Starting phenix.real_space_refine on Sun Apr 7 07:27:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/04_2024/7qfp_13946.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/04_2024/7qfp_13946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/04_2024/7qfp_13946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/04_2024/7qfp_13946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/04_2024/7qfp_13946.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/04_2024/7qfp_13946.pdb" } resolution = 3.7 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= -0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 6363 2.51 5 N 1670 2.21 5 O 1940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A ASP 502": "OD1" <-> "OD2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 640": "OD1" <-> "OD2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 834": "OD1" <-> "OD2" Residue "A PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 881": "OD1" <-> "OD2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 962": "OD1" <-> "OD2" Residue "A TYR 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1044": "OD1" <-> "OD2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A GLU 1083": "OE1" <-> "OE2" Residue "A ASP 1100": "OD1" <-> "OD2" Residue "A PHE 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A PHE 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9996 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1233, 9996 Classifications: {'peptide': 1233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 1199} Chain breaks: 1 Time building chain proxies: 5.69, per 1000 atoms: 0.57 Number of scatterers: 9996 At special positions: 0 Unit cell: (94.6, 99.76, 122.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1940 8.00 N 1670 7.00 C 6363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 443 " 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 Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 18 sheets defined 26.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.941A pdb=" N LEU A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 3.606A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.779A pdb=" N ASN A 187 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 238 removed outlier: 3.794A pdb=" N THR A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.509A pdb=" N LEU A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 305 removed outlier: 3.977A pdb=" N TYR A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.696A pdb=" N LYS A 317 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.613A pdb=" N PHE A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 removed outlier: 3.721A pdb=" N LEU A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.658A pdb=" N VAL A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 3.898A pdb=" N TYR A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 588 through 605 removed outlier: 4.952A pdb=" N GLN A 594 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 removed outlier: 4.643A pdb=" N ALA A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 710 removed outlier: 3.836A pdb=" N VAL A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 699 " --> pdb=" O TRP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 729 removed outlier: 3.762A pdb=" N PHE A 714 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 Processing helix chain 'A' and resid 760 through 817 removed outlier: 4.624A pdb=" N ASN A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 793 " --> pdb=" O LYS A 789 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 798 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG A 800 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 801 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 836 Processing helix chain 'A' and resid 945 through 949 Processing helix chain 'A' and resid 1072 through 1083 removed outlier: 3.510A pdb=" N ILE A1076 " --> pdb=" O ASP A1072 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A1077 " --> pdb=" O GLU A1073 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A1078 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A1082 " --> pdb=" O THR A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1176 removed outlier: 3.853A pdb=" N LEU A1176 " --> pdb=" O LYS A1173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 removed outlier: 6.729A pdb=" N TRP A 57 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 201 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.662A pdb=" N VAL A 422 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 250 removed outlier: 3.531A pdb=" N ILE A 250 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 264 " --> pdb=" O ILE A 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA9, first strand: chain 'A' and resid 889 through 891 Processing sheet with id=AB1, first strand: chain 'A' and resid 905 through 906 removed outlier: 3.565A pdb=" N PHE A 905 " --> pdb=" O ILE A1061 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1008 through 1012 removed outlier: 3.602A pdb=" N ILE A 934 " --> pdb=" O ILE A1012 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 990 through 993 removed outlier: 3.781A pdb=" N PHE A 992 " --> pdb=" O ILE A 976 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 976 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 975 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 968 " --> pdb=" O THR A 979 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 981 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TRP A 967 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASN A 958 " --> pdb=" O TRP A 967 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 969 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 954 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR A 954 " --> pdb=" O VAL A1051 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A1051 " --> pdb=" O TYR A 954 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE A 956 " --> pdb=" O LYS A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1019 through 1024 removed outlier: 6.474A pdb=" N SER A1020 " --> pdb=" O GLN A1031 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A1031 " --> pdb=" O SER A1020 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A1022 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A1029 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1104 through 1107 Processing sheet with id=AB6, first strand: chain 'A' and resid 1113 through 1117 removed outlier: 3.600A pdb=" N ASN A1127 " --> pdb=" O PHE A1114 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASP A1116 " --> pdb=" O ILE A1125 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE A1125 " --> pdb=" O ASP A1116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1168 through 1169 removed outlier: 3.506A pdb=" N PHE A1177 " --> pdb=" O PHE A1169 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1204 through 1209 removed outlier: 3.533A pdb=" N LYS A1219 " --> pdb=" O VAL A1204 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A1218 " --> pdb=" O ILE A1226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1228 through 1229 248 hydrogen bonds defined for protein. 678 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: 3.30 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2831 1.33 - 1.46: 2025 1.46 - 1.58: 5299 1.58 - 1.70: 0 1.70 - 1.83: 38 Bond restraints: 10193 Sorted by residual: bond pdb=" C VAL A 545 " pdb=" N PRO A 546 " ideal model delta sigma weight residual 1.332 1.398 -0.066 1.30e-02 5.92e+03 2.58e+01 bond pdb=" N PRO A 941 " pdb=" CA PRO A 941 " ideal model delta sigma weight residual 1.469 1.523 -0.054 1.28e-02 6.10e+03 1.80e+01 bond pdb=" N PRO A 498 " pdb=" CA PRO A 498 " ideal model delta sigma weight residual 1.479 1.541 -0.062 1.56e-02 4.11e+03 1.57e+01 bond pdb=" N VAL A1204 " pdb=" CA VAL A1204 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.18e-02 7.18e+03 1.21e+01 bond pdb=" N ILE A 509 " pdb=" CA ILE A 509 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.14e+01 ... (remaining 10188 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.16: 159 106.16 - 113.11: 5311 113.11 - 120.07: 3961 120.07 - 127.02: 4311 127.02 - 133.98: 68 Bond angle restraints: 13810 Sorted by residual: angle pdb=" C VAL A 545 " pdb=" N PRO A 546 " pdb=" CA PRO A 546 " ideal model delta sigma weight residual 119.76 127.20 -7.44 1.03e+00 9.43e-01 5.22e+01 angle pdb=" C ILE A 940 " pdb=" N PRO A 941 " pdb=" CA PRO A 941 " ideal model delta sigma weight residual 119.84 128.85 -9.01 1.25e+00 6.40e-01 5.20e+01 angle pdb=" N ASN A 964 " pdb=" CA ASN A 964 " pdb=" C ASN A 964 " ideal model delta sigma weight residual 113.23 106.16 7.07 1.22e+00 6.72e-01 3.35e+01 angle pdb=" N ILE A 864 " pdb=" CA ILE A 864 " pdb=" C ILE A 864 " ideal model delta sigma weight residual 110.53 115.93 -5.40 9.40e-01 1.13e+00 3.30e+01 angle pdb=" N ASP A 484 " pdb=" CA ASP A 484 " pdb=" C ASP A 484 " ideal model delta sigma weight residual 113.18 106.42 6.76 1.21e+00 6.83e-01 3.12e+01 ... (remaining 13805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 5298 16.92 - 33.85: 637 33.85 - 50.77: 156 50.77 - 67.69: 31 67.69 - 84.61: 11 Dihedral angle restraints: 6133 sinusoidal: 2483 harmonic: 3650 Sorted by residual: dihedral pdb=" CB CYS A 429 " pdb=" SG CYS A 429 " pdb=" SG CYS A 443 " pdb=" CB CYS A 443 " ideal model delta sinusoidal sigma weight residual -86.00 -158.43 72.43 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" C ASN A 265 " pdb=" N ASN A 265 " pdb=" CA ASN A 265 " pdb=" CB ASN A 265 " ideal model delta harmonic sigma weight residual -122.60 -134.43 11.83 0 2.50e+00 1.60e-01 2.24e+01 dihedral pdb=" C ASP A 486 " pdb=" N ASP A 486 " pdb=" CA ASP A 486 " pdb=" CB ASP A 486 " ideal model delta harmonic sigma weight residual -122.60 -134.28 11.68 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 6130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1120 0.074 - 0.149: 298 0.149 - 0.223: 84 0.223 - 0.297: 25 0.297 - 0.371: 9 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA ASN A 265 " pdb=" N ASN A 265 " pdb=" C ASN A 265 " pdb=" CB ASN A 265 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA ASP A 486 " pdb=" N ASP A 486 " pdb=" C ASP A 486 " pdb=" CB ASP A 486 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA ASP A 944 " pdb=" N ASP A 944 " pdb=" C ASP A 944 " pdb=" CB ASP A 944 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 1533 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 391 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLY A 391 " -0.062 2.00e-02 2.50e+03 pdb=" O GLY A 391 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR A 392 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 171 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A 172 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 314 " 0.047 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 315 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " 0.041 5.00e-02 4.00e+02 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 539 2.71 - 3.26: 10159 3.26 - 3.81: 16402 3.81 - 4.35: 19915 4.35 - 4.90: 31467 Nonbonded interactions: 78482 Sorted by model distance: nonbonded pdb=" N GLU A 267 " pdb=" OE1 GLU A 267 " model vdw 2.167 2.520 nonbonded pdb=" O ARG A 419 " pdb=" NH1 ARG A 419 " model vdw 2.186 2.520 nonbonded pdb=" N GLN A 371 " pdb=" OE1 GLN A 371 " model vdw 2.249 2.520 nonbonded pdb=" O ASN A 27 " pdb=" ND2 ASN A 27 " model vdw 2.253 2.520 nonbonded pdb=" O ALA A 604 " pdb=" OH TYR A 622 " model vdw 2.288 2.440 ... (remaining 78477 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.510 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.350 Find NCS groups from input model: 0.270 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.007 0.066 10193 Z= 0.418 Angle : 1.109 10.154 13810 Z= 0.746 Chirality : 0.081 0.371 1536 Planarity : 0.006 0.074 1793 Dihedral : 15.770 84.612 3778 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.57 % Allowed : 12.53 % Favored : 86.90 % Rotamer: Outliers : 4.14 % Allowed : 12.86 % Favored : 83.00 % Cbeta Deviations : 0.34 % 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: -4.48 (0.19), residues: 1229 helix: -2.54 (0.21), residues: 333 sheet: -2.82 (0.47), residues: 98 loop : -3.41 (0.18), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 937 HIS 0.004 0.001 HIS A 229 PHE 0.012 0.001 PHE A 905 TYR 0.021 0.002 TYR A 233 ARG 0.004 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 211 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: A 442 ILE cc_start: 0.8815 (tt) cc_final: 0.8204 (tt) REVERT: A 503 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: A 578 ASN cc_start: 0.9012 (m110) cc_final: 0.8456 (p0) REVERT: A 637 ASN cc_start: 0.7768 (p0) cc_final: 0.7498 (p0) REVERT: A 645 LEU cc_start: 0.7880 (mt) cc_final: 0.7608 (mt) REVERT: A 689 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8567 (pttt) REVERT: A 693 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7907 (mt-10) REVERT: A 758 LYS cc_start: 0.4694 (OUTLIER) cc_final: 0.4486 (pttm) REVERT: A 870 LEU cc_start: 0.8615 (tp) cc_final: 0.8403 (tt) REVERT: A 1044 ASP cc_start: 0.9154 (p0) cc_final: 0.8867 (p0) REVERT: A 1076 ILE cc_start: 0.8187 (mm) cc_final: 0.7918 (mm) REVERT: A 1101 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5375 (mmmt) REVERT: A 1114 PHE cc_start: 0.7803 (t80) cc_final: 0.7429 (t80) REVERT: A 1163 ASP cc_start: 0.7158 (t0) cc_final: 0.6800 (t0) REVERT: A 1201 PHE cc_start: 0.8283 (m-80) cc_final: 0.7550 (m-80) outliers start: 47 outliers final: 15 residues processed: 252 average time/residue: 0.2393 time to fit residues: 83.1687 Evaluate side-chains 146 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1101 LYS Chi-restraints excluded: chain A residue 1186 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 37 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 111 optimal weight: 0.4980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 158 GLN A 214 ASN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 400 ASN A 407 ASN A 448 ASN A 585 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A 711 ASN A 715 ASN A 765 ASN A 805 ASN A 837 ASN A 871 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** A 974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 ASN A1027 ASN A1082 ASN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 GLN A1224 ASN A1251 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10193 Z= 0.169 Angle : 0.636 7.963 13810 Z= 0.336 Chirality : 0.046 0.169 1536 Planarity : 0.004 0.065 1793 Dihedral : 7.352 69.723 1377 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.85 % Favored : 90.07 % Rotamer: Outliers : 4.05 % Allowed : 18.77 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.21), residues: 1229 helix: -1.00 (0.27), residues: 327 sheet: -2.24 (0.46), residues: 108 loop : -3.33 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1241 HIS 0.002 0.000 HIS A 236 PHE 0.029 0.002 PHE A 670 TYR 0.021 0.001 TYR A1023 ARG 0.005 0.001 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.5602 (mmm) cc_final: 0.5313 (mmm) REVERT: A 158 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8075 (mm110) REVERT: A 460 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: A 555 THR cc_start: 0.6956 (OUTLIER) cc_final: 0.6679 (t) REVERT: A 578 ASN cc_start: 0.8967 (m110) cc_final: 0.8338 (p0) REVERT: A 600 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: A 645 LEU cc_start: 0.7910 (mt) cc_final: 0.7657 (mt) REVERT: A 653 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: A 689 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8548 (pttt) REVERT: A 857 PHE cc_start: 0.7891 (t80) cc_final: 0.7586 (t80) REVERT: A 870 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8042 (tt) REVERT: A 1044 ASP cc_start: 0.9153 (p0) cc_final: 0.8927 (p0) REVERT: A 1070 GLU cc_start: 0.3879 (OUTLIER) cc_final: 0.3505 (tp30) REVERT: A 1103 TYR cc_start: 0.4855 (m-80) cc_final: 0.4300 (m-80) REVERT: A 1163 ASP cc_start: 0.7026 (t0) cc_final: 0.6552 (t0) REVERT: A 1207 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.4788 (mtt) outliers start: 46 outliers final: 18 residues processed: 174 average time/residue: 0.2141 time to fit residues: 53.2730 Evaluate side-chains 139 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain A residue 1237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 10193 Z= 0.437 Angle : 0.814 13.757 13810 Z= 0.434 Chirality : 0.050 0.165 1536 Planarity : 0.005 0.070 1793 Dihedral : 6.663 58.167 1343 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.03 % Favored : 83.89 % Rotamer: Outliers : 5.64 % Allowed : 21.76 % Favored : 72.60 % 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: -3.71 (0.21), residues: 1229 helix: -0.94 (0.27), residues: 337 sheet: -2.37 (0.46), residues: 99 loop : -3.41 (0.19), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 592 HIS 0.006 0.001 HIS A1041 PHE 0.025 0.003 PHE A 428 TYR 0.026 0.002 TYR A 324 ARG 0.009 0.001 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 97 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6656 (mmm) cc_final: 0.6126 (mmm) REVERT: A 123 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 368 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8881 (m-80) REVERT: A 460 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: A 637 ASN cc_start: 0.8866 (m-40) cc_final: 0.8662 (t0) REVERT: A 645 LEU cc_start: 0.8070 (mt) cc_final: 0.7707 (mt) REVERT: A 1044 ASP cc_start: 0.9115 (p0) cc_final: 0.8853 (p0) REVERT: A 1070 GLU cc_start: 0.4515 (OUTLIER) cc_final: 0.4138 (tp30) outliers start: 64 outliers final: 33 residues processed: 148 average time/residue: 0.2305 time to fit residues: 48.9844 Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 93 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 741 ASN Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1239 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 217 ASN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN A 903 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10193 Z= 0.197 Angle : 0.643 13.734 13810 Z= 0.332 Chirality : 0.045 0.164 1536 Planarity : 0.004 0.051 1793 Dihedral : 5.706 48.089 1337 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.23 % Favored : 88.69 % Rotamer: Outliers : 4.14 % Allowed : 23.88 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.22), residues: 1229 helix: -0.35 (0.29), residues: 328 sheet: -2.36 (0.46), residues: 104 loop : -3.27 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 978 HIS 0.003 0.001 HIS A1041 PHE 0.017 0.001 PHE A 211 TYR 0.020 0.001 TYR A1023 ARG 0.007 0.001 ARG A1062 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 114 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6655 (mmm) cc_final: 0.6218 (mmm) REVERT: A 123 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 368 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8816 (m-80) REVERT: A 460 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: A 645 LEU cc_start: 0.7869 (mt) cc_final: 0.7558 (mt) REVERT: A 1044 ASP cc_start: 0.9122 (p0) cc_final: 0.8825 (p0) REVERT: A 1063 TYR cc_start: 0.7195 (m-80) cc_final: 0.6988 (m-80) REVERT: A 1070 GLU cc_start: 0.4091 (OUTLIER) cc_final: 0.3876 (tp30) outliers start: 47 outliers final: 31 residues processed: 150 average time/residue: 0.1990 time to fit residues: 43.9870 Evaluate side-chains 132 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1237 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0070 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 140 GLN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 10193 Z= 0.385 Angle : 0.759 12.817 13810 Z= 0.399 Chirality : 0.048 0.168 1536 Planarity : 0.005 0.049 1793 Dihedral : 6.227 59.627 1337 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.84 % Favored : 83.08 % Rotamer: Outliers : 6.87 % Allowed : 23.17 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.22), residues: 1229 helix: -0.59 (0.28), residues: 329 sheet: -2.37 (0.49), residues: 98 loop : -3.40 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1257 HIS 0.003 0.001 HIS A 73 PHE 0.022 0.002 PHE A 209 TYR 0.023 0.002 TYR A 324 ARG 0.003 0.000 ARG A1062 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 94 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6769 (mmm) cc_final: 0.6193 (mmm) REVERT: A 123 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 324 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7228 (p90) REVERT: A 419 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7781 (tpt90) REVERT: A 460 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: A 645 LEU cc_start: 0.7959 (mt) cc_final: 0.7622 (mt) REVERT: A 788 MET cc_start: 0.8876 (mmm) cc_final: 0.8595 (mmm) REVERT: A 898 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8341 (m-10) REVERT: A 943 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: A 1044 ASP cc_start: 0.9166 (p0) cc_final: 0.8898 (p0) outliers start: 78 outliers final: 49 residues processed: 154 average time/residue: 0.2017 time to fit residues: 45.8229 Evaluate side-chains 144 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 90 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 741 ASN Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1239 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 0.0070 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10193 Z= 0.272 Angle : 0.682 11.609 13810 Z= 0.355 Chirality : 0.046 0.194 1536 Planarity : 0.004 0.048 1793 Dihedral : 5.941 53.712 1337 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.73 % Favored : 85.19 % Rotamer: Outliers : 5.46 % Allowed : 25.81 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.22), residues: 1229 helix: -0.38 (0.28), residues: 328 sheet: -2.29 (0.49), residues: 97 loop : -3.36 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 937 HIS 0.002 0.001 HIS A 73 PHE 0.014 0.002 PHE A 209 TYR 0.016 0.002 TYR A1023 ARG 0.003 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 96 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6690 (mmm) cc_final: 0.6173 (mmm) REVERT: A 123 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 460 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: A 637 ASN cc_start: 0.8472 (t0) cc_final: 0.8218 (t0) REVERT: A 645 LEU cc_start: 0.7941 (mt) cc_final: 0.7602 (mt) REVERT: A 898 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8336 (m-10) REVERT: A 1022 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 1044 ASP cc_start: 0.9153 (p0) cc_final: 0.8903 (p0) REVERT: A 1257 TRP cc_start: 0.5979 (m100) cc_final: 0.5719 (m100) outliers start: 62 outliers final: 56 residues processed: 146 average time/residue: 0.2119 time to fit residues: 44.9061 Evaluate side-chains 149 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 90 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10193 Z= 0.199 Angle : 0.657 10.532 13810 Z= 0.334 Chirality : 0.045 0.200 1536 Planarity : 0.004 0.048 1793 Dihedral : 5.624 53.978 1337 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.16 % Favored : 85.76 % Rotamer: Outliers : 4.93 % Allowed : 26.43 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.23), residues: 1229 helix: -0.16 (0.29), residues: 329 sheet: -2.27 (0.49), residues: 92 loop : -3.29 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 937 HIS 0.002 0.000 HIS A1041 PHE 0.014 0.001 PHE A 211 TYR 0.016 0.001 TYR A1023 ARG 0.005 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 98 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6604 (mmm) cc_final: 0.6143 (mmm) REVERT: A 123 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 460 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: A 600 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: A 637 ASN cc_start: 0.8421 (t0) cc_final: 0.7640 (t0) REVERT: A 645 LEU cc_start: 0.7910 (mt) cc_final: 0.7559 (mt) REVERT: A 721 MET cc_start: 0.8495 (tpp) cc_final: 0.8288 (tpp) REVERT: A 1022 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8956 (tt) REVERT: A 1044 ASP cc_start: 0.9137 (p0) cc_final: 0.8878 (p0) REVERT: A 1070 GLU cc_start: 0.4375 (tp30) cc_final: 0.4034 (tp30) outliers start: 56 outliers final: 44 residues processed: 143 average time/residue: 0.2015 time to fit residues: 42.3526 Evaluate side-chains 139 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 92 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 600 PHE Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10193 Z= 0.255 Angle : 0.669 9.258 13810 Z= 0.349 Chirality : 0.046 0.173 1536 Planarity : 0.004 0.043 1793 Dihedral : 5.711 54.227 1337 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.13 % Favored : 84.78 % Rotamer: Outliers : 5.37 % Allowed : 27.14 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.22), residues: 1229 helix: -0.18 (0.29), residues: 329 sheet: -2.20 (0.49), residues: 97 loop : -3.29 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1257 HIS 0.002 0.001 HIS A1264 PHE 0.017 0.002 PHE A 571 TYR 0.022 0.002 TYR A 743 ARG 0.005 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 94 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6733 (mmm) cc_final: 0.6244 (mmm) REVERT: A 123 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 460 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: A 637 ASN cc_start: 0.8451 (t0) cc_final: 0.7791 (t0) REVERT: A 645 LEU cc_start: 0.7935 (mt) cc_final: 0.7582 (mt) REVERT: A 898 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: A 1022 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8959 (tt) REVERT: A 1044 ASP cc_start: 0.9124 (p0) cc_final: 0.8893 (p0) REVERT: A 1070 GLU cc_start: 0.4478 (tp30) cc_final: 0.4275 (tp30) REVERT: A 1257 TRP cc_start: 0.6028 (m100) cc_final: 0.5814 (m100) outliers start: 61 outliers final: 52 residues processed: 146 average time/residue: 0.2050 time to fit residues: 44.4564 Evaluate side-chains 145 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 90 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 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 80 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10193 Z= 0.218 Angle : 0.671 10.212 13810 Z= 0.343 Chirality : 0.046 0.174 1536 Planarity : 0.004 0.047 1793 Dihedral : 5.657 53.865 1337 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.08 % Favored : 85.76 % Rotamer: Outliers : 5.55 % Allowed : 26.61 % Favored : 67.84 % 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: -3.23 (0.23), residues: 1229 helix: -0.15 (0.29), residues: 329 sheet: -2.37 (0.50), residues: 96 loop : -3.22 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 937 HIS 0.001 0.000 HIS A 73 PHE 0.020 0.002 PHE A 571 TYR 0.025 0.001 TYR A 743 ARG 0.005 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 94 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6540 (mmm) cc_final: 0.6069 (mmm) REVERT: A 460 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: A 637 ASN cc_start: 0.8426 (t0) cc_final: 0.7644 (t0) REVERT: A 645 LEU cc_start: 0.7891 (mt) cc_final: 0.7516 (mt) REVERT: A 898 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8391 (m-10) REVERT: A 928 LYS cc_start: 0.8059 (pttm) cc_final: 0.7754 (ptpp) REVERT: A 1022 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8965 (tt) REVERT: A 1044 ASP cc_start: 0.9110 (p0) cc_final: 0.8876 (p0) REVERT: A 1180 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: A 1257 TRP cc_start: 0.6033 (m100) cc_final: 0.5800 (m100) outliers start: 63 outliers final: 54 residues processed: 148 average time/residue: 0.2089 time to fit residues: 45.6168 Evaluate side-chains 149 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 91 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10193 Z= 0.190 Angle : 0.657 9.974 13810 Z= 0.337 Chirality : 0.046 0.295 1536 Planarity : 0.003 0.047 1793 Dihedral : 5.521 52.953 1337 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.43 % Favored : 86.49 % Rotamer: Outliers : 5.11 % Allowed : 26.87 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.23), residues: 1229 helix: 0.02 (0.30), residues: 330 sheet: -2.25 (0.48), residues: 106 loop : -3.20 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 937 HIS 0.001 0.000 HIS A1041 PHE 0.015 0.002 PHE A 571 TYR 0.024 0.001 TYR A 743 ARG 0.005 0.000 ARG A 863 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 93 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6530 (mmm) cc_final: 0.6174 (mmm) REVERT: A 430 LYS cc_start: 0.8494 (tttt) cc_final: 0.7995 (ptmt) REVERT: A 460 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: A 637 ASN cc_start: 0.8398 (t0) cc_final: 0.7722 (t0) REVERT: A 645 LEU cc_start: 0.7898 (mt) cc_final: 0.7541 (mt) REVERT: A 721 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7170 (mmm) REVERT: A 898 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8355 (m-10) REVERT: A 1022 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8951 (tt) REVERT: A 1044 ASP cc_start: 0.9111 (p0) cc_final: 0.8879 (p0) REVERT: A 1257 TRP cc_start: 0.6031 (m100) cc_final: 0.5790 (m100) outliers start: 58 outliers final: 47 residues processed: 142 average time/residue: 0.1964 time to fit residues: 41.5563 Evaluate side-chains 144 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 93 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1027 ASN Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 12 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.0270 chunk 5 optimal weight: 7.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 80 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.105605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.083145 restraints weight = 36386.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.085742 restraints weight = 20574.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.087455 restraints weight = 14273.293| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 10193 Z= 0.165 Angle : 0.658 9.963 13810 Z= 0.332 Chirality : 0.046 0.307 1536 Planarity : 0.003 0.049 1793 Dihedral : 5.288 49.073 1337 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.47 % Favored : 88.45 % Rotamer: Outliers : 3.70 % Allowed : 28.28 % Favored : 68.02 % 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: -2.94 (0.23), residues: 1229 helix: 0.24 (0.30), residues: 330 sheet: -2.11 (0.48), residues: 104 loop : -3.14 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 978 HIS 0.002 0.000 HIS A1175 PHE 0.016 0.001 PHE A 211 TYR 0.022 0.001 TYR A 743 ARG 0.005 0.000 ARG A 863 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.31 seconds wall clock time: 41 minutes 2.68 seconds (2462.68 seconds total)