Starting phenix.real_space_refine on Tue Jun 10 03:22:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j6j_5925/06_2025/3j6j_5925.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j6j_5925/06_2025/3j6j_5925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j6j_5925/06_2025/3j6j_5925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j6j_5925/06_2025/3j6j_5925.map" model { file = "/net/cci-nas-00/data/ceres_data/3j6j_5925/06_2025/3j6j_5925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j6j_5925/06_2025/3j6j_5925.cif" } resolution = 3.64 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= 0.032 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6344 atoms to isotropic. 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 48 5.16 5 C 4040 2.51 5 N 1088 2.21 5 O 1168 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-5710/modules/chem_data/mon_lib" Total number of atoms: 6344 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "I" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Time building chain proxies: 3.98, per 1000 atoms: 0.63 Number of scatterers: 6344 At special positions: 0 Unit cell: (99, 96.8, 80.3, 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 48 16.00 O 1168 8.00 N 1088 7.00 C 4040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 782.5 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.052A pdb=" N PHE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 15 through 20' Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.686A pdb=" N HIS A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 3.651A pdb=" N TYR A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.903A pdb=" N CYS B 20 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.101A pdb=" N ASP B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.529A pdb=" N TRP B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.660A pdb=" N TYR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.673A pdb=" N SER B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.705A pdb=" N ASP C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.660A pdb=" N HIS C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.600A pdb=" N TYR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.667A pdb=" N PHE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 20' Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 35 through 50 removed outlier: 4.090A pdb=" N ASP D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 removed outlier: 3.502A pdb=" N TRP D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.953A pdb=" N PHE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 20' Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 35 through 50 removed outlier: 4.123A pdb=" N ASP E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 removed outlier: 3.865A pdb=" N TRP E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.836A pdb=" N TYR E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 15 through 20 removed outlier: 3.834A pdb=" N PHE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 15 through 20' Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 35 through 50 removed outlier: 3.985A pdb=" N ASP G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 63 removed outlier: 3.666A pdb=" N TRP G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 removed outlier: 3.537A pdb=" N TYR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.613A pdb=" N TYR G 95 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 15 through 20 removed outlier: 3.668A pdb=" N PHE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS I 20 " --> pdb=" O PHE I 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 15 through 20' Processing helix chain 'I' and resid 23 through 28 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 35 through 50 removed outlier: 3.889A pdb=" N ASP I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 63 removed outlier: 3.992A pdb=" N TRP I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 removed outlier: 3.655A pdb=" N TYR I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 94 Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 15 through 20 removed outlier: 3.564A pdb=" N PHE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS L 20 " --> pdb=" O PHE L 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 15 through 20' Processing helix chain 'L' and resid 23 through 28 Processing helix chain 'L' and resid 35 through 50 removed outlier: 3.997A pdb=" N ASP L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 63 removed outlier: 3.570A pdb=" N TRP L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 79 removed outlier: 3.710A pdb=" N TYR L 71 " --> pdb=" O GLY L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 94 396 hydrogen bonds defined for protein. 1185 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: 1.53 Time building geometry restraints manager: 1.81 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: 2016 1.33 - 1.46: 1206 1.46 - 1.58: 3218 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 6496 Sorted by residual: bond pdb=" C LEU L 28 " pdb=" N PRO L 29 " ideal model delta sigma weight residual 1.336 1.419 -0.083 1.20e-02 6.94e+03 4.81e+01 bond pdb=" N PRO L 29 " pdb=" CD PRO L 29 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.93e+00 bond pdb=" C ILE D 12 " pdb=" O ILE D 12 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.80e+00 bond pdb=" C ILE B 12 " pdb=" O ILE B 12 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.80e+00 bond pdb=" N CYS D 20 " pdb=" CA CYS D 20 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.62e+00 ... (remaining 6491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 8697 4.20 - 8.41: 137 8.41 - 12.61: 5 12.61 - 16.81: 0 16.81 - 21.02: 1 Bond angle restraints: 8840 Sorted by residual: angle pdb=" N ARG A 37 " pdb=" CA ARG A 37 " pdb=" C ARG A 37 " ideal model delta sigma weight residual 111.36 119.53 -8.17 1.09e+00 8.42e-01 5.61e+01 angle pdb=" C LEU D 31 " pdb=" N PRO D 32 " pdb=" CA PRO D 32 " ideal model delta sigma weight residual 119.87 127.63 -7.76 1.04e+00 9.25e-01 5.57e+01 angle pdb=" N ASN A 51 " pdb=" CA ASN A 51 " pdb=" C ASN A 51 " ideal model delta sigma weight residual 111.03 118.81 -7.78 1.11e+00 8.12e-01 4.91e+01 angle pdb=" CA PRO L 29 " pdb=" N PRO L 29 " pdb=" CD PRO L 29 " ideal model delta sigma weight residual 112.00 102.49 9.51 1.40e+00 5.10e-01 4.61e+01 angle pdb=" C LEU L 28 " pdb=" N PRO L 29 " pdb=" CA PRO L 29 " ideal model delta sigma weight residual 118.85 111.48 7.37 1.09e+00 8.42e-01 4.57e+01 ... (remaining 8835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 3418 16.97 - 33.94: 279 33.94 - 50.91: 111 50.91 - 67.88: 45 67.88 - 84.85: 3 Dihedral angle restraints: 3856 sinusoidal: 1536 harmonic: 2320 Sorted by residual: dihedral pdb=" CG ARG I 64 " pdb=" CD ARG I 64 " pdb=" NE ARG I 64 " pdb=" CZ ARG I 64 " ideal model delta sinusoidal sigma weight residual -90.00 -10.80 -79.20 2 1.50e+01 4.44e-03 2.06e+01 dihedral pdb=" CG ARG G 64 " pdb=" CD ARG G 64 " pdb=" NE ARG G 64 " pdb=" CZ ARG G 64 " ideal model delta sinusoidal sigma weight residual -90.00 -12.28 -77.72 2 1.50e+01 4.44e-03 2.04e+01 dihedral pdb=" CA LEU I 48 " pdb=" C LEU I 48 " pdb=" N SER I 49 " pdb=" CA SER I 49 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 770 0.069 - 0.137: 170 0.137 - 0.206: 23 0.206 - 0.275: 4 0.275 - 0.343: 1 Chirality restraints: 968 Sorted by residual: chirality pdb=" CA LEU L 28 " pdb=" N LEU L 28 " pdb=" C LEU L 28 " pdb=" CB LEU L 28 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ARG A 37 " pdb=" N ARG A 37 " pdb=" C ARG A 37 " pdb=" CB ARG A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PHE D 19 " pdb=" N PHE D 19 " pdb=" C PHE D 19 " pdb=" CB PHE D 19 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 965 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 57 " -0.013 2.00e-02 2.50e+03 1.56e-02 3.63e+00 pdb=" CG HIS G 57 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS G 57 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS G 57 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS G 57 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS G 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 36 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ALA G 36 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA G 36 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG G 37 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 20 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.67e+00 pdb=" C CYS A 20 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS A 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 21 " 0.010 2.00e-02 2.50e+03 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 24 2.24 - 2.91: 2828 2.91 - 3.57: 10141 3.57 - 4.24: 15508 4.24 - 4.90: 26180 Nonbonded interactions: 54681 Sorted by model distance: nonbonded pdb=" NH2 ARG A 37 " pdb=" OE2 GLU B 26 " model vdw 1.578 3.120 nonbonded pdb=" OE1 GLN B 39 " pdb=" CZ2 TRP C 56 " model vdw 1.753 3.340 nonbonded pdb=" OE1 GLN C 39 " pdb=" CZ2 TRP G 56 " model vdw 1.889 3.340 nonbonded pdb=" CD ARG A 37 " pdb=" NH1 ARG C 52 " model vdw 1.961 3.520 nonbonded pdb=" NH1 ARG B 37 " pdb=" NH1 ARG B 41 " model vdw 2.006 3.200 ... (remaining 54676 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.190 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.009 0.408 6497 Z= 0.676 Angle : 1.414 21.017 8840 Z= 0.997 Chirality : 0.058 0.343 968 Planarity : 0.005 0.036 1144 Dihedral : 15.900 84.850 2352 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 0.92 % Allowed : 4.08 % Favored : 95.00 % Rotamer: Outliers : 6.10 % Allowed : 9.16 % Favored : 84.74 % 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: -1.46 (0.26), residues: 760 helix: -0.53 (0.19), residues: 536 sheet: None (None), residues: 0 loop : -1.78 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 56 HIS 0.019 0.003 HIS G 57 PHE 0.021 0.002 PHE I 72 TYR 0.026 0.003 TYR G 30 ARG 0.012 0.001 ARG L 64 Details of bonding type rmsd hydrogen bonds : bond 0.23138 ( 396) hydrogen bonds : angle 8.11236 ( 1185) covalent geometry : bond 0.00704 ( 6496) covalent geometry : angle 1.41398 ( 8840) Misc. bond : bond 0.40765 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 516 time to evaluate : 0.773 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.9289 (mmtt) cc_final: 0.9074 (mmtm) REVERT: A 66 PRO cc_start: 0.9215 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: A 77 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8379 (mtp85) REVERT: A 82 VAL cc_start: 0.9016 (t) cc_final: 0.8698 (p) REVERT: B 14 ARG cc_start: 0.9034 (ttp-110) cc_final: 0.8738 (mtm-85) REVERT: B 24 VAL cc_start: 0.9299 (t) cc_final: 0.8624 (t) REVERT: B 35 THR cc_start: 0.9204 (m) cc_final: 0.8680 (m) REVERT: B 38 ASP cc_start: 0.9603 (t0) cc_final: 0.9261 (m-30) REVERT: B 77 ARG cc_start: 0.8949 (mtt-85) cc_final: 0.8473 (mmt90) REVERT: B 83 ASP cc_start: 0.9129 (m-30) cc_final: 0.8784 (m-30) REVERT: B 95 TYR cc_start: 0.8993 (m-80) cc_final: 0.8391 (m-80) REVERT: B 96 GLN cc_start: 0.7958 (mt0) cc_final: 0.7754 (mm-40) REVERT: C 3 PHE cc_start: 0.7767 (t80) cc_final: 0.7242 (t80) REVERT: C 21 ASN cc_start: 0.9164 (m110) cc_final: 0.8558 (m-40) REVERT: C 31 LEU cc_start: 0.9161 (mt) cc_final: 0.8903 (mt) REVERT: C 41 ARG cc_start: 0.9284 (ttt180) cc_final: 0.8894 (tpp80) REVERT: C 53 ASP cc_start: 0.9613 (m-30) cc_final: 0.9190 (m-30) REVERT: D 3 PHE cc_start: 0.8490 (t80) cc_final: 0.7684 (t80) REVERT: D 14 ARG cc_start: 0.8780 (ttp-110) cc_final: 0.8449 (mtm-85) REVERT: D 21 ASN cc_start: 0.9174 (m110) cc_final: 0.8873 (m-40) REVERT: D 35 THR cc_start: 0.8773 (m) cc_final: 0.8411 (p) REVERT: D 40 ASP cc_start: 0.8091 (m-30) cc_final: 0.7796 (m-30) REVERT: D 54 THR cc_start: 0.9471 (m) cc_final: 0.9148 (p) REVERT: E 9 TYR cc_start: 0.9417 (t80) cc_final: 0.9077 (t80) REVERT: E 23 ASP cc_start: 0.9264 (t70) cc_final: 0.9057 (t0) REVERT: E 35 THR cc_start: 0.8651 (m) cc_final: 0.8180 (p) REVERT: E 60 ASN cc_start: 0.9546 (t0) cc_final: 0.9279 (m110) REVERT: E 87 GLU cc_start: 0.8960 (tt0) cc_final: 0.8664 (tp30) REVERT: E 90 SER cc_start: 0.9179 (t) cc_final: 0.8827 (p) REVERT: G 5 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7779 (mt-10) REVERT: G 24 VAL cc_start: 0.9330 (t) cc_final: 0.9022 (m) REVERT: G 28 LEU cc_start: 0.9350 (mt) cc_final: 0.9050 (mt) REVERT: G 35 THR cc_start: 0.8615 (m) cc_final: 0.8237 (p) REVERT: G 76 LEU cc_start: 0.9456 (mt) cc_final: 0.9015 (mt) REVERT: I 14 ARG cc_start: 0.9140 (ttp-110) cc_final: 0.8839 (mtm-85) REVERT: I 24 VAL cc_start: 0.9488 (t) cc_final: 0.9102 (m) REVERT: I 53 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: I 60 ASN cc_start: 0.9562 (t0) cc_final: 0.9317 (m110) REVERT: I 72 PHE cc_start: 0.9444 (t80) cc_final: 0.9172 (t80) REVERT: I 90 SER cc_start: 0.8871 (t) cc_final: 0.8571 (p) REVERT: L 21 ASN cc_start: 0.8869 (m110) cc_final: 0.8508 (m-40) REVERT: L 28 LEU cc_start: 0.8607 (mt) cc_final: 0.8371 (mt) REVERT: L 31 LEU cc_start: 0.9130 (mt) cc_final: 0.8905 (mt) REVERT: L 40 ASP cc_start: 0.8676 (m-30) cc_final: 0.8423 (m-30) REVERT: L 41 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8294 (ttm170) outliers start: 42 outliers final: 3 residues processed: 524 average time/residue: 0.2214 time to fit residues: 143.7508 Evaluate side-chains 467 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 462 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain L residue 41 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 57 HIS A 63 GLN A 96 GLN B 21 ASN B 60 ASN C 21 ASN C 57 HIS ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 21 ASN D 96 GLN E 39 GLN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS L 21 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN L 60 ASN L 96 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.070662 restraints weight = 21890.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072878 restraints weight = 11138.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074431 restraints weight = 6797.991| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6497 Z= 0.169 Angle : 0.742 9.420 8840 Z= 0.389 Chirality : 0.044 0.196 968 Planarity : 0.006 0.053 1144 Dihedral : 6.131 58.210 896 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.58 % Favored : 98.16 % Rotamer: Outliers : 8.28 % Allowed : 23.98 % Favored : 67.73 % 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: 1.38 (0.28), residues: 760 helix: 0.98 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 1.17 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 56 HIS 0.002 0.001 HIS C 57 PHE 0.034 0.003 PHE G 59 TYR 0.024 0.002 TYR L 92 ARG 0.007 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 396) hydrogen bonds : angle 4.89167 ( 1185) covalent geometry : bond 0.00379 ( 6496) covalent geometry : angle 0.74249 ( 8840) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 513 time to evaluate : 0.660 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: symmetry clash revert: symmetry clash REVERT: A 8 THR cc_start: 0.9594 (m) cc_final: 0.9367 (p) REVERT: A 37 ARG cc_start: 0.8535 (ttp80) cc_final: 0.7337 (ttp80) REVERT: A 51 ASN cc_start: 0.8228 (p0) cc_final: 0.7565 (t0) REVERT: A 55 LEU cc_start: 0.8849 (mt) cc_final: 0.8391 (mt) REVERT: A 58 LEU cc_start: 0.9635 (tt) cc_final: 0.9315 (tp) REVERT: A 61 THR cc_start: 0.9651 (m) cc_final: 0.9423 (p) REVERT: A 64 ARG cc_start: 0.8731 (tpp80) cc_final: 0.8498 (tpp80) REVERT: A 66 PRO cc_start: 0.9474 (Cg_exo) cc_final: 0.9228 (Cg_endo) REVERT: A 90 SER cc_start: 0.9561 (t) cc_final: 0.9292 (p) REVERT: A 96 GLN cc_start: 0.7687 (mt0) cc_final: 0.7311 (mm110) REVERT: B 9 TYR cc_start: 0.9124 (t80) cc_final: 0.8369 (t80) REVERT: B 16 PHE cc_start: 0.8721 (t80) cc_final: 0.7278 (t80) REVERT: B 42 LEU cc_start: 0.9510 (mt) cc_final: 0.9293 (mt) REVERT: B 51 ASN cc_start: 0.8162 (p0) cc_final: 0.7942 (t0) REVERT: B 77 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.8507 (mmt-90) REVERT: B 82 VAL cc_start: 0.9021 (m) cc_final: 0.8387 (t) REVERT: B 86 ASP cc_start: 0.8740 (m-30) cc_final: 0.8212 (m-30) REVERT: C 7 LYS cc_start: 0.9110 (mmtt) cc_final: 0.8907 (mmtm) REVERT: C 9 TYR cc_start: 0.8839 (t80) cc_final: 0.8536 (t80) REVERT: C 15 ASN cc_start: 0.9349 (m110) cc_final: 0.8923 (m110) REVERT: C 35 THR cc_start: 0.9077 (m) cc_final: 0.8230 (p) REVERT: C 38 ASP cc_start: 0.9173 (m-30) cc_final: 0.8280 (m-30) REVERT: C 41 ARG cc_start: 0.8877 (ttt180) cc_final: 0.8543 (ttp-170) REVERT: C 53 ASP cc_start: 0.8602 (m-30) cc_final: 0.8295 (m-30) REVERT: D 8 THR cc_start: 0.9581 (m) cc_final: 0.9356 (p) REVERT: D 9 TYR cc_start: 0.9095 (t80) cc_final: 0.8816 (t80) REVERT: D 16 PHE cc_start: 0.8558 (t80) cc_final: 0.8182 (t80) REVERT: D 42 LEU cc_start: 0.9503 (mt) cc_final: 0.9257 (mm) REVERT: D 53 ASP cc_start: 0.8537 (m-30) cc_final: 0.8301 (m-30) REVERT: D 57 HIS cc_start: 0.9242 (m-70) cc_final: 0.8867 (m-70) REVERT: E 5 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8399 (mt-10) REVERT: E 7 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9159 (mmtm) REVERT: E 42 LEU cc_start: 0.9363 (mt) cc_final: 0.9141 (mm) REVERT: E 51 ASN cc_start: 0.8696 (p0) cc_final: 0.8133 (t0) REVERT: E 77 ARG cc_start: 0.9149 (ttm110) cc_final: 0.8532 (mmt90) REVERT: E 95 TYR cc_start: 0.9190 (m-80) cc_final: 0.8902 (m-80) REVERT: G 5 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7867 (mt-10) REVERT: G 8 THR cc_start: 0.9421 (m) cc_final: 0.9079 (p) REVERT: G 9 TYR cc_start: 0.8886 (t80) cc_final: 0.8586 (t80) REVERT: G 28 LEU cc_start: 0.9370 (mt) cc_final: 0.9007 (mt) REVERT: G 31 LEU cc_start: 0.9184 (mt) cc_final: 0.8942 (mm) REVERT: G 59 PHE cc_start: 0.9019 (m-80) cc_final: 0.8412 (m-80) REVERT: G 60 ASN cc_start: 0.9424 (t0) cc_final: 0.9079 (m110) REVERT: G 66 PRO cc_start: 0.9461 (Cg_exo) cc_final: 0.9169 (Cg_endo) REVERT: G 76 LEU cc_start: 0.9630 (mt) cc_final: 0.9380 (mt) REVERT: G 77 ARG cc_start: 0.9355 (tpp80) cc_final: 0.8906 (mmt90) REVERT: I 5 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8242 (mt-10) REVERT: I 9 TYR cc_start: 0.9151 (t80) cc_final: 0.8845 (t80) REVERT: I 15 ASN cc_start: 0.9237 (m110) cc_final: 0.8962 (m110) REVERT: I 38 ASP cc_start: 0.9261 (m-30) cc_final: 0.8732 (p0) REVERT: I 60 ASN cc_start: 0.9453 (t0) cc_final: 0.9239 (t0) REVERT: I 64 ARG cc_start: 0.8647 (tpp80) cc_final: 0.8444 (tpp80) REVERT: I 77 ARG cc_start: 0.9282 (ttm110) cc_final: 0.8716 (mmt90) REVERT: I 90 SER cc_start: 0.9377 (t) cc_final: 0.9031 (p) REVERT: I 96 GLN cc_start: 0.8272 (mt0) cc_final: 0.7677 (tp40) REVERT: L 5 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8415 (mt-10) REVERT: L 8 THR cc_start: 0.9665 (m) cc_final: 0.9417 (p) REVERT: L 14 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.6562 (mtp-110) REVERT: L 23 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8338 (t70) REVERT: L 26 GLU cc_start: 0.8268 (mp0) cc_final: 0.7487 (mp0) REVERT: L 37 ARG cc_start: 0.8480 (tmm-80) cc_final: 0.8215 (tmt170) REVERT: L 41 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7926 (ttm110) REVERT: L 53 ASP cc_start: 0.8895 (m-30) cc_final: 0.8246 (m-30) REVERT: L 54 THR cc_start: 0.9385 (m) cc_final: 0.8984 (p) REVERT: L 59 PHE cc_start: 0.9419 (m-80) cc_final: 0.8675 (m-80) REVERT: L 86 ASP cc_start: 0.8168 (m-30) cc_final: 0.7908 (m-30) outliers start: 57 outliers final: 29 residues processed: 523 average time/residue: 0.2129 time to fit residues: 138.2016 Evaluate side-chains 522 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 491 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 40 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 21 ASN B 96 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 63 GLN D 51 ASN E 60 ASN G 39 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.072376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.064196 restraints weight = 22688.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066287 restraints weight = 11471.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.067737 restraints weight = 7035.381| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.7915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6497 Z= 0.235 Angle : 0.760 12.123 8840 Z= 0.392 Chirality : 0.045 0.191 968 Planarity : 0.007 0.084 1144 Dihedral : 4.758 19.676 884 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.18 % Favored : 98.68 % Rotamer: Outliers : 10.17 % Allowed : 27.18 % Favored : 62.65 % 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: 1.36 (0.29), residues: 760 helix: 0.74 (0.19), residues: 600 sheet: None (None), residues: 0 loop : 2.16 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 56 HIS 0.003 0.001 HIS A 57 PHE 0.038 0.003 PHE D 3 TYR 0.024 0.002 TYR L 92 ARG 0.016 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 396) hydrogen bonds : angle 4.77945 ( 1185) covalent geometry : bond 0.00528 ( 6496) covalent geometry : angle 0.76002 ( 8840) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 506 time to evaluate : 0.679 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 THR cc_start: 0.9751 (m) cc_final: 0.9548 (p) REVERT: A 14 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: A 43 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.9048 (mtt90) REVERT: A 52 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.8327 (ptp-110) REVERT: A 55 LEU cc_start: 0.8635 (mt) cc_final: 0.8180 (mt) REVERT: A 64 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8483 (tpp80) REVERT: A 77 ARG cc_start: 0.8855 (mmt-90) cc_final: 0.8591 (mmt-90) REVERT: A 82 VAL cc_start: 0.9420 (p) cc_final: 0.9175 (t) REVERT: A 87 GLU cc_start: 0.9402 (tp30) cc_final: 0.9126 (tp30) REVERT: B 9 TYR cc_start: 0.9185 (t80) cc_final: 0.8697 (t80) REVERT: B 14 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8283 (mtm-85) REVERT: B 38 ASP cc_start: 0.8989 (m-30) cc_final: 0.8711 (m-30) REVERT: B 53 ASP cc_start: 0.8474 (m-30) cc_final: 0.8031 (m-30) REVERT: B 63 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8814 (pp30) REVERT: C 9 TYR cc_start: 0.9067 (t80) cc_final: 0.8542 (t80) REVERT: C 10 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9094 (ptmm) REVERT: C 35 THR cc_start: 0.9117 (m) cc_final: 0.8533 (p) REVERT: C 38 ASP cc_start: 0.8839 (m-30) cc_final: 0.8348 (m-30) REVERT: C 41 ARG cc_start: 0.8751 (ttt180) cc_final: 0.8535 (ttp-170) REVERT: C 86 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8498 (p0) REVERT: D 37 ARG cc_start: 0.8906 (ttt180) cc_final: 0.8436 (tmm-80) REVERT: D 41 ARG cc_start: 0.8898 (ttp-170) cc_final: 0.8345 (ttp-170) REVERT: D 53 ASP cc_start: 0.8529 (m-30) cc_final: 0.8282 (m-30) REVERT: D 57 HIS cc_start: 0.9199 (m-70) cc_final: 0.8915 (m-70) REVERT: E 51 ASN cc_start: 0.9021 (p0) cc_final: 0.8724 (p0) REVERT: E 77 ARG cc_start: 0.9125 (ttm110) cc_final: 0.8617 (mmt90) REVERT: G 1 MET cc_start: 0.8198 (ttm) cc_final: 0.7871 (ttm) REVERT: G 9 TYR cc_start: 0.9326 (t80) cc_final: 0.9069 (t80) REVERT: G 38 ASP cc_start: 0.8871 (m-30) cc_final: 0.8632 (m-30) REVERT: G 70 GLU cc_start: 0.8264 (pp20) cc_final: 0.8028 (pp20) REVERT: G 71 TYR cc_start: 0.9254 (m-80) cc_final: 0.8682 (m-80) REVERT: G 72 PHE cc_start: 0.9501 (t80) cc_final: 0.9262 (t80) REVERT: G 76 LEU cc_start: 0.9737 (mt) cc_final: 0.9468 (mt) REVERT: G 77 ARG cc_start: 0.9335 (tpp80) cc_final: 0.8953 (mmt90) REVERT: G 90 SER cc_start: 0.9473 (OUTLIER) cc_final: 0.9105 (p) REVERT: I 9 TYR cc_start: 0.9124 (t80) cc_final: 0.8797 (t80) REVERT: I 14 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: I 38 ASP cc_start: 0.9232 (m-30) cc_final: 0.8734 (p0) REVERT: I 41 ARG cc_start: 0.8882 (mmm-85) cc_final: 0.8541 (mmm-85) REVERT: I 71 TYR cc_start: 0.9361 (m-80) cc_final: 0.9127 (m-80) REVERT: I 77 ARG cc_start: 0.9274 (ttm110) cc_final: 0.8885 (mmt180) REVERT: I 95 TYR cc_start: 0.9253 (m-80) cc_final: 0.8867 (m-80) REVERT: I 96 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8218 (tp40) REVERT: L 8 THR cc_start: 0.9747 (m) cc_final: 0.9535 (p) REVERT: L 41 ARG cc_start: 0.8665 (ttm170) cc_final: 0.8362 (ttm110) REVERT: L 55 LEU cc_start: 0.9508 (tp) cc_final: 0.9151 (tp) REVERT: L 59 PHE cc_start: 0.9324 (m-80) cc_final: 0.9005 (m-80) REVERT: L 64 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8630 (mmm-85) REVERT: L 82 VAL cc_start: 0.8981 (p) cc_final: 0.8762 (t) REVERT: L 95 TYR cc_start: 0.9101 (m-80) cc_final: 0.8873 (m-10) outliers start: 70 outliers final: 40 residues processed: 518 average time/residue: 0.2150 time to fit residues: 138.4369 Evaluate side-chains 532 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 487 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 39 GLN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.062592 restraints weight = 23565.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.064648 restraints weight = 11783.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066024 restraints weight = 7199.714| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.8581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6497 Z= 0.192 Angle : 0.704 9.697 8840 Z= 0.367 Chirality : 0.044 0.187 968 Planarity : 0.006 0.054 1144 Dihedral : 4.623 21.738 880 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.58 % Favored : 98.29 % Rotamer: Outliers : 7.99 % Allowed : 34.74 % Favored : 57.27 % 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: 1.37 (0.29), residues: 760 helix: 0.66 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.58 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 56 HIS 0.001 0.000 HIS C 57 PHE 0.024 0.002 PHE D 16 TYR 0.017 0.002 TYR B 92 ARG 0.008 0.001 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 396) hydrogen bonds : angle 4.50158 ( 1185) covalent geometry : bond 0.00435 ( 6496) covalent geometry : angle 0.70380 ( 8840) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 496 time to evaluate : 0.716 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 5 GLU cc_start: 0.8678 (mt-10) cc_final: 0.7964 (tt0) REVERT: A 53 ASP cc_start: 0.8670 (m-30) cc_final: 0.8466 (m-30) REVERT: A 55 LEU cc_start: 0.8528 (mt) cc_final: 0.8281 (mt) REVERT: A 87 GLU cc_start: 0.9341 (tp30) cc_final: 0.9103 (tp30) REVERT: B 9 TYR cc_start: 0.9201 (t80) cc_final: 0.8694 (t80) REVERT: B 14 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8186 (mtm-85) REVERT: B 53 ASP cc_start: 0.8511 (m-30) cc_final: 0.8262 (m-30) REVERT: B 63 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8722 (tt0) REVERT: B 93 GLN cc_start: 0.9272 (tm-30) cc_final: 0.9047 (tm-30) REVERT: C 9 TYR cc_start: 0.9215 (t80) cc_final: 0.8818 (t80) REVERT: C 10 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9130 (ptmm) REVERT: C 35 THR cc_start: 0.9150 (m) cc_final: 0.8404 (p) REVERT: C 38 ASP cc_start: 0.8812 (m-30) cc_final: 0.8177 (m-30) REVERT: C 41 ARG cc_start: 0.8765 (ttt180) cc_final: 0.8553 (ttp-170) REVERT: C 53 ASP cc_start: 0.8697 (m-30) cc_final: 0.8459 (m-30) REVERT: C 60 ASN cc_start: 0.9520 (t0) cc_final: 0.9194 (m110) REVERT: C 86 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8542 (p0) REVERT: C 96 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7513 (tp-100) REVERT: D 14 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.8188 (mtm-85) REVERT: D 41 ARG cc_start: 0.9027 (ttp-170) cc_final: 0.8603 (ttp-170) REVERT: D 53 ASP cc_start: 0.8587 (m-30) cc_final: 0.8382 (m-30) REVERT: D 57 HIS cc_start: 0.9142 (m-70) cc_final: 0.8867 (m-70) REVERT: D 77 ARG cc_start: 0.9223 (ttm110) cc_final: 0.8870 (mmt90) REVERT: E 52 ARG cc_start: 0.9128 (ttm-80) cc_final: 0.8882 (ttm-80) REVERT: E 77 ARG cc_start: 0.9094 (ttm110) cc_final: 0.8829 (mmt90) REVERT: G 1 MET cc_start: 0.8248 (ttm) cc_final: 0.7958 (ttm) REVERT: G 9 TYR cc_start: 0.9257 (t80) cc_final: 0.8976 (t80) REVERT: G 60 ASN cc_start: 0.9465 (t0) cc_final: 0.9224 (m110) REVERT: G 72 PHE cc_start: 0.9499 (t80) cc_final: 0.9081 (t80) REVERT: G 76 LEU cc_start: 0.9732 (mt) cc_final: 0.9389 (mt) REVERT: G 77 ARG cc_start: 0.9312 (tpp80) cc_final: 0.9029 (mmt90) REVERT: I 14 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.7814 (mtm-85) REVERT: I 38 ASP cc_start: 0.9144 (m-30) cc_final: 0.8839 (m-30) REVERT: I 41 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8312 (tpp80) REVERT: I 77 ARG cc_start: 0.9313 (ttm110) cc_final: 0.8992 (mmt90) REVERT: I 95 TYR cc_start: 0.9234 (m-80) cc_final: 0.9025 (m-80) REVERT: I 96 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8280 (mm-40) REVERT: L 7 LYS cc_start: 0.9407 (ttmm) cc_final: 0.9146 (ttpt) REVERT: L 41 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8490 (ttm110) REVERT: L 64 ARG cc_start: 0.9038 (mmm-85) cc_final: 0.8659 (mmm-85) outliers start: 55 outliers final: 36 residues processed: 505 average time/residue: 0.2021 time to fit residues: 127.7506 Evaluate side-chains 523 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 482 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 96 GLN C 51 ASN C 63 GLN C 96 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** 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 = 0.3089 r_free = 0.3089 target = 0.071052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.062610 restraints weight = 23020.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.064693 restraints weight = 11857.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.066069 restraints weight = 7340.477| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.9074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6497 Z= 0.170 Angle : 0.703 9.841 8840 Z= 0.367 Chirality : 0.043 0.189 968 Planarity : 0.005 0.047 1144 Dihedral : 4.523 21.750 880 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 7.70 % Allowed : 37.06 % Favored : 55.23 % 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: 1.18 (0.30), residues: 760 helix: 0.50 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.73 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 56 HIS 0.001 0.000 HIS C 57 PHE 0.022 0.002 PHE E 3 TYR 0.028 0.002 TYR I 9 ARG 0.008 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 396) hydrogen bonds : angle 4.43724 ( 1185) covalent geometry : bond 0.00390 ( 6496) covalent geometry : angle 0.70287 ( 8840) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 497 time to evaluate : 0.740 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 5 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7985 (tt0) REVERT: A 30 TYR cc_start: 0.9243 (m-10) cc_final: 0.9009 (m-10) REVERT: A 55 LEU cc_start: 0.8554 (mt) cc_final: 0.8321 (mt) REVERT: A 87 GLU cc_start: 0.9371 (tp30) cc_final: 0.9138 (tp30) REVERT: A 91 VAL cc_start: 0.9344 (t) cc_final: 0.9071 (p) REVERT: B 14 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8183 (mtm-85) REVERT: B 39 GLN cc_start: 0.9246 (pt0) cc_final: 0.8347 (pp30) REVERT: B 53 ASP cc_start: 0.8572 (m-30) cc_final: 0.8360 (m-30) REVERT: B 63 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8701 (pp30) REVERT: B 84 LEU cc_start: 0.9282 (tp) cc_final: 0.9044 (tp) REVERT: C 9 TYR cc_start: 0.9196 (t80) cc_final: 0.8916 (t80) REVERT: C 10 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9100 (ptmm) REVERT: C 35 THR cc_start: 0.9108 (m) cc_final: 0.8378 (p) REVERT: C 38 ASP cc_start: 0.8740 (m-30) cc_final: 0.8132 (m-30) REVERT: C 41 ARG cc_start: 0.8844 (ttt180) cc_final: 0.8428 (ttp-110) REVERT: C 53 ASP cc_start: 0.8479 (m-30) cc_final: 0.8158 (m-30) REVERT: C 77 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8893 (mmt-90) REVERT: C 96 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7654 (tp-100) REVERT: D 14 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.8217 (mtm-85) REVERT: D 39 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8516 (pp30) REVERT: D 41 ARG cc_start: 0.9120 (ttp-170) cc_final: 0.8749 (ttp-170) REVERT: D 43 ARG cc_start: 0.8976 (mtp180) cc_final: 0.8739 (mtt180) REVERT: D 77 ARG cc_start: 0.9222 (ttm110) cc_final: 0.8906 (mmt90) REVERT: D 87 GLU cc_start: 0.9162 (tp30) cc_final: 0.8894 (tp30) REVERT: E 51 ASN cc_start: 0.8956 (p0) cc_final: 0.8595 (p0) REVERT: E 71 TYR cc_start: 0.9520 (m-80) cc_final: 0.9173 (m-80) REVERT: E 77 ARG cc_start: 0.9153 (ttm110) cc_final: 0.8938 (mmt90) REVERT: G 1 MET cc_start: 0.8299 (ttm) cc_final: 0.7957 (ttm) REVERT: G 9 TYR cc_start: 0.9300 (t80) cc_final: 0.9020 (t80) REVERT: G 76 LEU cc_start: 0.9710 (mt) cc_final: 0.9459 (mt) REVERT: G 77 ARG cc_start: 0.9344 (tpp80) cc_final: 0.9047 (mmt90) REVERT: I 1 MET cc_start: 0.8234 (tpp) cc_final: 0.7852 (mmp) REVERT: I 14 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.7918 (mtm-85) REVERT: I 38 ASP cc_start: 0.9215 (m-30) cc_final: 0.8870 (m-30) REVERT: I 60 ASN cc_start: 0.9545 (t0) cc_final: 0.9260 (m110) REVERT: I 77 ARG cc_start: 0.9328 (ttm110) cc_final: 0.9069 (mmt-90) REVERT: I 96 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8270 (mm-40) REVERT: L 23 ASP cc_start: 0.8932 (t70) cc_final: 0.8699 (t70) REVERT: L 26 GLU cc_start: 0.7993 (mp0) cc_final: 0.7492 (mp0) REVERT: L 41 ARG cc_start: 0.8896 (ttm170) cc_final: 0.8588 (ttm110) REVERT: L 64 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8713 (mmm-85) outliers start: 53 outliers final: 41 residues processed: 506 average time/residue: 0.2162 time to fit residues: 137.0355 Evaluate side-chains 527 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 482 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 51 ASN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 63 GLN ** L 51 ASN ** 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 = 0.3095 r_free = 0.3095 target = 0.070468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.062055 restraints weight = 22783.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064083 restraints weight = 11890.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.065455 restraints weight = 7387.784| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.9421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6497 Z= 0.163 Angle : 0.731 10.679 8840 Z= 0.380 Chirality : 0.043 0.184 968 Planarity : 0.005 0.046 1144 Dihedral : 4.466 22.929 880 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 8.28 % Allowed : 39.68 % Favored : 52.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.30), residues: 760 helix: 0.38 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.74 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 56 HIS 0.002 0.000 HIS A 57 PHE 0.027 0.002 PHE E 3 TYR 0.032 0.002 TYR I 9 ARG 0.008 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 396) hydrogen bonds : angle 4.50304 ( 1185) covalent geometry : bond 0.00375 ( 6496) covalent geometry : angle 0.73056 ( 8840) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 487 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8621 (mt-10) cc_final: 0.7995 (tt0) REVERT: A 14 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.7940 (mtm-85) REVERT: A 55 LEU cc_start: 0.8513 (mt) cc_final: 0.8083 (mt) REVERT: A 77 ARG cc_start: 0.9111 (mmt90) cc_final: 0.8903 (mmt180) REVERT: A 87 GLU cc_start: 0.9310 (tp30) cc_final: 0.8984 (tp30) REVERT: B 14 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8239 (mtm-85) REVERT: B 17 SER cc_start: 0.9506 (p) cc_final: 0.9305 (m) REVERT: B 38 ASP cc_start: 0.8841 (m-30) cc_final: 0.8027 (m-30) REVERT: B 39 GLN cc_start: 0.9191 (pt0) cc_final: 0.8403 (pp30) REVERT: B 41 ARG cc_start: 0.8438 (ttm110) cc_final: 0.7657 (ptp-170) REVERT: B 63 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8450 (pp30) REVERT: B 84 LEU cc_start: 0.9256 (tp) cc_final: 0.9012 (tp) REVERT: C 9 TYR cc_start: 0.9224 (t80) cc_final: 0.8828 (t80) REVERT: C 10 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9112 (ptmm) REVERT: C 14 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.8145 (mtm-85) REVERT: C 35 THR cc_start: 0.9089 (m) cc_final: 0.8381 (p) REVERT: C 38 ASP cc_start: 0.8656 (m-30) cc_final: 0.8001 (m-30) REVERT: C 41 ARG cc_start: 0.8783 (ttt180) cc_final: 0.8359 (ttp-110) REVERT: C 53 ASP cc_start: 0.8417 (m-30) cc_final: 0.8110 (m-30) REVERT: C 77 ARG cc_start: 0.9162 (ttm110) cc_final: 0.8864 (mmt90) REVERT: C 87 GLU cc_start: 0.9129 (tp30) cc_final: 0.8870 (tp30) REVERT: D 39 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8668 (pp30) REVERT: D 41 ARG cc_start: 0.9160 (ttp-170) cc_final: 0.8837 (ttp-170) REVERT: D 77 ARG cc_start: 0.9177 (ttm110) cc_final: 0.8928 (mmt90) REVERT: D 87 GLU cc_start: 0.9139 (tp30) cc_final: 0.8924 (tp30) REVERT: D 91 VAL cc_start: 0.9296 (t) cc_final: 0.9053 (p) REVERT: E 14 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.8101 (mtm-85) REVERT: E 52 ARG cc_start: 0.9242 (ttm-80) cc_final: 0.8980 (tpp80) REVERT: G 1 MET cc_start: 0.8264 (ttm) cc_final: 0.7908 (ttm) REVERT: G 9 TYR cc_start: 0.9360 (t80) cc_final: 0.8955 (t80) REVERT: G 77 ARG cc_start: 0.9260 (tpp80) cc_final: 0.9049 (mmt90) REVERT: I 1 MET cc_start: 0.8208 (tpp) cc_final: 0.7864 (mmp) REVERT: I 9 TYR cc_start: 0.9019 (t80) cc_final: 0.8660 (t80) REVERT: I 15 ASN cc_start: 0.9175 (m110) cc_final: 0.8924 (m110) REVERT: I 38 ASP cc_start: 0.9023 (m-30) cc_final: 0.8778 (m-30) REVERT: I 64 ARG cc_start: 0.8610 (tpp80) cc_final: 0.8154 (tpp80) REVERT: I 77 ARG cc_start: 0.9279 (ttm110) cc_final: 0.9046 (mmt-90) REVERT: L 9 TYR cc_start: 0.9396 (t80) cc_final: 0.8886 (t80) REVERT: L 41 ARG cc_start: 0.8856 (ttm170) cc_final: 0.8631 (ttm110) REVERT: L 64 ARG cc_start: 0.9007 (mmm-85) cc_final: 0.8670 (mmm-85) outliers start: 57 outliers final: 41 residues processed: 500 average time/residue: 0.2112 time to fit residues: 131.9695 Evaluate side-chains 523 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 479 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN C 63 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 51 ASN I 60 ASN I 96 GLN L 39 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.070998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.062569 restraints weight = 22530.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064591 restraints weight = 11627.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.066010 restraints weight = 7174.638| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.9656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6497 Z= 0.166 Angle : 0.761 10.444 8840 Z= 0.393 Chirality : 0.044 0.186 968 Planarity : 0.005 0.053 1144 Dihedral : 4.472 23.113 880 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.50 % Favored : 97.37 % Rotamer: Outliers : 7.56 % Allowed : 40.55 % Favored : 51.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.29), residues: 760 helix: 0.37 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 1.13 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 56 HIS 0.001 0.000 HIS I 57 PHE 0.029 0.002 PHE I 16 TYR 0.023 0.003 TYR L 92 ARG 0.010 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 396) hydrogen bonds : angle 4.54965 ( 1185) covalent geometry : bond 0.00385 ( 6496) covalent geometry : angle 0.76063 ( 8840) Misc. bond : bond 0.00074 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 485 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.7924 (mtm-85) REVERT: A 77 ARG cc_start: 0.9132 (mmt90) cc_final: 0.8887 (mmt180) REVERT: A 87 GLU cc_start: 0.9319 (tp30) cc_final: 0.9064 (tp30) REVERT: B 14 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8278 (mtm-85) REVERT: B 38 ASP cc_start: 0.8907 (m-30) cc_final: 0.8079 (m-30) REVERT: B 41 ARG cc_start: 0.8493 (ttm110) cc_final: 0.7665 (ptp-170) REVERT: B 51 ASN cc_start: 0.8516 (p0) cc_final: 0.8215 (p0) REVERT: B 63 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8476 (pp30) REVERT: B 84 LEU cc_start: 0.9249 (tp) cc_final: 0.9045 (tp) REVERT: C 9 TYR cc_start: 0.9252 (t80) cc_final: 0.8861 (t80) REVERT: C 10 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9185 (ptmm) REVERT: C 14 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8224 (mtm-85) REVERT: C 35 THR cc_start: 0.8979 (m) cc_final: 0.8262 (p) REVERT: C 38 ASP cc_start: 0.8680 (m-30) cc_final: 0.8026 (m-30) REVERT: C 41 ARG cc_start: 0.8865 (ttt180) cc_final: 0.8377 (ttp-110) REVERT: C 77 ARG cc_start: 0.9231 (ttm110) cc_final: 0.8917 (mmt90) REVERT: D 10 LYS cc_start: 0.9488 (ptpt) cc_final: 0.9014 (ttpp) REVERT: D 14 ARG cc_start: 0.8671 (mtp-110) cc_final: 0.8204 (mtm-85) REVERT: D 39 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8702 (pp30) REVERT: D 41 ARG cc_start: 0.9173 (ttp-170) cc_final: 0.8867 (ttp-170) REVERT: D 77 ARG cc_start: 0.9233 (ttm110) cc_final: 0.8985 (mmt90) REVERT: D 91 VAL cc_start: 0.9306 (t) cc_final: 0.9066 (p) REVERT: E 5 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8514 (tt0) REVERT: E 52 ARG cc_start: 0.9347 (ttm-80) cc_final: 0.9100 (tpp80) REVERT: E 61 THR cc_start: 0.9522 (m) cc_final: 0.9180 (p) REVERT: G 1 MET cc_start: 0.8281 (ttm) cc_final: 0.8018 (ttm) REVERT: G 9 TYR cc_start: 0.9416 (t80) cc_final: 0.9080 (t80) REVERT: G 14 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8183 (mtm-85) REVERT: G 77 ARG cc_start: 0.9282 (tpp80) cc_final: 0.9019 (mmt90) REVERT: I 1 MET cc_start: 0.8328 (tpp) cc_final: 0.7864 (mmp) REVERT: I 9 TYR cc_start: 0.8954 (t80) cc_final: 0.8704 (t80) REVERT: I 15 ASN cc_start: 0.9241 (m110) cc_final: 0.8819 (m110) REVERT: I 38 ASP cc_start: 0.9093 (m-30) cc_final: 0.8803 (m-30) REVERT: I 64 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8166 (tpp80) REVERT: I 77 ARG cc_start: 0.9333 (ttm110) cc_final: 0.8965 (mmt90) REVERT: L 9 TYR cc_start: 0.9365 (t80) cc_final: 0.8860 (t80) REVERT: L 41 ARG cc_start: 0.8970 (ttm170) cc_final: 0.8727 (ttm110) REVERT: L 64 ARG cc_start: 0.9082 (mmm-85) cc_final: 0.8725 (mmm-85) outliers start: 52 outliers final: 40 residues processed: 496 average time/residue: 0.2276 time to fit residues: 141.7883 Evaluate side-chains 517 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 474 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN C 63 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 96 GLN L 39 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.062031 restraints weight = 22892.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064071 restraints weight = 11842.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.065471 restraints weight = 7338.065| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.9798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6497 Z= 0.194 Angle : 0.806 13.430 8840 Z= 0.413 Chirality : 0.045 0.185 968 Planarity : 0.006 0.054 1144 Dihedral : 4.561 23.203 880 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Rotamer: Outliers : 7.85 % Allowed : 40.55 % Favored : 51.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.29), residues: 760 helix: 0.33 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 1.08 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 56 HIS 0.002 0.001 HIS I 57 PHE 0.029 0.002 PHE E 3 TYR 0.024 0.003 TYR L 95 ARG 0.016 0.001 ARG I 14 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 396) hydrogen bonds : angle 4.71243 ( 1185) covalent geometry : bond 0.00450 ( 6496) covalent geometry : angle 0.80595 ( 8840) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 482 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLN cc_start: 0.8947 (pp30) cc_final: 0.8433 (pp30) REVERT: A 65 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8344 (mmt180) REVERT: A 77 ARG cc_start: 0.9145 (mmt90) cc_final: 0.8882 (mmt180) REVERT: A 87 GLU cc_start: 0.9322 (tp30) cc_final: 0.9076 (tp30) REVERT: B 9 TYR cc_start: 0.8924 (t80) cc_final: 0.8624 (t80) REVERT: B 14 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8217 (mtm-85) REVERT: B 63 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8599 (pp30) REVERT: C 7 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8859 (mtmm) REVERT: C 9 TYR cc_start: 0.9327 (t80) cc_final: 0.8931 (t80) REVERT: C 10 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9171 (ptmm) REVERT: C 14 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8227 (mtm-85) REVERT: C 35 THR cc_start: 0.9046 (m) cc_final: 0.8359 (p) REVERT: C 38 ASP cc_start: 0.8671 (m-30) cc_final: 0.8044 (m-30) REVERT: C 41 ARG cc_start: 0.8866 (ttt180) cc_final: 0.8385 (ttp-110) REVERT: C 77 ARG cc_start: 0.9238 (ttm110) cc_final: 0.8888 (mmt90) REVERT: D 10 LYS cc_start: 0.9494 (ptpt) cc_final: 0.8525 (ttpp) REVERT: D 14 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.8300 (mtm-85) REVERT: D 39 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8757 (pp30) REVERT: D 41 ARG cc_start: 0.9159 (ttp-170) cc_final: 0.8830 (ttp-170) REVERT: D 77 ARG cc_start: 0.9254 (ttm110) cc_final: 0.8975 (mmt90) REVERT: E 5 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8513 (tt0) REVERT: E 14 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.8180 (mtm-85) REVERT: E 52 ARG cc_start: 0.9410 (ttm-80) cc_final: 0.8993 (tpp80) REVERT: E 61 THR cc_start: 0.9516 (m) cc_final: 0.9192 (p) REVERT: E 63 GLN cc_start: 0.9662 (OUTLIER) cc_final: 0.9360 (pp30) REVERT: G 1 MET cc_start: 0.8342 (ttm) cc_final: 0.8017 (ttm) REVERT: G 7 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8805 (mtpp) REVERT: G 9 TYR cc_start: 0.9472 (t80) cc_final: 0.9072 (t80) REVERT: G 14 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8224 (mtm-85) REVERT: G 77 ARG cc_start: 0.9293 (tpp80) cc_final: 0.8978 (mmt90) REVERT: I 5 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8628 (mt-10) REVERT: I 9 TYR cc_start: 0.8973 (t80) cc_final: 0.8728 (t80) REVERT: I 38 ASP cc_start: 0.9091 (m-30) cc_final: 0.8755 (m-30) REVERT: I 77 ARG cc_start: 0.9369 (ttm110) cc_final: 0.9112 (mmt-90) REVERT: I 96 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.8001 (mm-40) REVERT: L 7 LYS cc_start: 0.9258 (ptmm) cc_final: 0.8955 (ttpt) REVERT: L 9 TYR cc_start: 0.9352 (t80) cc_final: 0.8882 (t80) REVERT: L 41 ARG cc_start: 0.9010 (ttm170) cc_final: 0.8759 (ttm110) REVERT: L 64 ARG cc_start: 0.9077 (mmm-85) cc_final: 0.8732 (mmm-85) outliers start: 54 outliers final: 44 residues processed: 495 average time/residue: 0.2111 time to fit residues: 130.2287 Evaluate side-chains 521 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 472 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN D 51 ASN E 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 51 ASN I 63 GLN I 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.071167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.062554 restraints weight = 22877.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.064604 restraints weight = 11826.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.066067 restraints weight = 7332.227| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 1.0057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6497 Z= 0.176 Angle : 0.843 16.852 8840 Z= 0.423 Chirality : 0.045 0.184 968 Planarity : 0.006 0.064 1144 Dihedral : 4.615 22.791 880 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.63 % Favored : 97.24 % Rotamer: Outliers : 8.43 % Allowed : 40.55 % Favored : 51.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 760 helix: 0.24 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 1.01 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.001 0.000 HIS E 57 PHE 0.033 0.002 PHE E 3 TYR 0.025 0.002 TYR E 9 ARG 0.011 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 396) hydrogen bonds : angle 4.75817 ( 1185) covalent geometry : bond 0.00416 ( 6496) covalent geometry : angle 0.84259 ( 8840) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 486 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8394 (mtp-110) cc_final: 0.8037 (mtm-85) REVERT: A 37 ARG cc_start: 0.9175 (ttp80) cc_final: 0.8609 (ttp80) REVERT: A 39 GLN cc_start: 0.8942 (pp30) cc_final: 0.8360 (pp30) REVERT: A 41 ARG cc_start: 0.9042 (ttp80) cc_final: 0.8438 (ttm110) REVERT: A 65 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8245 (mmt180) REVERT: A 77 ARG cc_start: 0.9140 (mmt90) cc_final: 0.8873 (mmt180) REVERT: A 87 GLU cc_start: 0.9298 (tp30) cc_final: 0.9049 (tp30) REVERT: B 9 TYR cc_start: 0.8931 (t80) cc_final: 0.8650 (t80) REVERT: B 14 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8357 (mtp-110) REVERT: B 41 ARG cc_start: 0.8486 (ttm110) cc_final: 0.7366 (ptp-170) REVERT: B 63 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8531 (pp30) REVERT: C 9 TYR cc_start: 0.9336 (t80) cc_final: 0.8966 (t80) REVERT: C 10 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9148 (ptmm) REVERT: C 14 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.8248 (mtm-85) REVERT: C 35 THR cc_start: 0.8973 (m) cc_final: 0.8256 (p) REVERT: C 38 ASP cc_start: 0.8617 (m-30) cc_final: 0.8086 (m-30) REVERT: C 41 ARG cc_start: 0.8871 (ttt180) cc_final: 0.8555 (ttp-170) REVERT: C 65 ARG cc_start: 0.8285 (mmt-90) cc_final: 0.8041 (mmt-90) REVERT: C 77 ARG cc_start: 0.9242 (ttm110) cc_final: 0.8879 (mmt90) REVERT: D 9 TYR cc_start: 0.9321 (t80) cc_final: 0.9051 (t80) REVERT: D 14 ARG cc_start: 0.8741 (mtp-110) cc_final: 0.8528 (mtm-85) REVERT: D 39 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8855 (pp30) REVERT: D 41 ARG cc_start: 0.9136 (ttp-170) cc_final: 0.8809 (ttp-170) REVERT: D 54 THR cc_start: 0.9605 (m) cc_final: 0.9361 (p) REVERT: D 71 TYR cc_start: 0.9322 (m-80) cc_final: 0.8981 (m-10) REVERT: D 77 ARG cc_start: 0.9208 (ttm110) cc_final: 0.8923 (mmt90) REVERT: E 5 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8305 (tt0) REVERT: E 9 TYR cc_start: 0.8820 (t80) cc_final: 0.8517 (t80) REVERT: E 14 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8145 (mtm-85) REVERT: E 52 ARG cc_start: 0.9411 (ttm-80) cc_final: 0.9022 (tpp80) REVERT: E 61 THR cc_start: 0.9487 (m) cc_final: 0.9176 (p) REVERT: E 63 GLN cc_start: 0.9616 (OUTLIER) cc_final: 0.9346 (pp30) REVERT: E 87 GLU cc_start: 0.9192 (tp30) cc_final: 0.8977 (tp30) REVERT: G 1 MET cc_start: 0.8314 (ttm) cc_final: 0.7994 (ttm) REVERT: G 9 TYR cc_start: 0.9434 (t80) cc_final: 0.9072 (t80) REVERT: G 14 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8099 (mtm-85) REVERT: G 77 ARG cc_start: 0.9251 (tpp80) cc_final: 0.8975 (mmt90) REVERT: I 5 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8608 (mt-10) REVERT: I 15 ASN cc_start: 0.9256 (m110) cc_final: 0.8954 (m110) REVERT: I 38 ASP cc_start: 0.9083 (m-30) cc_final: 0.8790 (m-30) REVERT: I 77 ARG cc_start: 0.9359 (ttm110) cc_final: 0.9092 (mmt-90) REVERT: L 9 TYR cc_start: 0.9314 (t80) cc_final: 0.8797 (t80) REVERT: L 41 ARG cc_start: 0.9033 (ttm170) cc_final: 0.8781 (ttm110) REVERT: L 59 PHE cc_start: 0.9377 (m-10) cc_final: 0.9173 (m-80) REVERT: L 64 ARG cc_start: 0.9087 (mmm-85) cc_final: 0.8735 (mmm-85) outliers start: 58 outliers final: 46 residues processed: 501 average time/residue: 0.2089 time to fit residues: 130.1295 Evaluate side-chains 531 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 481 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN D 51 ASN D 63 GLN E 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN I 39 GLN I 63 GLN I 96 GLN L 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.061939 restraints weight = 23143.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.063967 restraints weight = 12100.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.065363 restraints weight = 7542.698| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 1.0135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6497 Z= 0.199 Angle : 0.873 16.426 8840 Z= 0.443 Chirality : 0.047 0.183 968 Planarity : 0.006 0.064 1144 Dihedral : 4.740 22.728 880 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.76 % Favored : 97.11 % Rotamer: Outliers : 7.99 % Allowed : 40.70 % Favored : 51.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.30), residues: 760 helix: 0.11 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.48 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.001 0.000 HIS D 57 PHE 0.036 0.003 PHE E 3 TYR 0.027 0.002 TYR D 95 ARG 0.011 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 396) hydrogen bonds : angle 4.93093 ( 1185) covalent geometry : bond 0.00464 ( 6496) covalent geometry : angle 0.87322 ( 8840) Misc. bond : bond 0.00068 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 481 time to evaluate : 0.662 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 14 ARG cc_start: 0.8332 (mtp-110) cc_final: 0.8027 (mtm-85) REVERT: A 37 ARG cc_start: 0.9180 (ttp80) cc_final: 0.8706 (ttp80) REVERT: A 39 GLN cc_start: 0.8947 (pp30) cc_final: 0.8346 (pp30) REVERT: A 41 ARG cc_start: 0.9008 (ttp80) cc_final: 0.8461 (ttm110) REVERT: A 77 ARG cc_start: 0.9122 (mmt90) cc_final: 0.8868 (mmt180) REVERT: A 91 VAL cc_start: 0.9394 (t) cc_final: 0.9193 (p) REVERT: B 9 TYR cc_start: 0.8982 (t80) cc_final: 0.8187 (t80) REVERT: B 14 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8173 (mtm-85) REVERT: B 41 ARG cc_start: 0.8470 (ttm110) cc_final: 0.7317 (ptp-170) REVERT: B 77 ARG cc_start: 0.9147 (mmt180) cc_final: 0.8784 (mmt180) REVERT: C 9 TYR cc_start: 0.9365 (t80) cc_final: 0.9018 (t80) REVERT: C 10 LYS cc_start: 0.9485 (OUTLIER) cc_final: 0.9158 (ptmm) REVERT: C 14 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8245 (mtm-85) REVERT: C 35 THR cc_start: 0.9018 (m) cc_final: 0.8288 (p) REVERT: C 38 ASP cc_start: 0.8534 (m-30) cc_final: 0.8000 (m-30) REVERT: C 41 ARG cc_start: 0.8823 (ttt180) cc_final: 0.8536 (ttp-170) REVERT: C 65 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.8042 (mmt-90) REVERT: D 14 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8476 (mtm-85) REVERT: D 39 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8797 (pp30) REVERT: D 41 ARG cc_start: 0.9116 (ttp-170) cc_final: 0.8801 (ttp-170) REVERT: D 71 TYR cc_start: 0.9269 (m-80) cc_final: 0.9042 (m-80) REVERT: D 77 ARG cc_start: 0.9182 (ttm110) cc_final: 0.8888 (mmt90) REVERT: E 5 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8173 (tt0) REVERT: E 52 ARG cc_start: 0.9351 (ttm-80) cc_final: 0.8955 (tpp80) REVERT: E 61 THR cc_start: 0.9416 (m) cc_final: 0.9151 (p) REVERT: E 63 GLN cc_start: 0.9612 (OUTLIER) cc_final: 0.9331 (pp30) REVERT: E 87 GLU cc_start: 0.9244 (tp30) cc_final: 0.9036 (tp30) REVERT: G 1 MET cc_start: 0.8291 (ttm) cc_final: 0.8031 (ttm) REVERT: G 9 TYR cc_start: 0.9465 (t80) cc_final: 0.9125 (t80) REVERT: G 14 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7939 (mtm-85) REVERT: G 77 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8920 (mmt90) REVERT: I 1 MET cc_start: 0.7889 (tpp) cc_final: 0.7602 (mmp) REVERT: I 5 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8580 (mt-10) REVERT: I 15 ASN cc_start: 0.9204 (m110) cc_final: 0.8874 (m110) REVERT: I 38 ASP cc_start: 0.8931 (m-30) cc_final: 0.8569 (m-30) REVERT: I 64 ARG cc_start: 0.8644 (tpp80) cc_final: 0.8227 (mmt90) REVERT: I 77 ARG cc_start: 0.9321 (ttm110) cc_final: 0.9032 (mmt90) REVERT: L 41 ARG cc_start: 0.9010 (ttm170) cc_final: 0.8762 (ttm110) REVERT: L 64 ARG cc_start: 0.9047 (mmm-85) cc_final: 0.8644 (mmm-85) REVERT: L 87 GLU cc_start: 0.9302 (tp30) cc_final: 0.9076 (tp30) outliers start: 55 outliers final: 39 residues processed: 498 average time/residue: 0.2114 time to fit residues: 130.8406 Evaluate side-chains 517 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 474 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.070435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.061482 restraints weight = 23259.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063591 restraints weight = 12063.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.065031 restraints weight = 7533.995| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 1.0172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6497 Z= 0.184 Angle : 0.894 13.336 8840 Z= 0.452 Chirality : 0.046 0.182 968 Planarity : 0.006 0.059 1144 Dihedral : 4.735 23.017 880 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 6.40 % Allowed : 43.46 % Favored : 50.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.29), residues: 760 helix: 0.03 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.44 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 56 HIS 0.002 0.001 HIS D 57 PHE 0.035 0.003 PHE E 3 TYR 0.032 0.002 TYR D 95 ARG 0.011 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 396) hydrogen bonds : angle 4.98493 ( 1185) covalent geometry : bond 0.00436 ( 6496) covalent geometry : angle 0.89448 ( 8840) Misc. bond : bond 0.00051 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2855.23 seconds wall clock time: 50 minutes 38.93 seconds (3038.93 seconds total)