Starting phenix.real_space_refine on Wed Sep 25 10:08:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/09_2024/7qfp_13946.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/09_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_13946/09_2024/7qfp_13946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/09_2024/7qfp_13946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/09_2024/7qfp_13946.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qfp_13946/09_2024/7qfp_13946.cif" } 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. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.21, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 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: 1.22 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: 3.44 Time building geometry restraints manager: 3.15 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: 0.00 - 2.03: 12717 2.03 - 4.06: 968 4.06 - 6.09: 93 6.09 - 8.12: 21 8.12 - 10.15: 11 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 3.120 nonbonded pdb=" O ARG A 419 " pdb=" NH1 ARG A 419 " model vdw 2.186 3.120 nonbonded pdb=" N GLN A 371 " pdb=" OE1 GLN A 371 " model vdw 2.249 3.120 nonbonded pdb=" O ASN A 27 " pdb=" ND2 ASN A 27 " model vdw 2.253 3.120 nonbonded pdb=" O ALA A 604 " pdb=" OH TYR A 622 " model vdw 2.288 3.040 ... (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: 1.710 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.780 ------------------------------------------------------------------------------- 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 : 1.190 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: 0.2306 time to fit residues: 80.1916 Evaluate side-chains 146 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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: 0.6980 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 214 ASN A 291 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN A 382 ASN A 400 ASN A 407 ASN A 448 ASN A 685 ASN A 711 ASN A 715 ASN A 727 ASN A 765 ASN A 805 ASN A 837 ASN A 871 ASN A 952 ASN A1025 ASN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 GLN A1251 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10193 Z= 0.187 Angle : 0.669 7.699 13810 Z= 0.356 Chirality : 0.047 0.179 1536 Planarity : 0.004 0.065 1793 Dihedral : 7.352 74.654 1377 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.33 % Favored : 89.59 % Rotamer: Outliers : 3.52 % Allowed : 17.89 % Favored : 78.59 % 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: -3.78 (0.20), residues: 1229 helix: -1.20 (0.26), residues: 327 sheet: -2.29 (0.45), residues: 108 loop : -3.34 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1241 HIS 0.002 0.001 HIS A 229 PHE 0.030 0.002 PHE A 670 TYR 0.020 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 184 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 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: A 53 MET cc_start: 0.5709 (mmm) cc_final: 0.5357 (mmm) REVERT: A 158 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8040 (mm110) REVERT: A 266 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8573 (mt) REVERT: A 555 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6640 (t) REVERT: A 578 ASN cc_start: 0.8958 (m110) cc_final: 0.8361 (p0) REVERT: A 600 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: A 637 ASN cc_start: 0.7739 (p0) cc_final: 0.7501 (p0) REVERT: A 645 LEU cc_start: 0.7894 (mt) cc_final: 0.7607 (mt) REVERT: A 689 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8587 (pttt) REVERT: A 758 LYS cc_start: 0.4667 (OUTLIER) cc_final: 0.4258 (pttm) REVERT: A 870 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8072 (tt) REVERT: A 1022 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7921 (tt) REVERT: A 1044 ASP cc_start: 0.9138 (p0) cc_final: 0.8837 (p0) REVERT: A 1163 ASP cc_start: 0.7026 (t0) cc_final: 0.6665 (t0) outliers start: 40 outliers final: 17 residues processed: 169 average time/residue: 0.2127 time to fit residues: 51.5732 Evaluate side-chains 132 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 266 ILE 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 486 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 503 GLU 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 727 ASN Chi-restraints excluded: chain A residue 758 LYS 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 1022 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1138 LEU 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: 2.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 407 ASN A 510 GLN A 727 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A 981 GLN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10193 Z= 0.235 Angle : 0.667 14.652 13810 Z= 0.350 Chirality : 0.046 0.195 1536 Planarity : 0.004 0.056 1793 Dihedral : 6.413 74.143 1350 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.21 % Favored : 87.71 % Rotamer: Outliers : 4.49 % Allowed : 19.82 % Favored : 75.68 % 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: -3.37 (0.22), residues: 1229 helix: -0.55 (0.29), residues: 324 sheet: -2.21 (0.44), residues: 118 loop : -3.20 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1241 HIS 0.002 0.001 HIS A 73 PHE 0.022 0.002 PHE A 211 TYR 0.022 0.001 TYR A1180 ARG 0.005 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 167 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 116 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: 0.6335 (mmm) cc_final: 0.5917 (mmm) REVERT: A 55 ASN cc_start: 0.8576 (t0) cc_final: 0.7894 (t0) REVERT: A 123 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 350 SER cc_start: 0.8835 (p) cc_final: 0.8485 (t) REVERT: A 460 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: A 578 ASN cc_start: 0.9009 (m110) cc_final: 0.8340 (p0) REVERT: A 600 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: A 637 ASN cc_start: 0.7680 (p0) cc_final: 0.7450 (p0) REVERT: A 645 LEU cc_start: 0.8024 (mt) cc_final: 0.7709 (mt) REVERT: A 758 LYS cc_start: 0.4639 (OUTLIER) cc_final: 0.4237 (pttm) REVERT: A 1044 ASP cc_start: 0.9111 (p0) cc_final: 0.8879 (p0) REVERT: A 1070 GLU cc_start: 0.4640 (tp30) cc_final: 0.4195 (tp30) REVERT: A 1163 ASP cc_start: 0.7203 (t0) cc_final: 0.6709 (t0) REVERT: A 1207 MET cc_start: 0.5255 (OUTLIER) cc_final: 0.4917 (mtt) outliers start: 51 outliers final: 26 residues processed: 150 average time/residue: 0.2115 time to fit residues: 45.9426 Evaluate side-chains 133 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 458 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 500 LEU Chi-restraints excluded: chain A residue 503 GLU 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 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 758 LYS Chi-restraints excluded: chain A residue 889 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 1042 VAL Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain A residue 1237 VAL 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: 9.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 0.0570 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 634 GLN A 727 ASN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN A1041 HIS ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10193 Z= 0.282 Angle : 0.690 12.918 13810 Z= 0.362 Chirality : 0.047 0.160 1536 Planarity : 0.004 0.051 1793 Dihedral : 6.320 75.481 1342 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.10 % Favored : 86.82 % Rotamer: Outliers : 4.76 % Allowed : 21.32 % Favored : 73.92 % 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: -3.39 (0.22), residues: 1229 helix: -0.63 (0.28), residues: 344 sheet: -2.11 (0.48), residues: 91 loop : -3.25 (0.19), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1241 HIS 0.003 0.001 HIS A1264 PHE 0.019 0.002 PHE A1114 TYR 0.018 0.002 TYR A 743 ARG 0.008 0.001 ARG A 863 *********************** 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 160 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 106 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6485 (mmm) cc_final: 0.6001 (mmm) REVERT: A 123 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 350 SER cc_start: 0.9012 (p) cc_final: 0.8654 (t) REVERT: A 460 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: A 600 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: A 637 ASN cc_start: 0.7761 (p0) cc_final: 0.7514 (p0) REVERT: A 645 LEU cc_start: 0.7970 (mt) cc_final: 0.7611 (mt) REVERT: A 1044 ASP cc_start: 0.9157 (p0) cc_final: 0.8951 (p0) REVERT: A 1070 GLU cc_start: 0.4578 (tp30) cc_final: 0.4032 (tp30) REVERT: A 1163 ASP cc_start: 0.7381 (t0) cc_final: 0.6866 (t0) REVERT: A 1166 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: A 1207 MET cc_start: 0.5425 (OUTLIER) cc_final: 0.5053 (mtt) outliers start: 54 outliers final: 30 residues processed: 146 average time/residue: 0.2179 time to fit residues: 45.5813 Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 126 LYS 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 458 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 503 GLU 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 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1207 MET 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: 0.5980 chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 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 112 ASN A 217 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: 0.7574 moved from start: 0.4219 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= 0.180 Angle : 0.634 12.669 13810 Z= 0.326 Chirality : 0.045 0.158 1536 Planarity : 0.004 0.052 1793 Dihedral : 5.588 77.269 1336 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.15 % Favored : 88.77 % Rotamer: Outliers : 3.96 % Allowed : 22.03 % Favored : 74.01 % 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: -3.13 (0.22), residues: 1229 helix: -0.20 (0.29), residues: 335 sheet: -2.24 (0.43), residues: 115 loop : -3.13 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1241 HIS 0.001 0.000 HIS A 817 PHE 0.019 0.001 PHE A1067 TYR 0.026 0.001 TYR A1180 ARG 0.003 0.000 ARG A 863 *********************** 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 159 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8004 (tm-30) REVERT: A 268 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: A 350 SER cc_start: 0.8973 (p) cc_final: 0.8583 (t) REVERT: A 600 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: A 637 ASN cc_start: 0.7632 (p0) cc_final: 0.7391 (p0) REVERT: A 645 LEU cc_start: 0.7803 (mt) cc_final: 0.7497 (mt) REVERT: A 741 ASN cc_start: 0.9316 (m-40) cc_final: 0.8710 (p0) REVERT: A 788 MET cc_start: 0.8751 (mmm) cc_final: 0.8510 (mmm) REVERT: A 903 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7953 (t0) REVERT: A 1044 ASP cc_start: 0.9160 (p0) cc_final: 0.8940 (p0) REVERT: A 1070 GLU cc_start: 0.4438 (tp30) cc_final: 0.4131 (tp30) REVERT: A 1163 ASP cc_start: 0.7421 (t0) cc_final: 0.7096 (t0) REVERT: A 1166 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6470 (m-80) outliers start: 45 outliers final: 28 residues processed: 150 average time/residue: 0.2013 time to fit residues: 44.4105 Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 278 ASN 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 486 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 GLU 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 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 903 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 1089 LEU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1237 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10193 Z= 0.292 Angle : 0.695 11.669 13810 Z= 0.362 Chirality : 0.047 0.154 1536 Planarity : 0.004 0.045 1793 Dihedral : 5.859 82.603 1336 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 4.32 % Allowed : 23.52 % Favored : 72.16 % 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: -3.19 (0.22), residues: 1229 helix: -0.30 (0.29), residues: 334 sheet: -1.86 (0.52), residues: 85 loop : -3.19 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1241 HIS 0.002 0.001 HIS A 73 PHE 0.018 0.002 PHE A 571 TYR 0.021 0.002 TYR A 743 ARG 0.007 0.001 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 150 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 101 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 350 SER cc_start: 0.9144 (p) cc_final: 0.8768 (t) REVERT: A 460 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: A 600 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: A 637 ASN cc_start: 0.7751 (p0) cc_final: 0.7515 (p0) REVERT: A 645 LEU cc_start: 0.7878 (mt) cc_final: 0.7551 (mt) REVERT: A 741 ASN cc_start: 0.9366 (m-40) cc_final: 0.8817 (p0) REVERT: A 930 LYS cc_start: 0.8020 (tppt) cc_final: 0.7747 (tppt) REVERT: A 938 VAL cc_start: 0.9332 (t) cc_final: 0.9109 (m) REVERT: A 1044 ASP cc_start: 0.9147 (p0) cc_final: 0.8943 (p0) REVERT: A 1070 GLU cc_start: 0.4460 (tp30) cc_final: 0.3912 (tp30) REVERT: A 1163 ASP cc_start: 0.7490 (t0) cc_final: 0.7157 (t0) REVERT: A 1166 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6538 (m-80) outliers start: 49 outliers final: 32 residues processed: 139 average time/residue: 0.2122 time to fit residues: 43.0698 Evaluate side-chains 132 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 278 ASN 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 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 503 GLU 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 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 868 SER 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 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1237 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10193 Z= 0.200 Angle : 0.650 11.296 13810 Z= 0.332 Chirality : 0.046 0.162 1536 Planarity : 0.004 0.047 1793 Dihedral : 5.738 90.647 1336 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 4.05 % Allowed : 23.44 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.23), residues: 1229 helix: -0.15 (0.29), residues: 335 sheet: -1.99 (0.50), residues: 98 loop : -3.06 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1241 HIS 0.001 0.000 HIS A 817 PHE 0.013 0.001 PHE A1114 TYR 0.026 0.001 TYR A1180 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 149 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 103 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 350 SER cc_start: 0.9093 (p) cc_final: 0.8658 (t) REVERT: A 460 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: A 600 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: A 637 ASN cc_start: 0.7658 (p0) cc_final: 0.7411 (p0) REVERT: A 645 LEU cc_start: 0.7857 (mt) cc_final: 0.7547 (mt) REVERT: A 741 ASN cc_start: 0.9344 (m-40) cc_final: 0.8795 (p0) REVERT: A 788 MET cc_start: 0.8759 (mmm) cc_final: 0.8500 (mmm) REVERT: A 898 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: A 903 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8057 (t0) REVERT: A 938 VAL cc_start: 0.9321 (t) cc_final: 0.9120 (m) REVERT: A 1044 ASP cc_start: 0.9144 (p0) cc_final: 0.8936 (p0) REVERT: A 1070 GLU cc_start: 0.4710 (tp30) cc_final: 0.4112 (tp30) REVERT: A 1163 ASP cc_start: 0.7541 (t0) cc_final: 0.7144 (t0) REVERT: A 1166 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: A 1257 TRP cc_start: 0.5780 (m100) cc_final: 0.5511 (m100) outliers start: 46 outliers final: 35 residues processed: 142 average time/residue: 0.2041 time to fit residues: 42.5257 Evaluate side-chains 138 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 348 LEU 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 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 503 GLU 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 609 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 903 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 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1237 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.0020 chunk 113 optimal weight: 6.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5088 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= 0.206 Angle : 0.658 11.198 13810 Z= 0.337 Chirality : 0.046 0.159 1536 Planarity : 0.004 0.049 1793 Dihedral : 5.721 93.671 1336 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 4.14 % Allowed : 23.79 % Favored : 72.07 % 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: -2.98 (0.23), residues: 1229 helix: -0.11 (0.29), residues: 335 sheet: -1.75 (0.53), residues: 90 loop : -3.07 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1241 HIS 0.001 0.001 HIS A 73 PHE 0.025 0.002 PHE A 571 TYR 0.026 0.001 TYR A 743 ARG 0.004 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 152 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 105 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8003 (tm-30) REVERT: A 350 SER cc_start: 0.9097 (p) cc_final: 0.8648 (t) REVERT: A 460 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.6284 (m-80) REVERT: A 637 ASN cc_start: 0.7698 (p0) cc_final: 0.7436 (p0) REVERT: A 645 LEU cc_start: 0.7845 (mt) cc_final: 0.7539 (mt) REVERT: A 741 ASN cc_start: 0.9352 (m-40) cc_final: 0.8749 (p0) REVERT: A 788 MET cc_start: 0.8753 (mmm) cc_final: 0.8478 (mmm) REVERT: A 898 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8270 (m-10) REVERT: A 903 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8042 (t0) REVERT: A 1044 ASP cc_start: 0.9151 (p0) cc_final: 0.8945 (p0) REVERT: A 1149 VAL cc_start: -0.1801 (OUTLIER) cc_final: -0.2180 (m) REVERT: A 1163 ASP cc_start: 0.7528 (t0) cc_final: 0.7157 (t0) REVERT: A 1166 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6535 (m-80) outliers start: 47 outliers final: 38 residues processed: 143 average time/residue: 0.2050 time to fit residues: 42.7207 Evaluate side-chains 137 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 94 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 348 LEU 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 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 503 GLU 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 609 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 898 TYR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 903 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 956 ILE Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1237 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 407 ASN ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10193 Z= 0.175 Angle : 0.650 11.280 13810 Z= 0.330 Chirality : 0.045 0.160 1536 Planarity : 0.004 0.052 1793 Dihedral : 5.604 93.489 1336 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.64 % Favored : 88.28 % Rotamer: Outliers : 3.44 % Allowed : 25.11 % Favored : 71.45 % 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: -2.93 (0.23), residues: 1229 helix: -0.04 (0.29), residues: 336 sheet: -1.92 (0.55), residues: 87 loop : -3.02 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1241 HIS 0.002 0.000 HIS A 973 PHE 0.019 0.001 PHE A 571 TYR 0.028 0.001 TYR A 743 ARG 0.004 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 148 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 109 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: A 637 ASN cc_start: 0.7693 (p0) cc_final: 0.7436 (p0) REVERT: A 645 LEU cc_start: 0.7815 (mt) cc_final: 0.7494 (mt) REVERT: A 741 ASN cc_start: 0.9358 (m-40) cc_final: 0.8705 (p0) REVERT: A 788 MET cc_start: 0.8705 (mmm) cc_final: 0.8413 (mmm) REVERT: A 903 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 1044 ASP cc_start: 0.9148 (p0) cc_final: 0.8933 (p0) REVERT: A 1149 VAL cc_start: -0.1960 (OUTLIER) cc_final: -0.2344 (m) REVERT: A 1163 ASP cc_start: 0.7508 (t0) cc_final: 0.7087 (t0) REVERT: A 1166 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6530 (m-80) outliers start: 39 outliers final: 34 residues processed: 143 average time/residue: 0.2048 time to fit residues: 43.3077 Evaluate side-chains 140 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 102 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 348 LEU 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 460 TYR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 503 GLU 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 609 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 917 ILE 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 1125 ILE Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 TYR 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 71 optimal weight: 0.0970 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5223 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= 0.168 Angle : 0.665 11.155 13810 Z= 0.336 Chirality : 0.046 0.166 1536 Planarity : 0.004 0.053 1793 Dihedral : 5.522 97.208 1336 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 3.17 % Allowed : 25.73 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.23), residues: 1229 helix: 0.13 (0.30), residues: 330 sheet: -1.57 (0.56), residues: 85 loop : -2.92 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1241 HIS 0.001 0.000 HIS A 817 PHE 0.017 0.001 PHE A 211 TYR 0.028 0.001 TYR A 743 ARG 0.003 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 148 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8650 (t0) cc_final: 0.7850 (t0) REVERT: A 460 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.6321 (m-80) REVERT: A 600 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: A 637 ASN cc_start: 0.7656 (p0) cc_final: 0.7395 (p0) REVERT: A 645 LEU cc_start: 0.7872 (mt) cc_final: 0.7507 (mt) REVERT: A 741 ASN cc_start: 0.9365 (m-40) cc_final: 0.8731 (p0) REVERT: A 788 MET cc_start: 0.8628 (mmm) cc_final: 0.8347 (mmm) REVERT: A 903 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8007 (t0) REVERT: A 960 MET cc_start: 0.5529 (mmp) cc_final: 0.5175 (mmp) REVERT: A 1149 VAL cc_start: -0.1994 (OUTLIER) cc_final: -0.2506 (m) REVERT: A 1163 ASP cc_start: 0.7477 (t0) cc_final: 0.7018 (t0) REVERT: A 1166 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6345 (m-80) outliers start: 36 outliers final: 30 residues processed: 144 average time/residue: 0.2039 time to fit residues: 43.4841 Evaluate side-chains 139 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 348 LEU 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 460 TYR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 503 GLU 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 609 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 917 ILE 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 1125 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1166 TYR 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: 1.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.105929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.083009 restraints weight = 36002.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.085549 restraints weight = 20445.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.087316 restraints weight = 14206.151| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5305 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= 0.202 Angle : 0.672 10.997 13810 Z= 0.342 Chirality : 0.046 0.157 1536 Planarity : 0.004 0.053 1793 Dihedral : 5.601 100.338 1336 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 3.70 % Allowed : 25.46 % Favored : 70.84 % 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: -2.86 (0.23), residues: 1229 helix: -0.02 (0.29), residues: 336 sheet: -2.02 (0.51), residues: 97 loop : -2.94 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1241 HIS 0.007 0.001 HIS A1041 PHE 0.016 0.002 PHE A1067 TYR 0.028 0.001 TYR A 743 ARG 0.007 0.000 ARG A 863 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.80 seconds wall clock time: 40 minutes 1.90 seconds (2401.90 seconds total)