0) cc_final: 0.6856 (mm-30) REVERT: A 799 LEU cc_start: 0.7760 (mp) cc_final: 0.7360 (tt) REVERT: A 864 ILE cc_start: 0.7809 (mm) cc_final: 0.7541 (mm) REVERT: A 875 MET cc_start: 0.7206 (ttp) cc_final: 0.6654 (ttt) REVERT: A 1131 GLN cc_start: 0.6503 (pt0) cc_final: 0.6273 (pt0) REVERT: B 29 ASP cc_start: 0.6319 (t0) cc_final: 0.6060 (t70) REVERT: B 79 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 226 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7458 (mtt180) outliers start: 8 outliers final: 5 residues processed: 122 average time/residue: 0.2199 time to fit residues: 38.7664 Evaluate side-chains 114 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS A 766 HIS ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9990 Z= 0.386 Angle : 0.603 9.310 13557 Z= 0.306 Chirality : 0.044 0.248 1527 Planarity : 0.004 0.046 1698 Dihedral : 9.503 176.267 1442 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.62 % Allowed : 11.06 % Favored : 87.32 % 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: -0.70 (0.25), residues: 1186 helix: -0.11 (0.21), residues: 580 sheet: 0.23 (0.45), residues: 147 loop : -1.00 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 260 HIS 0.007 0.001 HIS A 449 PHE 0.023 0.002 PHE A 113 TYR 0.019 0.002 TYR A1055 ARG 0.004 0.001 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 HIS cc_start: 0.8222 (p-80) cc_final: 0.7588 (p-80) REVERT: A 799 LEU cc_start: 0.8050 (mp) cc_final: 0.7813 (tt) REVERT: B 29 ASP cc_start: 0.6498 (t0) cc_final: 0.6163 (t70) REVERT: B 79 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7413 (mt-10) outliers start: 17 outliers final: 11 residues processed: 123 average time/residue: 0.2243 time to fit residues: 39.3897 Evaluate side-chains 117 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 7.9990 chunk 81 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1087 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9990 Z= 0.247 Angle : 0.535 9.480 13557 Z= 0.271 Chirality : 0.041 0.250 1527 Planarity : 0.004 0.041 1698 Dihedral : 8.959 171.253 1442 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.19 % Allowed : 12.96 % Favored : 84.84 % 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: -0.60 (0.25), residues: 1186 helix: 0.06 (0.21), residues: 587 sheet: 0.22 (0.45), residues: 147 loop : -1.08 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 260 HIS 0.004 0.001 HIS A1118 PHE 0.016 0.001 PHE A 646 TYR 0.010 0.001 TYR B 121 ARG 0.005 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.7726 (mp10) cc_final: 0.7391 (mp10) REVERT: A 535 HIS cc_start: 0.8314 (p-80) cc_final: 0.7664 (p-80) REVERT: A 875 MET cc_start: 0.7322 (ttp) cc_final: 0.6738 (ttt) REVERT: A 1131 GLN cc_start: 0.6923 (pt0) cc_final: 0.6619 (pp30) REVERT: B 29 ASP cc_start: 0.6267 (t0) cc_final: 0.5989 (t70) REVERT: B 79 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7455 (mt-10) outliers start: 23 outliers final: 14 residues processed: 130 average time/residue: 0.2189 time to fit residues: 41.3849 Evaluate side-chains 121 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A1087 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9990 Z= 0.238 Angle : 0.534 9.519 13557 Z= 0.268 Chirality : 0.041 0.252 1527 Planarity : 0.004 0.039 1698 Dihedral : 8.663 166.066 1442 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.10 % Allowed : 14.20 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1186 helix: 0.17 (0.22), residues: 578 sheet: 0.26 (0.45), residues: 147 loop : -1.06 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.004 0.001 HIS A1118 PHE 0.016 0.001 PHE A 113 TYR 0.010 0.001 TYR B 121 ARG 0.006 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.7744 (mp10) cc_final: 0.7397 (mp10) REVERT: A 535 HIS cc_start: 0.8336 (p-80) cc_final: 0.7721 (p-80) REVERT: A 769 MET cc_start: 0.4608 (tpt) cc_final: 0.4333 (tpp) REVERT: A 875 MET cc_start: 0.7286 (ttp) cc_final: 0.6844 (ttt) REVERT: A 1087 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7629 (tm130) REVERT: B 29 ASP cc_start: 0.6262 (t0) cc_final: 0.5958 (t70) REVERT: B 79 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7439 (mt-10) outliers start: 22 outliers final: 16 residues processed: 130 average time/residue: 0.2224 time to fit residues: 42.0775 Evaluate side-chains 126 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 67 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1087 GLN A1179 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9990 Z= 0.206 Angle : 0.517 9.519 13557 Z= 0.260 Chirality : 0.040 0.253 1527 Planarity : 0.003 0.037 1698 Dihedral : 8.415 160.316 1442 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.57 % Allowed : 14.39 % Favored : 83.03 % 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: -0.41 (0.25), residues: 1186 helix: 0.24 (0.22), residues: 578 sheet: 0.33 (0.46), residues: 147 loop : -1.02 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1095 HIS 0.005 0.001 HIS A1118 PHE 0.012 0.001 PHE A 113 TYR 0.010 0.001 TYR B 121 ARG 0.006 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7949 (p) REVERT: A 135 GLN cc_start: 0.7786 (mp10) cc_final: 0.7547 (mp10) REVERT: A 535 HIS cc_start: 0.8334 (p-80) cc_final: 0.7675 (p-80) REVERT: A 875 MET cc_start: 0.7294 (ttp) cc_final: 0.6855 (ttt) REVERT: A 1011 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 1104 PHE cc_start: 0.7721 (m-10) cc_final: 0.7402 (m-10) REVERT: B 29 ASP cc_start: 0.6247 (t0) cc_final: 0.5949 (t70) REVERT: B 79 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7272 (mt-10) outliers start: 27 outliers final: 21 residues processed: 141 average time/residue: 0.2235 time to fit residues: 46.5401 Evaluate side-chains 138 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1062 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 70 optimal weight: 0.0010 chunk 45 optimal weight: 0.5980 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9990 Z= 0.147 Angle : 0.493 9.485 13557 Z= 0.248 Chirality : 0.039 0.256 1527 Planarity : 0.003 0.037 1698 Dihedral : 8.060 151.312 1442 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.81 % Allowed : 15.73 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1186 helix: 0.44 (0.22), residues: 580 sheet: 0.38 (0.46), residues: 146 loop : -0.98 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1095 HIS 0.004 0.001 HIS A1118 PHE 0.011 0.001 PHE A 646 TYR 0.010 0.001 TYR B 121 ARG 0.007 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7854 (p) REVERT: A 535 HIS cc_start: 0.8329 (p-80) cc_final: 0.7655 (p-80) REVERT: A 875 MET cc_start: 0.7341 (ttp) cc_final: 0.6926 (ttt) REVERT: A 1055 TYR cc_start: 0.7992 (m-80) cc_final: 0.7612 (m-80) REVERT: A 1104 PHE cc_start: 0.7637 (m-10) cc_final: 0.7293 (m-10) REVERT: B 29 ASP cc_start: 0.6214 (t0) cc_final: 0.5932 (t70) REVERT: B 79 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7235 (mt-10) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.2200 time to fit residues: 42.1499 Evaluate side-chains 125 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9990 Z= 0.266 Angle : 0.534 9.571 13557 Z= 0.268 Chirality : 0.041 0.256 1527 Planarity : 0.004 0.039 1698 Dihedral : 7.967 141.596 1442 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.10 % Allowed : 16.40 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1186 helix: 0.31 (0.22), residues: 577 sheet: 0.32 (0.46), residues: 147 loop : -0.99 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1095 HIS 0.005 0.001 HIS A1118 PHE 0.024 0.002 PHE A 646 TYR 0.011 0.001 TYR A 974 ARG 0.007 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.7953 (p) REVERT: A 535 HIS cc_start: 0.8349 (p-80) cc_final: 0.7679 (p-80) REVERT: A 1055 TYR cc_start: 0.8022 (m-80) cc_final: 0.7715 (m-80) REVERT: A 1104 PHE cc_start: 0.7703 (m-10) cc_final: 0.7369 (m-10) REVERT: B 29 ASP cc_start: 0.6259 (t0) cc_final: 0.5930 (t70) outliers start: 22 outliers final: 15 residues processed: 131 average time/residue: 0.2178 time to fit residues: 41.0112 Evaluate side-chains 127 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9990 Z= 0.174 Angle : 0.508 9.714 13557 Z= 0.252 Chirality : 0.039 0.254 1527 Planarity : 0.003 0.039 1698 Dihedral : 7.721 133.034 1442 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.91 % Allowed : 16.49 % 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: -0.27 (0.25), residues: 1186 helix: 0.39 (0.22), residues: 577 sheet: 0.36 (0.47), residues: 147 loop : -0.99 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1095 HIS 0.005 0.001 HIS A1118 PHE 0.023 0.001 PHE B 108 TYR 0.010 0.001 TYR B 121 ARG 0.007 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7882 (p) REVERT: A 525 ARG cc_start: 0.6858 (ttm110) cc_final: 0.6649 (ttm170) REVERT: A 535 HIS cc_start: 0.8353 (p-80) cc_final: 0.7679 (p-80) REVERT: A 799 LEU cc_start: 0.7830 (tt) cc_final: 0.7487 (tt) REVERT: A 875 MET cc_start: 0.6981 (ttp) cc_final: 0.6444 (ttt) REVERT: A 1000 MET cc_start: 0.7824 (ttp) cc_final: 0.7601 (ttm) REVERT: A 1104 PHE cc_start: 0.7594 (m-10) cc_final: 0.7280 (m-10) REVERT: B 29 ASP cc_start: 0.6219 (t0) cc_final: 0.5911 (t70) REVERT: B 79 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7131 (mt-10) REVERT: B 228 LYS cc_start: 0.7695 (mtpt) cc_final: 0.7463 (mmmt) REVERT: B 348 HIS cc_start: 0.6954 (t-90) cc_final: 0.6745 (t70) outliers start: 20 outliers final: 14 residues processed: 130 average time/residue: 0.2420 time to fit residues: 45.4727 Evaluate side-chains 127 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9990 Z= 0.229 Angle : 0.529 10.440 13557 Z= 0.263 Chirality : 0.040 0.254 1527 Planarity : 0.004 0.039 1698 Dihedral : 7.650 125.760 1442 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.62 % Allowed : 16.97 % Favored : 81.41 % 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: -0.31 (0.25), residues: 1186 helix: 0.35 (0.22), residues: 577 sheet: 0.13 (0.46), residues: 153 loop : -0.92 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1095 HIS 0.005 0.001 HIS A1118 PHE 0.024 0.001 PHE B 108 TYR 0.011 0.001 TYR B 121 ARG 0.007 0.000 ARG A 525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7912 (p) REVERT: A 535 HIS cc_start: 0.8366 (p-80) cc_final: 0.7701 (p-80) REVERT: A 799 LEU cc_start: 0.8004 (tt) cc_final: 0.7678 (tt) REVERT: A 875 MET cc_start: 0.6997 (ttp) cc_final: 0.6505 (ttt) REVERT: A 1055 TYR cc_start: 0.8061 (m-80) cc_final: 0.7655 (m-80) REVERT: A 1104 PHE cc_start: 0.7622 (m-10) cc_final: 0.7120 (m-10) REVERT: B 29 ASP cc_start: 0.6246 (t0) cc_final: 0.5915 (t70) REVERT: B 79 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7146 (mt-10) REVERT: B 228 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7514 (mmmt) REVERT: B 348 HIS cc_start: 0.6952 (t-90) cc_final: 0.6740 (t70) outliers start: 17 outliers final: 14 residues processed: 127 average time/residue: 0.2192 time to fit residues: 40.1656 Evaluate side-chains 125 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.0040 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.237975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.232281 restraints weight = 9818.176| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 0.24 r_work: 0.4382 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.4306 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9990 Z= 0.167 Angle : 0.510 10.441 13557 Z= 0.252 Chirality : 0.039 0.255 1527 Planarity : 0.003 0.042 1698 Dihedral : 7.484 123.145 1442 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.81 % Allowed : 16.87 % Favored : 81.32 % 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: -0.21 (0.25), residues: 1186 helix: 0.46 (0.22), residues: 578 sheet: 0.14 (0.46), residues: 153 loop : -0.91 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1095 HIS 0.005 0.001 HIS A1118 PHE 0.024 0.001 PHE B 108 TYR 0.010 0.001 TYR B 121 ARG 0.005 0.000 ARG A 525 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2060.93 seconds wall clock time: 38 minutes 38.88 seconds (2318.88 seconds total)