Starting phenix.real_space_refine on Mon Apr 28 18:08:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a69_6987/04_2025/6a69_6987.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a69_6987/04_2025/6a69_6987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6a69_6987/04_2025/6a69_6987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a69_6987/04_2025/6a69_6987.map" model { file = "/net/cci-nas-00/data/ceres_data/6a69_6987/04_2025/6a69_6987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a69_6987/04_2025/6a69_6987.cif" } resolution = 4.11 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= 0.001 sd= 0.009 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 39 5.16 5 C 5045 2.51 5 N 1324 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7851 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 6839 Classifications: {'peptide': 911} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 36, 'TRANS': 847} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 998 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1014 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.52, per 1000 atoms: 0.70 Number of scatterers: 7851 At special positions: 0 Unit cell: (134.193, 103.645, 128.738, 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 39 16.00 O 1443 8.00 N 1324 7.00 C 5045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 200 " 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 Links applied NAG-ASN " NAG B 301 " - " ASN B 168 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 9 sheets defined 43.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 153 through 190 removed outlier: 3.994A pdb=" N ALA A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 362 through 397 removed outlier: 3.815A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.969A pdb=" N VAL A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.945A pdb=" N MET A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.733A pdb=" N CYS A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 removed outlier: 4.086A pdb=" N VAL A 563 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 625 through 632 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.842A pdb=" N LYS A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.973A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.857A pdb=" N LEU A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 834 through 877 removed outlier: 3.726A pdb=" N ILE A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 Processing helix chain 'A' and resid 896 through 903 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.672A pdb=" N LEU A 912 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 913 " --> pdb=" O SER A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 925 through 949 Processing helix chain 'A' and resid 970 through 990 removed outlier: 3.667A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1026 removed outlier: 4.004A pdb=" N LEU A1014 " --> pdb=" O CYS A1010 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A1025 " --> pdb=" O ILE A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1058 removed outlier: 3.913A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 245 removed outlier: 3.533A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.982A pdb=" N ILE A 472 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 707 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER A 474 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEU A 765 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N MET A 706 " --> pdb=" O LEU A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.866A pdb=" N GLU A 683 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 589 removed outlier: 3.650A pdb=" N MET A 585 " --> pdb=" O LYS A 601 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 613 through 616 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 126 removed outlier: 6.471A pdb=" N LYS B 144 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 143 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 6.202A pdb=" N GLU B 131 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 211 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 200 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 197 " --> pdb=" O LYS B 158 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2391 1.34 - 1.46: 1487 1.46 - 1.58: 4055 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 7994 Sorted by residual: bond pdb=" C TRP A 759 " pdb=" N PRO A 760 " ideal model delta sigma weight residual 1.331 1.364 -0.032 7.90e-03 1.60e+04 1.64e+01 bond pdb=" C ALA B 222 " pdb=" N PRO B 223 " ideal model delta sigma weight residual 1.333 1.363 -0.030 7.80e-03 1.64e+04 1.46e+01 bond pdb=" CG GLN A1020 " pdb=" CD GLN A1020 " ideal model delta sigma weight residual 1.516 1.452 0.064 2.50e-02 1.60e+03 6.61e+00 bond pdb=" CB TRP A 759 " pdb=" CG TRP A 759 " ideal model delta sigma weight residual 1.498 1.423 0.075 3.10e-02 1.04e+03 5.81e+00 bond pdb=" CB VAL A 792 " pdb=" CG2 VAL A 792 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.40e+00 ... (remaining 7989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 10327 2.96 - 5.91: 425 5.91 - 8.87: 86 8.87 - 11.82: 22 11.82 - 14.78: 6 Bond angle restraints: 10866 Sorted by residual: angle pdb=" C HIS A 965 " pdb=" N ALA A 966 " pdb=" CA ALA A 966 " ideal model delta sigma weight residual 121.70 134.77 -13.07 1.80e+00 3.09e-01 5.28e+01 angle pdb=" N HIS A 965 " pdb=" CA HIS A 965 " pdb=" C HIS A 965 " ideal model delta sigma weight residual 111.07 118.76 -7.69 1.07e+00 8.73e-01 5.17e+01 angle pdb=" C SER A 642 " pdb=" N GLU A 643 " pdb=" CA GLU A 643 " ideal model delta sigma weight residual 121.70 134.07 -12.37 1.80e+00 3.09e-01 4.72e+01 angle pdb=" N GLY A 228 " pdb=" CA GLY A 228 " pdb=" C GLY A 228 " ideal model delta sigma weight residual 111.42 121.78 -10.36 1.51e+00 4.39e-01 4.71e+01 angle pdb=" N PRO A 67 " pdb=" CA PRO A 67 " pdb=" CB PRO A 67 " ideal model delta sigma weight residual 103.00 110.36 -7.36 1.10e+00 8.26e-01 4.48e+01 ... (remaining 10861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 4389 15.21 - 30.42: 325 30.42 - 45.64: 74 45.64 - 60.85: 11 60.85 - 76.06: 4 Dihedral angle restraints: 4803 sinusoidal: 1822 harmonic: 2981 Sorted by residual: dihedral pdb=" CA VAL A 680 " pdb=" C VAL A 680 " pdb=" N GLY A 681 " pdb=" CA GLY A 681 " ideal model delta harmonic sigma weight residual 180.00 126.37 53.63 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA ASN A 565 " pdb=" C ASN A 565 " pdb=" N GLU A 566 " pdb=" CA GLU A 566 " ideal model delta harmonic sigma weight residual 0.00 44.37 -44.37 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA PHE A 953 " pdb=" C PHE A 953 " pdb=" N PHE A 954 " pdb=" CA PHE A 954 " ideal model delta harmonic sigma weight residual -180.00 -137.23 -42.77 0 5.00e+00 4.00e-02 7.32e+01 ... (remaining 4800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1015 0.080 - 0.160: 260 0.160 - 0.240: 28 0.240 - 0.320: 4 0.320 - 0.400: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CB ILE A1061 " pdb=" CA ILE A1061 " pdb=" CG1 ILE A1061 " pdb=" CG2 ILE A1061 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA HIS A 965 " pdb=" N HIS A 965 " pdb=" C HIS A 965 " pdb=" CB HIS A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL A 680 " pdb=" CA VAL A 680 " pdb=" CG1 VAL A 680 " pdb=" CG2 VAL A 680 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1305 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 94 " -0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO A 95 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 638 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 639 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 225 " 0.015 2.00e-02 2.50e+03 1.81e-02 8.22e+00 pdb=" CG TRP B 225 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 225 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 225 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 225 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 225 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 225 " 0.001 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2026 2.80 - 3.32: 7367 3.32 - 3.85: 12435 3.85 - 4.37: 13360 4.37 - 4.90: 22735 Nonbonded interactions: 57923 Sorted by model distance: nonbonded pdb=" O VAL A 515 " pdb=" OG SER A 519 " model vdw 2.275 3.040 nonbonded pdb=" O TYR A 513 " pdb=" OG1 THR A 516 " model vdw 2.308 3.040 nonbonded pdb=" O LEU A 947 " pdb=" NH1 ARG A 960 " model vdw 2.344 3.120 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 125 " model vdw 2.345 3.040 nonbonded pdb=" OE2 GLU B 135 " pdb=" NE2 GLN B 190 " model vdw 2.350 3.120 ... (remaining 57918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 0.630 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.011 0.105 7996 Z= 0.483 Angle : 1.480 14.780 10871 Z= 0.816 Chirality : 0.069 0.400 1308 Planarity : 0.009 0.077 1372 Dihedral : 11.870 76.061 2872 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.53 % Favored : 86.37 % Rotamer: Outliers : 1.81 % Allowed : 4.58 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.43 % Twisted Proline : 0.00 % Twisted General : 0.91 % 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: -4.69 (0.21), residues: 1021 helix: -2.43 (0.19), residues: 449 sheet: -2.74 (0.46), residues: 103 loop : -3.93 (0.22), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP B 225 HIS 0.009 0.003 HIS A 265 PHE 0.036 0.004 PHE A 953 TYR 0.032 0.003 TYR A 445 ARG 0.008 0.001 ARG A 272 Details of bonding type rmsd link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 1.63205 ( 3) hydrogen bonds : bond 0.17936 ( 358) hydrogen bonds : angle 7.61429 ( 1038) SS BOND : bond 0.00490 ( 1) SS BOND : angle 1.29656 ( 2) covalent geometry : bond 0.01075 ( 7994) covalent geometry : angle 1.48034 (10866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8688 (mt-10) REVERT: A 217 GLN cc_start: 0.8337 (tt0) cc_final: 0.7862 (tp40) REVERT: A 235 ASP cc_start: 0.8010 (m-30) cc_final: 0.7804 (t0) REVERT: A 466 MET cc_start: 0.8832 (tmm) cc_final: 0.8292 (tmm) REVERT: A 752 GLN cc_start: 0.8888 (tt0) cc_final: 0.8684 (tm-30) REVERT: A 814 MET cc_start: 0.8765 (mmp) cc_final: 0.8411 (mmp) REVERT: A 859 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8992 (tm-30) REVERT: A 887 MET cc_start: 0.8963 (tpp) cc_final: 0.8445 (tpp) REVERT: A 911 LEU cc_start: 0.9705 (mt) cc_final: 0.9472 (mp) REVERT: A 1017 PHE cc_start: 0.8919 (t80) cc_final: 0.8647 (t80) REVERT: B 218 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7903 (mtp-110) outliers start: 15 outliers final: 6 residues processed: 240 average time/residue: 0.1883 time to fit residues: 61.6267 Evaluate side-chains 145 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 540 HIS A 711 ASN A 886 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 HIS ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106305 restraints weight = 21735.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105435 restraints weight = 12473.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105692 restraints weight = 12313.762| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7996 Z= 0.155 Angle : 0.810 12.812 10871 Z= 0.420 Chirality : 0.047 0.197 1308 Planarity : 0.007 0.072 1372 Dihedral : 6.949 40.363 1111 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.33 % Favored : 91.47 % Rotamer: Outliers : 0.24 % Allowed : 3.74 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.24), residues: 1021 helix: -0.54 (0.23), residues: 462 sheet: -2.80 (0.42), residues: 113 loop : -3.59 (0.24), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 225 HIS 0.007 0.001 HIS A 971 PHE 0.025 0.002 PHE A 953 TYR 0.013 0.001 TYR B 244 ARG 0.010 0.001 ARG A 272 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 1.45971 ( 3) hydrogen bonds : bond 0.05484 ( 358) hydrogen bonds : angle 5.58062 ( 1038) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.22398 ( 2) covalent geometry : bond 0.00320 ( 7994) covalent geometry : angle 0.80961 (10866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8158 (mp0) REVERT: A 217 GLN cc_start: 0.8247 (tt0) cc_final: 0.7976 (tp40) REVERT: A 235 ASP cc_start: 0.8001 (m-30) cc_final: 0.7796 (t0) REVERT: A 268 GLU cc_start: 0.8222 (pp20) cc_final: 0.7921 (pp20) REVERT: A 421 ILE cc_start: 0.9599 (tp) cc_final: 0.9369 (tp) REVERT: A 466 MET cc_start: 0.8661 (tmm) cc_final: 0.7980 (tmm) REVERT: A 887 MET cc_start: 0.8889 (tpp) cc_final: 0.8518 (tpp) REVERT: A 964 LEU cc_start: 0.8829 (tt) cc_final: 0.8369 (tt) REVERT: A 1006 ASN cc_start: 0.8471 (m-40) cc_final: 0.7703 (m-40) REVERT: A 1049 MET cc_start: 0.7712 (mmt) cc_final: 0.7390 (tpp) REVERT: B 157 LYS cc_start: 0.6268 (tptp) cc_final: 0.5642 (mmmt) REVERT: B 199 GLU cc_start: 0.5410 (pt0) cc_final: 0.5198 (pt0) outliers start: 2 outliers final: 2 residues processed: 220 average time/residue: 0.1583 time to fit residues: 50.1899 Evaluate side-chains 135 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** 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 = 0.3802 r_free = 0.3802 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107784 restraints weight = 16210.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108398 restraints weight = 10068.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109306 restraints weight = 7398.244| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7996 Z= 0.141 Angle : 0.760 12.603 10871 Z= 0.394 Chirality : 0.046 0.190 1308 Planarity : 0.006 0.084 1372 Dihedral : 6.344 39.609 1111 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.71 % Favored : 90.10 % Rotamer: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.39 (0.25), residues: 1021 helix: 0.27 (0.24), residues: 455 sheet: -2.52 (0.43), residues: 113 loop : -3.42 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1041 HIS 0.005 0.001 HIS A 971 PHE 0.019 0.001 PHE A 953 TYR 0.011 0.001 TYR A 445 ARG 0.004 0.000 ARG B 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 1) link_NAG-ASN : angle 1.40147 ( 3) hydrogen bonds : bond 0.04649 ( 358) hydrogen bonds : angle 5.06000 ( 1038) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.41237 ( 2) covalent geometry : bond 0.00283 ( 7994) covalent geometry : angle 0.75966 (10866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8074 (mp0) REVERT: A 195 THR cc_start: 0.8540 (m) cc_final: 0.7797 (m) REVERT: A 268 GLU cc_start: 0.8298 (pp20) cc_final: 0.7906 (pp20) REVERT: A 463 CYS cc_start: 0.7971 (t) cc_final: 0.7620 (t) REVERT: A 466 MET cc_start: 0.8717 (tmm) cc_final: 0.8083 (tmm) REVERT: A 482 MET cc_start: 0.7733 (mmm) cc_final: 0.7435 (mmm) REVERT: A 905 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 928 MET cc_start: 0.8355 (tpp) cc_final: 0.7939 (tpp) REVERT: A 1006 ASN cc_start: 0.8439 (m-40) cc_final: 0.7123 (m-40) REVERT: A 1049 MET cc_start: 0.7846 (mmt) cc_final: 0.7345 (mtt) REVERT: B 162 MET cc_start: 0.7117 (pmm) cc_final: 0.6819 (pmm) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.1584 time to fit residues: 43.0776 Evaluate side-chains 130 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104709 restraints weight = 20124.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104620 restraints weight = 11426.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105050 restraints weight = 10349.403| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 7996 Z= 0.175 Angle : 0.755 12.216 10871 Z= 0.395 Chirality : 0.046 0.183 1308 Planarity : 0.006 0.084 1372 Dihedral : 6.102 42.263 1111 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.51 % Favored : 90.29 % Rotamer: Outliers : 0.24 % Allowed : 3.26 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.26 (0.25), residues: 1021 helix: 0.40 (0.25), residues: 458 sheet: -2.31 (0.43), residues: 113 loop : -3.44 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 225 HIS 0.003 0.001 HIS A 971 PHE 0.016 0.001 PHE A 954 TYR 0.017 0.001 TYR A 445 ARG 0.005 0.000 ARG A 997 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 1.07746 ( 3) hydrogen bonds : bond 0.04664 ( 358) hydrogen bonds : angle 4.94036 ( 1038) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.52302 ( 2) covalent geometry : bond 0.00398 ( 7994) covalent geometry : angle 0.75517 (10866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8082 (mp0) REVERT: A 217 GLN cc_start: 0.8061 (pp30) cc_final: 0.7761 (pp30) REVERT: A 268 GLU cc_start: 0.8012 (pp20) cc_final: 0.7795 (pp20) REVERT: A 466 MET cc_start: 0.8799 (tmm) cc_final: 0.8392 (tmm) REVERT: A 482 MET cc_start: 0.7865 (mmm) cc_final: 0.7478 (mmm) REVERT: A 757 LYS cc_start: 0.8427 (mmpt) cc_final: 0.8171 (mmtp) REVERT: A 887 MET cc_start: 0.9152 (tpp) cc_final: 0.8396 (tpp) REVERT: A 928 MET cc_start: 0.8330 (tpp) cc_final: 0.8062 (tpp) REVERT: A 1006 ASN cc_start: 0.8431 (m-40) cc_final: 0.7899 (m-40) REVERT: A 1049 MET cc_start: 0.7941 (mmt) cc_final: 0.7482 (mtt) REVERT: B 157 LYS cc_start: 0.6444 (tptp) cc_final: 0.5976 (mmmt) outliers start: 2 outliers final: 1 residues processed: 179 average time/residue: 0.1479 time to fit residues: 39.3133 Evaluate side-chains 130 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109435 restraints weight = 19052.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107019 restraints weight = 12855.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108435 restraints weight = 10347.908| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7996 Z= 0.133 Angle : 0.725 12.201 10871 Z= 0.376 Chirality : 0.045 0.182 1308 Planarity : 0.006 0.091 1372 Dihedral : 5.905 39.963 1111 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.63 % Favored : 91.18 % Rotamer: Outliers : 0.12 % Allowed : 1.81 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.26), residues: 1021 helix: 0.64 (0.25), residues: 459 sheet: -1.99 (0.45), residues: 115 loop : -3.24 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 404 HIS 0.005 0.001 HIS A 971 PHE 0.029 0.001 PHE A 953 TYR 0.019 0.001 TYR A 560 ARG 0.003 0.000 ARG A 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 1.00220 ( 3) hydrogen bonds : bond 0.04136 ( 358) hydrogen bonds : angle 4.68472 ( 1038) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.42479 ( 2) covalent geometry : bond 0.00276 ( 7994) covalent geometry : angle 0.72485 (10866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8091 (mp0) REVERT: A 268 GLU cc_start: 0.7834 (pp20) cc_final: 0.7621 (pp20) REVERT: A 466 MET cc_start: 0.8720 (tmm) cc_final: 0.8309 (tmm) REVERT: A 482 MET cc_start: 0.7833 (mmm) cc_final: 0.7510 (mmm) REVERT: A 711 ASN cc_start: 0.7699 (p0) cc_final: 0.7428 (p0) REVERT: A 887 MET cc_start: 0.9084 (tpp) cc_final: 0.8534 (tpp) REVERT: A 928 MET cc_start: 0.8179 (tpp) cc_final: 0.7853 (tpp) REVERT: A 998 ASN cc_start: 0.7962 (t0) cc_final: 0.7655 (t0) REVERT: A 1006 ASN cc_start: 0.8605 (m-40) cc_final: 0.7927 (m110) REVERT: A 1020 GLN cc_start: 0.8779 (tp40) cc_final: 0.8370 (tp40) REVERT: A 1049 MET cc_start: 0.7773 (mmt) cc_final: 0.7301 (mtt) REVERT: B 157 LYS cc_start: 0.6550 (tptp) cc_final: 0.5989 (mmmt) outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.1586 time to fit residues: 45.0400 Evaluate side-chains 137 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 87 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 17 optimal weight: 0.0030 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 265 HIS ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109888 restraints weight = 27660.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110135 restraints weight = 18677.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111196 restraints weight = 15090.433| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7996 Z= 0.126 Angle : 0.678 12.164 10871 Z= 0.354 Chirality : 0.044 0.182 1308 Planarity : 0.006 0.090 1372 Dihedral : 5.620 40.584 1111 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.75 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 1021 helix: 0.85 (0.25), residues: 458 sheet: -1.95 (0.46), residues: 110 loop : -3.12 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 404 HIS 0.005 0.001 HIS A 971 PHE 0.010 0.001 PHE A 652 TYR 0.009 0.001 TYR A 497 ARG 0.007 0.000 ARG A 699 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 1) link_NAG-ASN : angle 0.82036 ( 3) hydrogen bonds : bond 0.03777 ( 358) hydrogen bonds : angle 4.52706 ( 1038) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.47866 ( 2) covalent geometry : bond 0.00267 ( 7994) covalent geometry : angle 0.67814 (10866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8067 (mp0) REVERT: A 268 GLU cc_start: 0.7982 (pp20) cc_final: 0.7766 (pp20) REVERT: A 466 MET cc_start: 0.8737 (tmm) cc_final: 0.8206 (tmm) REVERT: A 482 MET cc_start: 0.7777 (mmm) cc_final: 0.7500 (mmm) REVERT: A 711 ASN cc_start: 0.7440 (p0) cc_final: 0.7212 (p0) REVERT: A 757 LYS cc_start: 0.8271 (mmpt) cc_final: 0.7870 (mptt) REVERT: A 887 MET cc_start: 0.9079 (tpp) cc_final: 0.8587 (tpp) REVERT: A 928 MET cc_start: 0.8168 (tpp) cc_final: 0.7870 (tpp) REVERT: A 1049 MET cc_start: 0.7907 (mmt) cc_final: 0.7414 (mtt) REVERT: B 141 MET cc_start: 0.6508 (mpp) cc_final: 0.6160 (mpp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1447 time to fit residues: 38.3310 Evaluate side-chains 131 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109169 restraints weight = 27601.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110154 restraints weight = 16380.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110884 restraints weight = 14134.631| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7996 Z= 0.126 Angle : 0.674 11.988 10871 Z= 0.350 Chirality : 0.044 0.181 1308 Planarity : 0.006 0.096 1372 Dihedral : 5.445 40.585 1111 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.14 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.26), residues: 1021 helix: 0.96 (0.25), residues: 459 sheet: -1.80 (0.45), residues: 118 loop : -3.03 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 PHE 0.011 0.001 PHE A 953 TYR 0.008 0.001 TYR A 497 ARG 0.002 0.000 ARG A 699 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 1) link_NAG-ASN : angle 0.81763 ( 3) hydrogen bonds : bond 0.03675 ( 358) hydrogen bonds : angle 4.42769 ( 1038) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.54031 ( 2) covalent geometry : bond 0.00272 ( 7994) covalent geometry : angle 0.67429 (10866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8072 (mp0) REVERT: A 194 PHE cc_start: 0.8774 (t80) cc_final: 0.8399 (t80) REVERT: A 268 GLU cc_start: 0.8090 (pp20) cc_final: 0.7838 (pp20) REVERT: A 466 MET cc_start: 0.8859 (tmm) cc_final: 0.8402 (tmm) REVERT: A 482 MET cc_start: 0.7659 (mmm) cc_final: 0.7394 (mmm) REVERT: A 485 MET cc_start: 0.7674 (pmm) cc_final: 0.7364 (pmm) REVERT: A 711 ASN cc_start: 0.7341 (p0) cc_final: 0.7057 (p0) REVERT: A 757 LYS cc_start: 0.8248 (mmpt) cc_final: 0.7825 (mptt) REVERT: A 887 MET cc_start: 0.9146 (tpp) cc_final: 0.8675 (tpp) REVERT: A 928 MET cc_start: 0.8013 (tpp) cc_final: 0.7737 (tpp) REVERT: B 141 MET cc_start: 0.6495 (mpp) cc_final: 0.6150 (mpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1450 time to fit residues: 38.0948 Evaluate side-chains 133 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.0370 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 0.0000 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 0.0000 overall best weight: 2.2070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN ** A 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104897 restraints weight = 30404.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107794 restraints weight = 20729.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107542 restraints weight = 15851.977| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7996 Z= 0.186 Angle : 0.734 11.638 10871 Z= 0.386 Chirality : 0.046 0.171 1308 Planarity : 0.006 0.097 1372 Dihedral : 5.611 42.615 1111 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.80 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.26), residues: 1021 helix: 0.92 (0.25), residues: 458 sheet: -1.66 (0.46), residues: 117 loop : -3.03 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.004 0.001 HIS A 965 PHE 0.015 0.002 PHE A 954 TYR 0.016 0.001 TYR A 445 ARG 0.003 0.000 ARG A 699 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 1) link_NAG-ASN : angle 0.83018 ( 3) hydrogen bonds : bond 0.04430 ( 358) hydrogen bonds : angle 4.66112 ( 1038) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.71469 ( 2) covalent geometry : bond 0.00431 ( 7994) covalent geometry : angle 0.73405 (10866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8063 (mp0) REVERT: A 268 GLU cc_start: 0.8150 (pp20) cc_final: 0.7802 (pp20) REVERT: A 466 MET cc_start: 0.8862 (tmm) cc_final: 0.8436 (tmm) REVERT: A 482 MET cc_start: 0.7648 (mmm) cc_final: 0.7372 (mmm) REVERT: A 485 MET cc_start: 0.7840 (pmm) cc_final: 0.7570 (pmm) REVERT: A 711 ASN cc_start: 0.7420 (p0) cc_final: 0.7162 (p0) REVERT: A 757 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7849 (mptt) REVERT: A 887 MET cc_start: 0.9142 (tpp) cc_final: 0.8282 (tpp) REVERT: A 1008 ILE cc_start: 0.9069 (mp) cc_final: 0.8726 (mm) REVERT: B 131 GLU cc_start: 0.6735 (tp30) cc_final: 0.6226 (tp30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1625 time to fit residues: 40.9987 Evaluate side-chains 128 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 47 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109943 restraints weight = 19831.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108835 restraints weight = 11071.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109733 restraints weight = 8975.620| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7996 Z= 0.132 Angle : 0.710 12.397 10871 Z= 0.365 Chirality : 0.044 0.179 1308 Planarity : 0.006 0.098 1372 Dihedral : 5.482 41.718 1111 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.04 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.27), residues: 1021 helix: 1.03 (0.25), residues: 460 sheet: -1.45 (0.47), residues: 118 loop : -3.01 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 404 HIS 0.004 0.001 HIS A 971 PHE 0.031 0.001 PHE A 953 TYR 0.013 0.001 TYR A 445 ARG 0.003 0.000 ARG A 187 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 1) link_NAG-ASN : angle 0.88179 ( 3) hydrogen bonds : bond 0.04006 ( 358) hydrogen bonds : angle 4.45079 ( 1038) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.56202 ( 2) covalent geometry : bond 0.00285 ( 7994) covalent geometry : angle 0.70978 (10866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7988 (mp0) REVERT: A 194 PHE cc_start: 0.8912 (t80) cc_final: 0.8607 (t80) REVERT: A 268 GLU cc_start: 0.8089 (pp20) cc_final: 0.7744 (pp20) REVERT: A 466 MET cc_start: 0.8844 (tmm) cc_final: 0.8470 (tmm) REVERT: A 482 MET cc_start: 0.7579 (mmm) cc_final: 0.7291 (mmm) REVERT: A 485 MET cc_start: 0.7582 (pmm) cc_final: 0.7250 (pmm) REVERT: A 711 ASN cc_start: 0.7352 (p0) cc_final: 0.7097 (p0) REVERT: A 757 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7848 (mptt) REVERT: A 887 MET cc_start: 0.9159 (tpp) cc_final: 0.8644 (tpp) REVERT: A 928 MET cc_start: 0.8174 (tpp) cc_final: 0.7876 (tpp) REVERT: A 1008 ILE cc_start: 0.9053 (mp) cc_final: 0.8686 (mm) REVERT: B 131 GLU cc_start: 0.6685 (tp30) cc_final: 0.6116 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1605 time to fit residues: 38.9212 Evaluate side-chains 128 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.143999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108843 restraints weight = 27531.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110138 restraints weight = 15397.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110804 restraints weight = 12332.493| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7996 Z= 0.130 Angle : 0.709 14.087 10871 Z= 0.365 Chirality : 0.044 0.177 1308 Planarity : 0.006 0.094 1372 Dihedral : 5.406 41.403 1111 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.43 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.27), residues: 1021 helix: 1.05 (0.25), residues: 461 sheet: -1.25 (0.48), residues: 118 loop : -2.95 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.005 0.001 HIS A 265 PHE 0.031 0.001 PHE A 953 TYR 0.013 0.001 TYR A 445 ARG 0.006 0.000 ARG A 187 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 1) link_NAG-ASN : angle 0.87501 ( 3) hydrogen bonds : bond 0.03841 ( 358) hydrogen bonds : angle 4.44128 ( 1038) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.60852 ( 2) covalent geometry : bond 0.00285 ( 7994) covalent geometry : angle 0.70910 (10866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7907 (mp0) REVERT: A 194 PHE cc_start: 0.8878 (t80) cc_final: 0.8585 (t80) REVERT: A 268 GLU cc_start: 0.8122 (pp20) cc_final: 0.7753 (pp20) REVERT: A 454 ASN cc_start: 0.9001 (m110) cc_final: 0.8767 (m110) REVERT: A 466 MET cc_start: 0.8738 (tmm) cc_final: 0.8404 (tmm) REVERT: A 482 MET cc_start: 0.7619 (mmm) cc_final: 0.7364 (mmm) REVERT: A 485 MET cc_start: 0.7706 (pmm) cc_final: 0.7433 (pmm) REVERT: A 711 ASN cc_start: 0.7365 (p0) cc_final: 0.7119 (p0) REVERT: A 757 LYS cc_start: 0.8287 (mmpt) cc_final: 0.7858 (mptt) REVERT: A 887 MET cc_start: 0.9165 (tpp) cc_final: 0.8787 (tpp) REVERT: A 928 MET cc_start: 0.8145 (tpp) cc_final: 0.7870 (tpp) REVERT: A 1008 ILE cc_start: 0.9016 (mp) cc_final: 0.8654 (mm) REVERT: B 131 GLU cc_start: 0.6634 (tp30) cc_final: 0.6097 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1632 time to fit residues: 39.5633 Evaluate side-chains 123 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 29 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.144729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109428 restraints weight = 23050.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110493 restraints weight = 11666.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110838 restraints weight = 9451.141| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7996 Z= 0.126 Angle : 0.700 12.820 10871 Z= 0.358 Chirality : 0.044 0.175 1308 Planarity : 0.005 0.092 1372 Dihedral : 5.289 41.188 1111 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.33 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.27), residues: 1021 helix: 1.06 (0.25), residues: 465 sheet: -1.08 (0.49), residues: 118 loop : -2.87 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1041 HIS 0.005 0.001 HIS A 265 PHE 0.031 0.001 PHE A 953 TYR 0.013 0.001 TYR A 497 ARG 0.004 0.000 ARG A 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 0.87243 ( 3) hydrogen bonds : bond 0.03674 ( 358) hydrogen bonds : angle 4.34383 ( 1038) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.61671 ( 2) covalent geometry : bond 0.00270 ( 7994) covalent geometry : angle 0.69981 (10866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2923.14 seconds wall clock time: 51 minutes 7.87 seconds (3067.87 seconds total)