Starting phenix.real_space_refine (version: dev) on Sun Feb 19 11:10:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/02_2023/7qfp_13946.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/02_2023/7qfp_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_13946/02_2023/7qfp_13946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/02_2023/7qfp_13946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/02_2023/7qfp_13946.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/02_2023/7qfp_13946.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 6.02, per 1000 atoms: 0.60 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: 4.60 Conformation dependent library (CDL) restraints added in 1.6 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: 0.60 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: 3.32 Time building geometry restraints manager: 4.83 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 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. 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: 1.500 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: 5.890 Check model and map are aligned: 0.150 Process input model: 30.120 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 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 % 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 *********************** 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 : 1.267 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 outliers start: 47 outliers final: 15 residues processed: 252 average time/residue: 0.2448 time to fit residues: 84.6116 Evaluate side-chains 136 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1321 time to fit residues: 4.9429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 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: 0.6420 ------------------------------------------------------------------------------- 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 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** A1162 ASN A1203 GLN A1224 ASN A1251 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10193 Z= 0.178 Angle : 0.646 7.966 13810 Z= 0.341 Chirality : 0.046 0.169 1536 Planarity : 0.004 0.065 1793 Dihedral : 5.157 20.008 1331 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.76 % Favored : 90.15 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.21), residues: 1229 helix: -1.05 (0.27), residues: 327 sheet: -2.25 (0.46), residues: 108 loop : -3.30 (0.19), residues: 794 *********************** 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 178 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 1.260 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 outliers start: 37 outliers final: 13 residues processed: 164 average time/residue: 0.2262 time to fit residues: 53.2102 Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1029 time to fit residues: 4.3592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 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 447 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 10193 Z= 0.389 Angle : 0.795 18.661 13810 Z= 0.416 Chirality : 0.048 0.185 1536 Planarity : 0.005 0.052 1793 Dihedral : 5.730 30.098 1331 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.38 % Favored : 84.54 % Rotamer Outliers : 4.49 % 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: -3.56 (0.22), residues: 1229 helix: -0.80 (0.27), residues: 336 sheet: -2.30 (0.46), residues: 99 loop : -3.31 (0.20), residues: 794 *********************** 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 158 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 107 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 20 residues processed: 145 average time/residue: 0.2220 time to fit residues: 45.6881 Evaluate side-chains 117 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1255 time to fit residues: 5.8462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** A1041 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10193 Z= 0.193 Angle : 0.647 12.036 13810 Z= 0.333 Chirality : 0.046 0.183 1536 Planarity : 0.004 0.051 1793 Dihedral : 5.282 28.914 1331 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.98 % Favored : 88.93 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.22), residues: 1229 helix: -0.30 (0.29), residues: 328 sheet: -1.90 (0.49), residues: 91 loop : -3.26 (0.19), residues: 810 *********************** 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 138 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 131 average time/residue: 0.2117 time to fit residues: 41.0798 Evaluate side-chains 112 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1164 time to fit residues: 5.0058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN A 579 ASN ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.095 10193 Z= 0.490 Angle : 0.834 12.536 13810 Z= 0.442 Chirality : 0.050 0.178 1536 Planarity : 0.005 0.058 1793 Dihedral : 6.110 28.791 1331 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 28.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 17.33 % Favored : 82.59 % Rotamer Outliers : 4.49 % 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: -3.74 (0.21), residues: 1229 helix: -0.84 (0.27), residues: 329 sheet: -2.43 (0.48), residues: 97 loop : -3.47 (0.19), residues: 803 *********************** 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 150 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 99 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 25 residues processed: 135 average time/residue: 0.2076 time to fit residues: 41.6558 Evaluate side-chains 114 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0969 time to fit residues: 6.0792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.0030 chunk 62 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 overall best weight: 0.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 10193 Z= 0.181 Angle : 0.660 10.757 13810 Z= 0.341 Chirality : 0.046 0.181 1536 Planarity : 0.004 0.052 1793 Dihedral : 5.264 28.295 1331 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.07 % Favored : 88.85 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.22), residues: 1229 helix: -0.13 (0.29), residues: 328 sheet: -1.68 (0.53), residues: 83 loop : -3.27 (0.19), residues: 818 *********************** 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 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 127 average time/residue: 0.2178 time to fit residues: 40.2344 Evaluate side-chains 106 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.381 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1085 time to fit residues: 3.3959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 10193 Z= 0.188 Angle : 0.658 10.545 13810 Z= 0.336 Chirality : 0.046 0.250 1536 Planarity : 0.003 0.047 1793 Dihedral : 5.068 27.320 1331 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.34 % Favored : 86.49 % Rotamer Outliers : 1.67 % 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: -3.06 (0.23), residues: 1229 helix: 0.08 (0.30), residues: 328 sheet: -2.04 (0.46), residues: 103 loop : -3.19 (0.20), residues: 798 *********************** 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 124 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 117 average time/residue: 0.2228 time to fit residues: 38.1910 Evaluate side-chains 111 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1226 time to fit residues: 4.0056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 10193 Z= 0.228 Angle : 0.687 10.277 13810 Z= 0.352 Chirality : 0.047 0.205 1536 Planarity : 0.004 0.067 1793 Dihedral : 5.154 26.591 1331 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.91 % Favored : 85.92 % Rotamer Outliers : 0.97 % 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: -3.09 (0.23), residues: 1229 helix: 0.05 (0.30), residues: 329 sheet: -2.20 (0.47), residues: 106 loop : -3.20 (0.20), residues: 794 *********************** 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 114 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.2088 time to fit residues: 34.5227 Evaluate side-chains 106 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1047 time to fit residues: 3.0552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 10193 Z= 0.213 Angle : 0.682 10.178 13810 Z= 0.346 Chirality : 0.046 0.187 1536 Planarity : 0.004 0.088 1793 Dihedral : 5.063 25.132 1331 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.00 % Favored : 85.92 % Rotamer Outliers : 1.06 % 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: -3.01 (0.23), residues: 1229 helix: 0.09 (0.30), residues: 331 sheet: -2.31 (0.47), residues: 99 loop : -3.12 (0.20), residues: 799 *********************** 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 115 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 110 average time/residue: 0.2042 time to fit residues: 33.5399 Evaluate side-chains 104 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1016 time to fit residues: 2.7870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.0040 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.0096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 10193 Z= 0.229 Angle : 0.696 10.344 13810 Z= 0.354 Chirality : 0.047 0.177 1536 Planarity : 0.004 0.080 1793 Dihedral : 5.096 24.459 1331 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.40 % Favored : 85.52 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.23), residues: 1229 helix: 0.09 (0.30), residues: 330 sheet: -1.92 (0.52), residues: 89 loop : -3.16 (0.20), residues: 810 ********************** 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 110 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.2272 time to fit residues: 37.3823 Evaluate side-chains 106 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1212 time to fit residues: 2.0207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.082562 restraints weight = 36296.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085121 restraints weight = 20926.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086833 restraints weight = 14585.511| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10193 Z= 0.172 Angle : 0.668 10.161 13810 Z= 0.337 Chirality : 0.046 0.207 1536 Planarity : 0.004 0.058 1793 Dihedral : 4.845 22.863 1331 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.88 % Favored : 88.04 % Rotamer Outliers : 0.35 % 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: -2.89 (0.23), residues: 1229 helix: 0.29 (0.30), residues: 330 sheet: -2.23 (0.48), residues: 99 loop : -3.07 (0.20), residues: 800 =============================================================================== Job complete usr+sys time: 1940.26 seconds wall clock time: 36 minutes 50.11 seconds (2210.11 seconds total)