Starting phenix.real_space_refine on Wed Sep 17 20:49:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j6j_5925/09_2025/3j6j_5925.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j6j_5925/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/3j6j_5925/09_2025/3j6j_5925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j6j_5925/09_2025/3j6j_5925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j6j_5925/09_2025/3j6j_5925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j6j_5925/09_2025/3j6j_5925.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.73, per 1000 atoms: 0.27 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: 0.57 Conformation dependent library (CDL) restraints added in 370.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.12 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: 0.86 Time building geometry restraints manager: 0.75 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: 0.00 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG L 64 TYR 0.026 0.003 TYR G 30 PHE 0.021 0.002 PHE I 72 TRP 0.015 0.002 TRP B 56 HIS 0.019 0.003 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00704 ( 6496) covalent geometry : angle 1.41398 ( 8840) hydrogen bonds : bond 0.23138 ( 396) hydrogen bonds : angle 8.11236 ( 1185) 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 : 0.251 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: 0.8380 (mtp85) REVERT: A 82 VAL cc_start: 0.9016 (t) cc_final: 0.8699 (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: 0.8613 (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: 0.9262 (m-30) REVERT: B 77 ARG cc_start: 0.8949 (mtt-85) cc_final: 0.8474 (mmt90) REVERT: B 83 ASP cc_start: 0.9129 (m-30) cc_final: 0.8783 (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: 0.8557 (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: D 3 PHE cc_start: 0.8490 (t80) cc_final: 0.7682 (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: 0.7797 (m-30) REVERT: D 54 THR cc_start: 0.9471 (m) cc_final: 0.9149 (p) REVERT: E 9 TYR cc_start: 0.9417 (t80) cc_final: 0.9076 (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: 0.8181 (p) REVERT: E 60 ASN cc_start: 0.9546 (t0) cc_final: 0.9280 (m110) REVERT: E 87 GLU cc_start: 0.8960 (tt0) cc_final: 0.8663 (tp30) REVERT: E 90 SER cc_start: 0.9179 (t) cc_final: 0.8824 (p) REVERT: G 5 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7780 (mt-10) REVERT: G 24 VAL cc_start: 0.9330 (t) cc_final: 0.9023 (m) REVERT: G 28 LEU cc_start: 0.9350 (mt) cc_final: 0.9049 (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: 0.9016 (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: 0.8793 (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: 0.8293 (ttm170) outliers start: 42 outliers final: 3 residues processed: 524 average time/residue: 0.1034 time to fit residues: 67.3889 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 : 0.254 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 B 96 GLN C 21 ASN C 57 HIS C 63 GLN C 96 GLN D 21 ASN D 96 GLN E 18 ASN E 39 GLN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS L 21 ASN L 39 GLN L 51 ASN L 60 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.076985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.068562 restraints weight = 22620.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070730 restraints weight = 11445.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072241 restraints weight = 6973.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073314 restraints weight = 4686.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.074160 restraints weight = 3333.287| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6497 Z= 0.209 Angle : 0.750 9.486 8840 Z= 0.396 Chirality : 0.044 0.194 968 Planarity : 0.007 0.056 1144 Dihedral : 5.948 49.217 896 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.45 % Favored : 98.29 % Rotamer: Outliers : 8.43 % Allowed : 23.69 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.28), residues: 760 helix: 1.01 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 1.24 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 64 TYR 0.024 0.003 TYR L 92 PHE 0.032 0.003 PHE G 59 TRP 0.023 0.002 TRP L 56 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6496) covalent geometry : angle 0.75029 ( 8840) hydrogen bonds : bond 0.04794 ( 396) hydrogen bonds : angle 5.00572 ( 1185) Misc. bond : bond 0.00398 ( 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 574 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 516 time to evaluate : 0.291 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: 0.9631 (m) cc_final: 0.9399 (p) REVERT: A 37 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7480 (ttp80) REVERT: A 51 ASN cc_start: 0.8261 (p0) cc_final: 0.7754 (t0) REVERT: A 52 ARG cc_start: 0.8675 (ptp-110) cc_final: 0.8231 (ptp-110) REVERT: A 55 LEU cc_start: 0.8838 (mt) cc_final: 0.8393 (mt) REVERT: A 63 GLN cc_start: 0.9427 (OUTLIER) cc_final: 0.9201 (pp30) REVERT: A 64 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8547 (tpp80) REVERT: A 96 GLN cc_start: 0.7667 (mt0) cc_final: 0.7350 (mm-40) REVERT: B 9 TYR cc_start: 0.9165 (t80) cc_final: 0.8383 (t80) REVERT: B 16 PHE cc_start: 0.8826 (t80) cc_final: 0.7463 (t80) REVERT: B 39 GLN cc_start: 0.9258 (pt0) cc_final: 0.8988 (pt0) REVERT: B 77 ARG cc_start: 0.8694 (mtt-85) cc_final: 0.8437 (mmt-90) REVERT: B 82 VAL cc_start: 0.9087 (m) cc_final: 0.8460 (t) REVERT: B 86 ASP cc_start: 0.8649 (m-30) cc_final: 0.8152 (m-30) REVERT: C 9 TYR cc_start: 0.8904 (t80) cc_final: 0.8587 (t80) REVERT: C 35 THR cc_start: 0.9140 (m) cc_final: 0.8544 (p) REVERT: C 38 ASP cc_start: 0.9111 (m-30) cc_final: 0.8223 (m-30) REVERT: C 96 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: D 7 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8682 (mmmm) REVERT: D 8 THR cc_start: 0.9612 (m) cc_final: 0.9393 (p) REVERT: D 9 TYR cc_start: 0.9169 (t80) cc_final: 0.8935 (t80) REVERT: D 14 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8507 (mtm-85) REVERT: D 16 PHE cc_start: 0.8723 (t80) cc_final: 0.8312 (t80) REVERT: D 42 LEU cc_start: 0.9534 (mt) cc_final: 0.9278 (mm) REVERT: D 53 ASP cc_start: 0.8444 (m-30) cc_final: 0.7514 (m-30) REVERT: D 57 HIS cc_start: 0.9201 (m-70) cc_final: 0.8857 (m-70) REVERT: E 5 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8386 (mt-10) REVERT: E 7 LYS cc_start: 0.9423 (mmtt) cc_final: 0.9092 (mmtm) REVERT: E 16 PHE cc_start: 0.8982 (t80) cc_final: 0.8669 (t80) REVERT: E 23 ASP cc_start: 0.8846 (t70) cc_final: 0.7808 (t0) REVERT: E 51 ASN cc_start: 0.8789 (p0) cc_final: 0.8205 (t0) REVERT: E 77 ARG cc_start: 0.9129 (ttm110) cc_final: 0.8567 (mmt90) REVERT: E 95 TYR cc_start: 0.9188 (m-80) cc_final: 0.8715 (m-80) REVERT: G 5 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7958 (mt-10) REVERT: G 8 THR cc_start: 0.9516 (m) cc_final: 0.9192 (p) REVERT: G 9 TYR cc_start: 0.8940 (t80) cc_final: 0.8624 (t80) REVERT: G 28 LEU cc_start: 0.9436 (mt) cc_final: 0.9230 (mt) REVERT: G 38 ASP cc_start: 0.8663 (m-30) cc_final: 0.8456 (m-30) REVERT: G 59 PHE cc_start: 0.9062 (m-80) cc_final: 0.8453 (m-80) REVERT: G 60 ASN cc_start: 0.9455 (t0) cc_final: 0.9109 (m110) REVERT: G 66 PRO cc_start: 0.9493 (Cg_exo) cc_final: 0.9248 (Cg_endo) REVERT: G 76 LEU cc_start: 0.9676 (mt) cc_final: 0.9459 (mt) REVERT: G 77 ARG cc_start: 0.9335 (tpp80) cc_final: 0.8940 (mmt90) REVERT: I 5 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8252 (mt-10) REVERT: I 9 TYR cc_start: 0.9193 (t80) cc_final: 0.8961 (t80) REVERT: I 14 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8264 (mtm-85) REVERT: I 38 ASP cc_start: 0.9244 (m-30) cc_final: 0.8765 (p0) REVERT: I 41 ARG cc_start: 0.8848 (mmm-85) cc_final: 0.8569 (mmm-85) REVERT: I 64 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8434 (tpp80) REVERT: I 77 ARG cc_start: 0.9262 (ttm110) cc_final: 0.8750 (mmt90) REVERT: I 90 SER cc_start: 0.9447 (t) cc_final: 0.9214 (p) REVERT: I 96 GLN cc_start: 0.8068 (mt0) cc_final: 0.7562 (tp40) REVERT: L 5 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8507 (mt-10) REVERT: L 8 THR cc_start: 0.9690 (m) cc_final: 0.9463 (p) REVERT: L 21 ASN cc_start: 0.8947 (m-40) cc_final: 0.8694 (m-40) REVERT: L 23 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8132 (t70) REVERT: L 26 GLU cc_start: 0.8322 (mp0) cc_final: 0.7560 (mp0) REVERT: L 37 ARG cc_start: 0.8547 (tmm-80) cc_final: 0.8018 (tmt170) REVERT: L 53 ASP cc_start: 0.8822 (m-30) cc_final: 0.8431 (m-30) REVERT: L 59 PHE cc_start: 0.9418 (m-80) cc_final: 0.8775 (m-80) REVERT: L 86 ASP cc_start: 0.8060 (m-30) cc_final: 0.7843 (m-30) REVERT: L 87 GLU cc_start: 0.8746 (tp30) cc_final: 0.8454 (tp30) outliers start: 58 outliers final: 31 residues processed: 527 average time/residue: 0.0991 time to fit residues: 64.9815 Evaluate side-chains 520 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 485 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 63 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 27 ILE 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 C residue 63 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain D residue 14 ARG 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 91 VAL Chi-restraints excluded: chain I residue 6 ASP 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 18 ASN 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 62 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 96 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 L 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066850 restraints weight = 22575.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068997 restraints weight = 11304.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070477 restraints weight = 6840.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.071563 restraints weight = 4552.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072319 restraints weight = 3222.861| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.7743 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= 0.157 Angle : 0.708 8.964 8840 Z= 0.366 Chirality : 0.043 0.220 968 Planarity : 0.006 0.054 1144 Dihedral : 4.577 18.592 880 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.32 % Favored : 98.42 % Rotamer: Outliers : 9.16 % Allowed : 29.07 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.29), residues: 760 helix: 0.86 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.25 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 43 TYR 0.020 0.002 TYR A 92 PHE 0.027 0.003 PHE G 59 TRP 0.018 0.001 TRP L 56 HIS 0.001 0.000 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6496) covalent geometry : angle 0.70805 ( 8840) hydrogen bonds : bond 0.04153 ( 396) hydrogen bonds : angle 4.60333 ( 1185) Misc. bond : bond 0.00009 ( 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 563 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 500 time to evaluate : 0.240 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: 0.9692 (m) cc_final: 0.9487 (p) REVERT: A 14 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.8050 (mtm-85) REVERT: A 43 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.9035 (mtt90) REVERT: A 51 ASN cc_start: 0.8157 (p0) cc_final: 0.7956 (t0) REVERT: A 52 ARG cc_start: 0.8627 (ptp-110) cc_final: 0.8354 (ptp-110) REVERT: A 55 LEU cc_start: 0.8666 (mt) cc_final: 0.8167 (mt) REVERT: B 9 TYR cc_start: 0.9131 (t80) cc_final: 0.8575 (t80) REVERT: B 14 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8228 (mtp-110) REVERT: B 38 ASP cc_start: 0.8754 (m-30) cc_final: 0.8150 (m-30) REVERT: B 53 ASP cc_start: 0.8286 (m-30) cc_final: 0.8057 (m-30) REVERT: B 63 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8838 (pp30) REVERT: B 82 VAL cc_start: 0.9098 (m) cc_final: 0.8708 (t) REVERT: B 93 GLN cc_start: 0.9297 (tm-30) cc_final: 0.9047 (tm-30) REVERT: C 9 TYR cc_start: 0.8998 (t80) cc_final: 0.8706 (t80) REVERT: C 35 THR cc_start: 0.8951 (m) cc_final: 0.8437 (p) REVERT: C 38 ASP cc_start: 0.8876 (m-30) cc_final: 0.7988 (m-30) REVERT: C 41 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8337 (ttp-110) REVERT: C 54 THR cc_start: 0.9456 (t) cc_final: 0.8993 (m) REVERT: C 60 ASN cc_start: 0.9464 (t0) cc_final: 0.9091 (m110) REVERT: C 80 GLU cc_start: 0.8418 (mp0) cc_final: 0.8180 (mp0) REVERT: C 86 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8514 (p0) REVERT: C 96 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: D 5 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8050 (mt-10) REVERT: D 7 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8535 (mmmm) REVERT: D 10 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8999 (ttpp) REVERT: D 41 ARG cc_start: 0.8723 (ttp-170) cc_final: 0.8305 (ttp-170) REVERT: D 43 ARG cc_start: 0.8936 (mtp180) cc_final: 0.8712 (mtt180) REVERT: D 53 ASP cc_start: 0.8496 (m-30) cc_final: 0.8192 (m-30) REVERT: D 57 HIS cc_start: 0.9140 (m-70) cc_final: 0.8873 (m-70) REVERT: D 77 ARG cc_start: 0.9168 (ttm110) cc_final: 0.8776 (mmt90) REVERT: D 95 TYR cc_start: 0.8886 (m-80) cc_final: 0.8084 (m-80) REVERT: E 7 LYS cc_start: 0.9349 (mmtt) cc_final: 0.9025 (mmtm) REVERT: E 16 PHE cc_start: 0.9062 (t80) cc_final: 0.8785 (t80) REVERT: E 77 ARG cc_start: 0.9144 (ttm110) cc_final: 0.8778 (mpt180) REVERT: E 95 TYR cc_start: 0.9172 (m-80) cc_final: 0.8458 (m-80) REVERT: E 96 GLN cc_start: 0.8657 (mt0) cc_final: 0.8315 (tp40) REVERT: G 8 THR cc_start: 0.9640 (m) cc_final: 0.9407 (p) REVERT: G 9 TYR cc_start: 0.9185 (t80) cc_final: 0.8817 (t80) REVERT: G 14 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8112 (mtm-85) REVERT: G 24 VAL cc_start: 0.9475 (m) cc_final: 0.9166 (p) REVERT: G 27 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9244 (tt) REVERT: G 76 LEU cc_start: 0.9700 (mt) cc_final: 0.9478 (mt) REVERT: G 77 ARG cc_start: 0.9310 (tpp80) cc_final: 0.8965 (mmt90) REVERT: I 9 TYR cc_start: 0.9042 (t80) cc_final: 0.8742 (t80) REVERT: I 14 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7960 (mtm-85) REVERT: I 37 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.6462 (ptm-80) REVERT: I 38 ASP cc_start: 0.9225 (m-30) cc_final: 0.8636 (p0) REVERT: I 41 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8337 (mmm-85) REVERT: I 77 ARG cc_start: 0.9201 (ttm110) cc_final: 0.8836 (mmt90) REVERT: I 95 TYR cc_start: 0.9218 (m-80) cc_final: 0.8874 (m-80) REVERT: I 96 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8109 (tp40) REVERT: L 8 THR cc_start: 0.9744 (m) cc_final: 0.9511 (p) REVERT: L 14 ARG cc_start: 0.8048 (ttp-110) cc_final: 0.7538 (mtm-85) REVERT: L 21 ASN cc_start: 0.9006 (m-40) cc_final: 0.8797 (m110) REVERT: L 23 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8057 (t70) REVERT: L 41 ARG cc_start: 0.8488 (ttm170) cc_final: 0.8176 (ttm110) REVERT: L 64 ARG cc_start: 0.9084 (mmm-85) cc_final: 0.8652 (mmm-85) REVERT: L 77 ARG cc_start: 0.8906 (mmt90) cc_final: 0.8585 (mmt180) REVERT: L 82 VAL cc_start: 0.8978 (p) cc_final: 0.8548 (t) REVERT: L 86 ASP cc_start: 0.8100 (m-30) cc_final: 0.7716 (m-30) REVERT: L 87 GLU cc_start: 0.8825 (tp30) cc_final: 0.8529 (tp30) outliers start: 63 outliers final: 34 residues processed: 516 average time/residue: 0.0977 time to fit residues: 63.0625 Evaluate side-chains 525 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 483 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 25 VAL 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 10 LYS Chi-restraints excluded: chain D residue 14 ARG 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 E residue 24 VAL Chi-restraints excluded: chain E residue 27 ILE 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 48 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 24 VAL 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 51 ASN 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 23 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 63 GLN C 96 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN G 18 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.071078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.062952 restraints weight = 23139.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.064983 restraints weight = 11556.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.066347 restraints weight = 7110.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067405 restraints weight = 4856.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068167 restraints weight = 3492.195| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.8452 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= 0.193 Angle : 0.712 9.829 8840 Z= 0.370 Chirality : 0.044 0.188 968 Planarity : 0.006 0.052 1144 Dihedral : 4.563 19.054 880 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.71 % Favored : 98.16 % Rotamer: Outliers : 9.45 % Allowed : 32.27 % Favored : 58.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.30), residues: 760 helix: 0.70 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.62 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 64 TYR 0.022 0.002 TYR C 95 PHE 0.024 0.003 PHE D 16 TRP 0.021 0.002 TRP L 56 HIS 0.001 0.000 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 6496) covalent geometry : angle 0.71209 ( 8840) hydrogen bonds : bond 0.04147 ( 396) hydrogen bonds : angle 4.48668 ( 1185) Misc. bond : bond 0.00137 ( 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 563 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 498 time to evaluate : 0.183 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 5 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7979 (tt0) REVERT: A 14 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: A 41 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8450 (ttm110) REVERT: A 43 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8953 (mtt90) REVERT: A 51 ASN cc_start: 0.8247 (p0) cc_final: 0.7617 (t0) REVERT: A 52 ARG cc_start: 0.8816 (ptp-110) cc_final: 0.8543 (ptp-110) REVERT: A 55 LEU cc_start: 0.8726 (mt) cc_final: 0.8180 (mt) REVERT: A 63 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9177 (pp30) REVERT: B 9 TYR cc_start: 0.9163 (t80) cc_final: 0.8725 (t80) REVERT: B 14 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8221 (mtm-85) REVERT: B 41 ARG cc_start: 0.8906 (ttp-110) cc_final: 0.8418 (ptp-170) REVERT: B 53 ASP cc_start: 0.8531 (m-30) cc_final: 0.7839 (m-30) REVERT: B 63 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8727 (tt0) REVERT: B 77 ARG cc_start: 0.8795 (mmt-90) cc_final: 0.8531 (mmt-90) REVERT: B 82 VAL cc_start: 0.8966 (m) cc_final: 0.8437 (t) REVERT: B 86 ASP cc_start: 0.8536 (m-30) cc_final: 0.8220 (m-30) REVERT: C 9 TYR cc_start: 0.9101 (t80) cc_final: 0.8724 (t80) REVERT: C 35 THR cc_start: 0.9125 (m) cc_final: 0.8573 (p) REVERT: C 38 ASP cc_start: 0.8954 (m-30) cc_final: 0.8148 (m-30) REVERT: C 41 ARG cc_start: 0.8661 (ttm110) cc_final: 0.8058 (ttp-170) REVERT: C 52 ARG cc_start: 0.9021 (mtp-110) cc_final: 0.8681 (mtp85) REVERT: C 54 THR cc_start: 0.9535 (t) cc_final: 0.9117 (m) REVERT: C 86 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8512 (p0) REVERT: D 14 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8141 (mtm-85) REVERT: D 35 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8741 (p) REVERT: D 41 ARG cc_start: 0.8950 (ttp-170) cc_final: 0.8446 (ttp-110) REVERT: D 57 HIS cc_start: 0.9168 (m-70) cc_final: 0.8883 (m-70) REVERT: D 77 ARG cc_start: 0.9245 (ttm110) cc_final: 0.8904 (mmt90) REVERT: E 7 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9012 (mmtm) REVERT: E 51 ASN cc_start: 0.8928 (p0) cc_final: 0.8582 (p0) REVERT: E 77 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8850 (mmt90) REVERT: E 95 TYR cc_start: 0.9297 (m-80) cc_final: 0.8281 (m-80) REVERT: E 96 GLN cc_start: 0.8790 (mt0) cc_final: 0.8436 (tp40) REVERT: G 1 MET cc_start: 0.8144 (ttm) cc_final: 0.7908 (ttm) REVERT: G 9 TYR cc_start: 0.9336 (t80) cc_final: 0.9110 (t80) REVERT: G 14 ARG cc_start: 0.8570 (mtp-110) cc_final: 0.8240 (mtp-110) REVERT: G 24 VAL cc_start: 0.9416 (m) cc_final: 0.8810 (p) REVERT: G 27 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9175 (tt) REVERT: G 28 LEU cc_start: 0.9564 (mt) cc_final: 0.9334 (mt) REVERT: G 76 LEU cc_start: 0.9713 (mt) cc_final: 0.9392 (mt) REVERT: G 77 ARG cc_start: 0.9388 (tpp80) cc_final: 0.9044 (mmt90) REVERT: I 14 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8005 (mtm-85) REVERT: I 38 ASP cc_start: 0.9111 (m-30) cc_final: 0.8903 (p0) REVERT: I 41 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8524 (mmm-85) REVERT: I 46 CYS cc_start: 0.9665 (OUTLIER) cc_final: 0.9416 (t) REVERT: I 77 ARG cc_start: 0.9314 (ttm110) cc_final: 0.8975 (mmt90) REVERT: I 95 TYR cc_start: 0.9234 (m-80) cc_final: 0.8958 (m-80) REVERT: L 10 LYS cc_start: 0.9361 (ttpp) cc_final: 0.9155 (ttpp) REVERT: L 14 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.7544 (mtm-85) REVERT: L 21 ASN cc_start: 0.9069 (m-40) cc_final: 0.8820 (m-40) REVERT: L 64 ARG cc_start: 0.9100 (mmm-85) cc_final: 0.8711 (mmm-85) REVERT: L 82 VAL cc_start: 0.8963 (p) cc_final: 0.8685 (t) REVERT: L 87 GLU cc_start: 0.8955 (tp30) cc_final: 0.8663 (tp30) outliers start: 65 outliers final: 36 residues processed: 508 average time/residue: 0.0989 time to fit residues: 63.1782 Evaluate side-chains 526 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 482 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 43 ARG 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 A residue 63 GLN Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU 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 14 ARG Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 51 ASN 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 6 ASP Chi-restraints excluded: chain I residue 14 ARG 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 52 ARG 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 62 LEU Chi-restraints excluded: chain L residue 90 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 58 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 63 GLN C 96 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN G 18 ASN G 51 ASN ** I 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 = 0.3115 r_free = 0.3115 target = 0.070997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062486 restraints weight = 23058.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.064570 restraints weight = 12023.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065961 restraints weight = 7538.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066993 restraints weight = 5191.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067808 restraints weight = 3792.955| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.8882 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= 0.154 Angle : 0.707 9.559 8840 Z= 0.367 Chirality : 0.043 0.186 968 Planarity : 0.006 0.094 1144 Dihedral : 4.459 20.257 880 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.37 % Favored : 97.50 % Rotamer: Outliers : 7.41 % Allowed : 35.90 % Favored : 56.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.30), residues: 760 helix: 0.59 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.57 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 37 TYR 0.028 0.002 TYR A 92 PHE 0.029 0.002 PHE B 16 TRP 0.017 0.001 TRP G 56 HIS 0.001 0.000 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6496) covalent geometry : angle 0.70711 ( 8840) hydrogen bonds : bond 0.04054 ( 396) hydrogen bonds : angle 4.34280 ( 1185) Misc. bond : bond 0.00073 ( 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 546 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 495 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8007 (tt0) REVERT: A 14 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.7978 (mtm-85) REVERT: A 41 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8369 (ttm110) REVERT: A 43 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8956 (mtt90) REVERT: A 51 ASN cc_start: 0.8178 (p0) cc_final: 0.7522 (t0) REVERT: A 52 ARG cc_start: 0.8650 (ptp-110) cc_final: 0.8361 (ptp-110) REVERT: A 55 LEU cc_start: 0.8658 (mt) cc_final: 0.8134 (mt) REVERT: B 14 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8218 (mtm-85) REVERT: B 17 SER cc_start: 0.9503 (p) cc_final: 0.9229 (m) REVERT: B 41 ARG cc_start: 0.8819 (ttp-110) cc_final: 0.8236 (ptp-170) REVERT: B 53 ASP cc_start: 0.8495 (m-30) cc_final: 0.8112 (m-30) REVERT: B 63 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8456 (pp30) REVERT: B 82 VAL cc_start: 0.9022 (m) cc_final: 0.8558 (t) REVERT: C 9 TYR cc_start: 0.9190 (t80) cc_final: 0.8835 (t80) REVERT: C 35 THR cc_start: 0.9100 (m) cc_final: 0.8713 (p) REVERT: C 38 ASP cc_start: 0.8770 (m-30) cc_final: 0.7881 (m-30) REVERT: C 41 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8189 (ttm110) REVERT: C 54 THR cc_start: 0.9415 (t) cc_final: 0.9019 (m) REVERT: C 72 PHE cc_start: 0.9534 (t80) cc_final: 0.9306 (t80) REVERT: C 77 ARG cc_start: 0.9080 (ttm110) cc_final: 0.8816 (mmt-90) REVERT: C 96 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7558 (tp-100) REVERT: D 14 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8296 (mtp-110) REVERT: D 41 ARG cc_start: 0.8973 (ttp-170) cc_final: 0.8531 (ttp-110) REVERT: D 77 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8836 (mmt90) REVERT: D 87 GLU cc_start: 0.9135 (tp30) cc_final: 0.8879 (tp30) REVERT: E 7 LYS cc_start: 0.9412 (mmtt) cc_final: 0.8982 (mmtm) REVERT: E 51 ASN cc_start: 0.8862 (p0) cc_final: 0.8501 (p0) REVERT: E 61 THR cc_start: 0.9526 (m) cc_final: 0.9238 (p) REVERT: E 70 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8858 (mp0) REVERT: E 95 TYR cc_start: 0.9238 (m-80) cc_final: 0.8291 (m-80) REVERT: G 1 MET cc_start: 0.8292 (ttm) cc_final: 0.7897 (ttm) REVERT: G 3 PHE cc_start: 0.9099 (t80) cc_final: 0.8798 (t80) REVERT: G 9 TYR cc_start: 0.9278 (t80) cc_final: 0.8980 (t80) REVERT: G 14 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8218 (mtp-110) REVERT: G 24 VAL cc_start: 0.9318 (m) cc_final: 0.8976 (p) REVERT: G 28 LEU cc_start: 0.9652 (mt) cc_final: 0.9440 (mt) REVERT: G 76 LEU cc_start: 0.9687 (mt) cc_final: 0.9478 (mt) REVERT: I 14 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7988 (mtm-85) REVERT: I 37 ARG cc_start: 0.8644 (ptm-80) cc_final: 0.8424 (ptm-80) REVERT: I 38 ASP cc_start: 0.9072 (m-30) cc_final: 0.8821 (m-30) REVERT: I 41 ARG cc_start: 0.8899 (mmm-85) cc_final: 0.8334 (mmm-85) REVERT: I 46 CYS cc_start: 0.9557 (t) cc_final: 0.9340 (t) REVERT: I 60 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8868 (m110) REVERT: L 10 LYS cc_start: 0.9349 (ttpp) cc_final: 0.8518 (ttpp) REVERT: L 14 ARG cc_start: 0.8233 (ttp-110) cc_final: 0.7882 (mtm-85) REVERT: L 21 ASN cc_start: 0.8960 (m-40) cc_final: 0.8683 (m-40) REVERT: L 26 GLU cc_start: 0.8319 (mp0) cc_final: 0.8112 (mp0) REVERT: L 38 ASP cc_start: 0.9004 (m-30) cc_final: 0.8675 (m-30) REVERT: L 41 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8308 (ttp-170) REVERT: L 64 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8675 (mmm-85) outliers start: 51 outliers final: 34 residues processed: 506 average time/residue: 0.1022 time to fit residues: 64.3360 Evaluate side-chains 518 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 479 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 43 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU 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 96 GLN Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ASN 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 6 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 46 CYS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 90 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN C 96 GLN D 63 GLN E 39 GLN G 18 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN I 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.061190 restraints weight = 22883.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.063280 restraints weight = 11989.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.064691 restraints weight = 7531.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.065734 restraints weight = 5205.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.066582 restraints weight = 3850.187| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.9228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6497 Z= 0.171 Angle : 0.734 9.563 8840 Z= 0.386 Chirality : 0.044 0.187 968 Planarity : 0.006 0.104 1144 Dihedral : 4.471 20.904 880 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.37 % Favored : 97.50 % Rotamer: Outliers : 7.41 % Allowed : 38.66 % Favored : 53.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.30), residues: 760 helix: 0.54 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.76 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 14 TYR 0.028 0.002 TYR L 95 PHE 0.027 0.002 PHE D 16 TRP 0.012 0.001 TRP L 56 HIS 0.001 0.000 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6496) covalent geometry : angle 0.73387 ( 8840) hydrogen bonds : bond 0.04151 ( 396) hydrogen bonds : angle 4.42768 ( 1185) Misc. bond : bond 0.00084 ( 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 533 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 482 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8191 (tt0) REVERT: A 14 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: A 30 TYR cc_start: 0.9223 (m-10) cc_final: 0.8914 (m-10) REVERT: A 41 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8471 (ttm110) REVERT: A 43 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.9098 (mtt90) REVERT: A 51 ASN cc_start: 0.8229 (p0) cc_final: 0.7474 (t0) REVERT: A 52 ARG cc_start: 0.8718 (ptp-110) cc_final: 0.8459 (ptp-110) REVERT: A 55 LEU cc_start: 0.8752 (mt) cc_final: 0.8152 (mt) REVERT: A 77 ARG cc_start: 0.9163 (mmt90) cc_final: 0.8889 (mmt180) REVERT: A 87 GLU cc_start: 0.9270 (tp30) cc_final: 0.9048 (tp30) REVERT: B 14 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8252 (mtm-85) REVERT: B 41 ARG cc_start: 0.8848 (ttp-110) cc_final: 0.8623 (ttm110) REVERT: B 53 ASP cc_start: 0.8695 (m-30) cc_final: 0.8353 (m-30) REVERT: B 63 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8499 (pp30) REVERT: B 77 ARG cc_start: 0.8776 (mmt180) cc_final: 0.8372 (mmt180) REVERT: B 84 LEU cc_start: 0.9267 (tp) cc_final: 0.9004 (tp) REVERT: C 9 TYR cc_start: 0.9192 (t80) cc_final: 0.8909 (t80) REVERT: C 35 THR cc_start: 0.9216 (m) cc_final: 0.8773 (p) REVERT: C 38 ASP cc_start: 0.8885 (m-30) cc_final: 0.8192 (m-30) REVERT: C 39 GLN cc_start: 0.9418 (pt0) cc_final: 0.9170 (tt0) REVERT: C 40 ASP cc_start: 0.9157 (t0) cc_final: 0.8712 (t0) REVERT: C 41 ARG cc_start: 0.8698 (ttm110) cc_final: 0.8413 (ttm110) REVERT: C 54 THR cc_start: 0.9478 (t) cc_final: 0.9100 (m) REVERT: C 77 ARG cc_start: 0.9243 (ttm110) cc_final: 0.8898 (mmt90) REVERT: C 96 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7522 (tp-100) REVERT: D 41 ARG cc_start: 0.9126 (ttp-170) cc_final: 0.8706 (ttp-110) REVERT: D 55 LEU cc_start: 0.9491 (tp) cc_final: 0.9250 (tp) REVERT: D 59 PHE cc_start: 0.8918 (m-10) cc_final: 0.8717 (m-80) REVERT: D 63 GLN cc_start: 0.9670 (OUTLIER) cc_final: 0.9316 (pp30) REVERT: D 77 ARG cc_start: 0.9265 (ttm110) cc_final: 0.9020 (mmt90) REVERT: D 87 GLU cc_start: 0.9212 (tp30) cc_final: 0.8883 (tp30) REVERT: E 14 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.8104 (mtm110) REVERT: E 26 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8799 (mp0) REVERT: E 61 THR cc_start: 0.9519 (m) cc_final: 0.9231 (p) REVERT: E 70 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9067 (mp0) REVERT: G 1 MET cc_start: 0.8263 (ttm) cc_final: 0.7958 (ttm) REVERT: G 9 TYR cc_start: 0.9299 (t80) cc_final: 0.9041 (t80) REVERT: G 14 ARG cc_start: 0.8617 (mtp-110) cc_final: 0.8232 (mtp-110) REVERT: G 24 VAL cc_start: 0.9279 (m) cc_final: 0.8977 (p) REVERT: G 77 ARG cc_start: 0.9097 (mmt90) cc_final: 0.8855 (mmt90) REVERT: I 1 MET cc_start: 0.8232 (tpp) cc_final: 0.7840 (mmt) REVERT: I 14 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7989 (mtm-85) REVERT: I 38 ASP cc_start: 0.9218 (m-30) cc_final: 0.8865 (m-30) REVERT: I 41 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8388 (mmm-85) REVERT: I 46 CYS cc_start: 0.9689 (t) cc_final: 0.9452 (t) REVERT: I 60 ASN cc_start: 0.9422 (OUTLIER) cc_final: 0.9127 (m110) REVERT: L 14 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7897 (mtm-85) REVERT: L 21 ASN cc_start: 0.9049 (m-40) cc_final: 0.8758 (m-40) REVERT: L 64 ARG cc_start: 0.9147 (mmm-85) cc_final: 0.8758 (mmm-85) REVERT: L 77 ARG cc_start: 0.9005 (mmt90) cc_final: 0.8666 (mmt180) outliers start: 51 outliers final: 35 residues processed: 493 average time/residue: 0.0990 time to fit residues: 61.1928 Evaluate side-chains 513 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 473 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 ARG 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 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 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 96 GLN Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 7 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN E 39 GLN G 18 ASN G 51 ASN I 18 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 = 0.3102 r_free = 0.3102 target = 0.070951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062494 restraints weight = 22853.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.064486 restraints weight = 11896.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065899 restraints weight = 7436.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.066970 restraints weight = 5114.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.067772 restraints weight = 3733.212| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.9434 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= 0.163 Angle : 0.748 9.726 8840 Z= 0.389 Chirality : 0.044 0.186 968 Planarity : 0.005 0.075 1144 Dihedral : 4.479 20.397 880 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.50 % Favored : 97.37 % Rotamer: Outliers : 7.12 % Allowed : 39.24 % Favored : 53.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.30), residues: 760 helix: 0.47 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.66 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 37 TYR 0.023 0.002 TYR I 9 PHE 0.025 0.002 PHE G 3 TRP 0.012 0.001 TRP L 56 HIS 0.000 0.000 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6496) covalent geometry : angle 0.74836 ( 8840) hydrogen bonds : bond 0.04063 ( 396) hydrogen bonds : angle 4.50601 ( 1185) Misc. bond : bond 0.00087 ( 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 526 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 477 time to evaluate : 0.250 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: 0.8706 (mt-10) cc_final: 0.8143 (tt0) REVERT: A 30 TYR cc_start: 0.9243 (m-10) cc_final: 0.9018 (m-10) REVERT: A 39 GLN cc_start: 0.9184 (pt0) cc_final: 0.8387 (pp30) REVERT: A 41 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8392 (ttm110) REVERT: A 43 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8822 (mtt90) REVERT: A 51 ASN cc_start: 0.8215 (p0) cc_final: 0.7905 (p0) REVERT: A 55 LEU cc_start: 0.8662 (mt) cc_final: 0.8434 (mt) REVERT: A 65 ARG cc_start: 0.8323 (mmt180) cc_final: 0.8049 (mmt180) REVERT: A 77 ARG cc_start: 0.9127 (mmt90) cc_final: 0.8919 (mmt180) REVERT: A 87 GLU cc_start: 0.9253 (tp30) cc_final: 0.9004 (tp30) REVERT: B 14 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8247 (mtm-85) REVERT: B 41 ARG cc_start: 0.8780 (ttp-110) cc_final: 0.8571 (ttm110) REVERT: B 53 ASP cc_start: 0.8593 (m-30) cc_final: 0.8258 (m-30) REVERT: B 77 ARG cc_start: 0.8692 (mmt180) cc_final: 0.8397 (mmt180) REVERT: B 87 GLU cc_start: 0.9175 (tp30) cc_final: 0.8773 (tp30) REVERT: C 7 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8782 (mtmm) REVERT: C 9 TYR cc_start: 0.9224 (t80) cc_final: 0.9013 (t80) REVERT: C 14 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8090 (mtm-85) REVERT: C 35 THR cc_start: 0.9214 (m) cc_final: 0.8804 (p) REVERT: C 38 ASP cc_start: 0.8797 (m-30) cc_final: 0.7957 (m-30) REVERT: C 41 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8285 (ttm110) REVERT: C 77 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8877 (mmt90) REVERT: C 96 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: D 14 ARG cc_start: 0.8617 (mtp-110) cc_final: 0.8350 (mtm-85) REVERT: D 41 ARG cc_start: 0.9089 (ttp-170) cc_final: 0.8686 (ttp-110) REVERT: D 77 ARG cc_start: 0.9204 (ttm110) cc_final: 0.9000 (mmt90) REVERT: D 87 GLU cc_start: 0.9151 (tp30) cc_final: 0.8902 (tp30) REVERT: E 5 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8446 (tt0) REVERT: E 14 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.8074 (mtm110) REVERT: E 52 ARG cc_start: 0.9289 (ttm-80) cc_final: 0.8977 (tpp80) REVERT: E 61 THR cc_start: 0.9528 (m) cc_final: 0.9217 (p) REVERT: G 1 MET cc_start: 0.8218 (ttm) cc_final: 0.7840 (ttm) REVERT: G 9 TYR cc_start: 0.9353 (t80) cc_final: 0.8918 (t80) REVERT: G 14 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8182 (mtp-110) REVERT: G 24 VAL cc_start: 0.9197 (m) cc_final: 0.8987 (p) REVERT: G 76 LEU cc_start: 0.9648 (mt) cc_final: 0.9390 (mp) REVERT: I 1 MET cc_start: 0.8284 (tpp) cc_final: 0.7948 (mmp) REVERT: I 9 TYR cc_start: 0.9054 (t80) cc_final: 0.8732 (t80) REVERT: I 14 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7973 (mtm-85) REVERT: I 38 ASP cc_start: 0.9081 (m-30) cc_final: 0.8796 (m-30) REVERT: I 41 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8560 (mmm-85) REVERT: I 46 CYS cc_start: 0.9638 (t) cc_final: 0.9435 (t) REVERT: I 60 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.9122 (m110) REVERT: L 14 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.8016 (mtm-85) REVERT: L 21 ASN cc_start: 0.8945 (m-40) cc_final: 0.8626 (m-40) REVERT: L 64 ARG cc_start: 0.9093 (mmm-85) cc_final: 0.8726 (mmm-85) REVERT: L 77 ARG cc_start: 0.8965 (mmt90) cc_final: 0.8706 (mmt180) outliers start: 49 outliers final: 33 residues processed: 489 average time/residue: 0.0985 time to fit residues: 60.2578 Evaluate side-chains 502 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 464 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 43 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU 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 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 96 GLN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 10 LYS 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 12 ILE Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 63 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN C 96 GLN G 18 ASN G 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.071075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.062280 restraints weight = 22629.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.064331 restraints weight = 11745.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065780 restraints weight = 7361.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066872 restraints weight = 5081.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067648 restraints weight = 3712.378| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.9690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6497 Z= 0.162 Angle : 0.794 9.941 8840 Z= 0.410 Chirality : 0.044 0.187 968 Planarity : 0.005 0.061 1144 Dihedral : 4.469 20.479 880 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.89 % Favored : 96.97 % Rotamer: Outliers : 5.67 % Allowed : 42.15 % Favored : 52.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.30), residues: 760 helix: 0.45 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.44 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 77 TYR 0.023 0.002 TYR D 92 PHE 0.024 0.002 PHE G 16 TRP 0.011 0.001 TRP L 56 HIS 0.001 0.000 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6496) covalent geometry : angle 0.79380 ( 8840) hydrogen bonds : bond 0.03974 ( 396) hydrogen bonds : angle 4.56577 ( 1185) Misc. bond : bond 0.00067 ( 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 520 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 481 time to evaluate : 0.246 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 5 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8198 (tt0) REVERT: A 14 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8237 (mtp-110) REVERT: A 37 ARG cc_start: 0.9220 (ttp80) cc_final: 0.7937 (ttp80) REVERT: A 39 GLN cc_start: 0.8851 (pt0) cc_final: 0.8496 (pp30) REVERT: A 41 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8024 (ttm110) REVERT: A 43 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8959 (mtt90) REVERT: A 51 ASN cc_start: 0.8178 (p0) cc_final: 0.7768 (p0) REVERT: A 55 LEU cc_start: 0.8792 (mt) cc_final: 0.8543 (mt) REVERT: A 77 ARG cc_start: 0.9158 (mmt90) cc_final: 0.8910 (mmt180) REVERT: A 82 VAL cc_start: 0.9244 (t) cc_final: 0.8966 (t) REVERT: A 86 ASP cc_start: 0.8959 (p0) cc_final: 0.8756 (p0) REVERT: A 87 GLU cc_start: 0.9268 (tp30) cc_final: 0.8953 (tp30) REVERT: B 14 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8400 (mtp-110) REVERT: B 26 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 41 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.8355 (ttm110) REVERT: B 53 ASP cc_start: 0.8607 (m-30) cc_final: 0.8303 (m-30) REVERT: B 77 ARG cc_start: 0.8696 (mmt180) cc_final: 0.8402 (mmt180) REVERT: B 87 GLU cc_start: 0.9217 (tp30) cc_final: 0.8821 (tp30) REVERT: C 9 TYR cc_start: 0.9181 (t80) cc_final: 0.8973 (t80) REVERT: C 14 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.8154 (mtm-85) REVERT: C 21 ASN cc_start: 0.8800 (m-40) cc_final: 0.7794 (t0) REVERT: C 39 GLN cc_start: 0.9399 (pt0) cc_final: 0.9171 (tt0) REVERT: C 41 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8280 (ttm110) REVERT: C 77 ARG cc_start: 0.9174 (ttm110) cc_final: 0.8863 (mmt90) REVERT: C 96 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: D 9 TYR cc_start: 0.9232 (t80) cc_final: 0.8830 (t80) REVERT: D 41 ARG cc_start: 0.9136 (ttp-170) cc_final: 0.8754 (ttp-110) REVERT: D 91 VAL cc_start: 0.9287 (t) cc_final: 0.9028 (p) REVERT: E 5 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8505 (tt0) REVERT: E 9 TYR cc_start: 0.8969 (t80) cc_final: 0.8704 (t80) REVERT: E 52 ARG cc_start: 0.9322 (ttm-80) cc_final: 0.9046 (tpp80) REVERT: E 61 THR cc_start: 0.9509 (m) cc_final: 0.9225 (p) REVERT: G 1 MET cc_start: 0.8088 (ttm) cc_final: 0.7733 (ttm) REVERT: G 9 TYR cc_start: 0.9320 (t80) cc_final: 0.8965 (t80) REVERT: G 14 ARG cc_start: 0.8563 (mtp-110) cc_final: 0.8190 (mtp-110) REVERT: G 76 LEU cc_start: 0.9587 (mt) cc_final: 0.9379 (mt) REVERT: G 77 ARG cc_start: 0.9157 (mmt90) cc_final: 0.8916 (mmt180) REVERT: I 1 MET cc_start: 0.8411 (tpp) cc_final: 0.8042 (mmp) REVERT: I 15 ASN cc_start: 0.9180 (m110) cc_final: 0.8809 (m110) REVERT: I 38 ASP cc_start: 0.9062 (m-30) cc_final: 0.8785 (m-30) REVERT: I 46 CYS cc_start: 0.9687 (t) cc_final: 0.9486 (t) REVERT: I 77 ARG cc_start: 0.9227 (mmt-90) cc_final: 0.8901 (mmt180) REVERT: L 21 ASN cc_start: 0.8932 (m-40) cc_final: 0.8607 (m-40) REVERT: L 64 ARG cc_start: 0.9125 (mmm-85) cc_final: 0.8719 (mmm-85) REVERT: L 77 ARG cc_start: 0.8992 (mmt90) cc_final: 0.8520 (mmt180) outliers start: 39 outliers final: 32 residues processed: 492 average time/residue: 0.0967 time to fit residues: 59.4987 Evaluate side-chains 501 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 467 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 43 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 7 LYS 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 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 96 GLN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 27 ILE 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 12 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 48 LEU 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 68 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN E 39 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN G 51 ASN I 39 GLN I 60 ASN 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 = 0.070130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.061423 restraints weight = 23320.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063468 restraints weight = 12052.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064905 restraints weight = 7542.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066035 restraints weight = 5190.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066649 restraints weight = 3774.616| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.9817 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= 0.190 Angle : 0.840 9.862 8840 Z= 0.438 Chirality : 0.046 0.188 968 Planarity : 0.006 0.067 1144 Dihedral : 4.633 20.338 880 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.63 % Favored : 97.24 % Rotamer: Outliers : 6.69 % Allowed : 42.88 % Favored : 50.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.30), residues: 760 helix: 0.43 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.26 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 14 TYR 0.027 0.003 TYR E 95 PHE 0.026 0.002 PHE A 16 TRP 0.016 0.002 TRP I 56 HIS 0.001 0.000 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 6496) covalent geometry : angle 0.84012 ( 8840) hydrogen bonds : bond 0.04212 ( 396) hydrogen bonds : angle 4.69979 ( 1185) Misc. bond : bond 0.00058 ( 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 519 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 473 time to evaluate : 0.239 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 5 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8197 (tt0) REVERT: A 14 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.8247 (mtp-110) REVERT: A 37 ARG cc_start: 0.9225 (ttp80) cc_final: 0.8531 (ttp80) REVERT: A 39 GLN cc_start: 0.8869 (pt0) cc_final: 0.8482 (pp30) REVERT: A 41 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8202 (ttp-110) REVERT: A 43 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8896 (mtt90) REVERT: A 51 ASN cc_start: 0.8347 (p0) cc_final: 0.7856 (p0) REVERT: A 55 LEU cc_start: 0.8796 (mt) cc_final: 0.8507 (mt) REVERT: A 77 ARG cc_start: 0.9173 (mmt90) cc_final: 0.8965 (mmt180) REVERT: A 86 ASP cc_start: 0.8967 (p0) cc_final: 0.8736 (p0) REVERT: A 87 GLU cc_start: 0.9285 (tp30) cc_final: 0.8991 (tp30) REVERT: B 14 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8195 (mtm-85) REVERT: B 38 ASP cc_start: 0.8893 (m-30) cc_final: 0.8423 (m-30) REVERT: B 41 ARG cc_start: 0.8748 (ttp-110) cc_final: 0.8498 (ttm110) REVERT: B 53 ASP cc_start: 0.8626 (m-30) cc_final: 0.8324 (m-30) REVERT: B 87 GLU cc_start: 0.9213 (tp30) cc_final: 0.8827 (tp30) REVERT: C 9 TYR cc_start: 0.9289 (t80) cc_final: 0.8930 (t80) REVERT: C 14 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: C 21 ASN cc_start: 0.8860 (m-40) cc_final: 0.7971 (t0) REVERT: C 41 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8322 (ttm110) REVERT: C 77 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8859 (mmt90) REVERT: C 96 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: D 9 TYR cc_start: 0.9290 (t80) cc_final: 0.8974 (t80) REVERT: D 41 ARG cc_start: 0.9138 (ttp-170) cc_final: 0.8738 (ttp-110) REVERT: D 59 PHE cc_start: 0.9042 (m-10) cc_final: 0.8814 (m-80) REVERT: D 93 GLN cc_start: 0.9278 (tm-30) cc_final: 0.9022 (tm-30) REVERT: E 5 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8517 (tt0) REVERT: E 37 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8248 (tmm-80) REVERT: E 41 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8239 (ttm110) REVERT: E 52 ARG cc_start: 0.9366 (ttm-80) cc_final: 0.9095 (tpp80) REVERT: E 61 THR cc_start: 0.9490 (m) cc_final: 0.9224 (p) REVERT: G 1 MET cc_start: 0.8072 (ttm) cc_final: 0.7794 (ttm) REVERT: G 5 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7729 (tt0) REVERT: G 9 TYR cc_start: 0.9348 (t80) cc_final: 0.9024 (t80) REVERT: G 14 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8234 (mtp-110) REVERT: G 70 GLU cc_start: 0.8282 (pp20) cc_final: 0.7993 (pp20) REVERT: G 71 TYR cc_start: 0.9353 (m-80) cc_final: 0.9055 (m-80) REVERT: I 1 MET cc_start: 0.8401 (tpp) cc_final: 0.8014 (mmp) REVERT: I 15 ASN cc_start: 0.9185 (m110) cc_final: 0.8913 (m110) REVERT: I 38 ASP cc_start: 0.9040 (m-30) cc_final: 0.8771 (m-30) REVERT: I 77 ARG cc_start: 0.9193 (mmt-90) cc_final: 0.8979 (mmt-90) REVERT: L 21 ASN cc_start: 0.8970 (m-40) cc_final: 0.8670 (m-40) REVERT: L 64 ARG cc_start: 0.9121 (mmm-85) cc_final: 0.8750 (mmm-85) REVERT: L 77 ARG cc_start: 0.9003 (mmt90) cc_final: 0.8530 (mmt180) outliers start: 46 outliers final: 35 residues processed: 483 average time/residue: 0.1005 time to fit residues: 60.5388 Evaluate side-chains 506 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 466 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 43 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 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 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU 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 C residue 96 GLN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 27 ILE 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 37 ARG Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 48 LEU 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 58 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 69 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN C 63 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN G 51 ASN I 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062495 restraints weight = 22381.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064547 restraints weight = 11909.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.066011 restraints weight = 7518.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067039 restraints weight = 5215.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067883 restraints weight = 3896.638| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 1.0015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6497 Z= 0.173 Angle : 0.876 10.523 8840 Z= 0.447 Chirality : 0.046 0.189 968 Planarity : 0.005 0.035 1144 Dihedral : 4.573 23.421 880 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.63 % Favored : 97.24 % Rotamer: Outliers : 5.52 % Allowed : 43.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.30), residues: 760 helix: 0.25 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.21 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 14 TYR 0.033 0.003 TYR I 9 PHE 0.030 0.003 PHE C 59 TRP 0.027 0.002 TRP C 56 HIS 0.001 0.000 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6496) covalent geometry : angle 0.87576 ( 8840) hydrogen bonds : bond 0.04178 ( 396) hydrogen bonds : angle 4.72858 ( 1185) Misc. bond : bond 0.00017 ( 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 517 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 479 time to evaluate : 0.250 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 5 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8232 (tt0) REVERT: A 14 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8145 (mtm110) REVERT: A 37 ARG cc_start: 0.9189 (ttp80) cc_final: 0.8092 (ttp80) REVERT: A 39 GLN cc_start: 0.8808 (pt0) cc_final: 0.8424 (pp30) REVERT: A 41 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8398 (ttm110) REVERT: A 51 ASN cc_start: 0.8262 (p0) cc_final: 0.7878 (p0) REVERT: A 55 LEU cc_start: 0.8759 (mt) cc_final: 0.8526 (mt) REVERT: A 77 ARG cc_start: 0.9160 (mmt90) cc_final: 0.8919 (mmt180) REVERT: A 87 GLU cc_start: 0.9238 (tp30) cc_final: 0.8995 (tp30) REVERT: B 9 TYR cc_start: 0.8810 (t80) cc_final: 0.8082 (t80) REVERT: B 14 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8315 (mtp-110) REVERT: B 38 ASP cc_start: 0.8872 (m-30) cc_final: 0.8510 (m-30) REVERT: B 39 GLN cc_start: 0.9036 (pt0) cc_final: 0.8688 (pp30) REVERT: B 53 ASP cc_start: 0.8606 (m-30) cc_final: 0.8320 (m-30) REVERT: B 87 GLU cc_start: 0.9203 (tp30) cc_final: 0.8802 (tp30) REVERT: C 9 TYR cc_start: 0.9192 (t80) cc_final: 0.8967 (t80) REVERT: C 14 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8069 (mtm-85) REVERT: C 21 ASN cc_start: 0.8804 (m-40) cc_final: 0.7956 (t0) REVERT: C 41 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8312 (ttm110) REVERT: C 53 ASP cc_start: 0.8987 (m-30) cc_final: 0.8783 (m-30) REVERT: D 10 LYS cc_start: 0.9401 (ttpp) cc_final: 0.8822 (ttpp) REVERT: D 14 ARG cc_start: 0.8317 (mtm110) cc_final: 0.7408 (mtm-85) REVERT: D 41 ARG cc_start: 0.9126 (ttp-170) cc_final: 0.8740 (ttp-110) REVERT: D 71 TYR cc_start: 0.9361 (m-80) cc_final: 0.8934 (m-10) REVERT: D 93 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8990 (tm-30) REVERT: E 5 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8440 (tt0) REVERT: E 14 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7844 (mtm110) REVERT: E 41 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8157 (ttp-110) REVERT: E 52 ARG cc_start: 0.9287 (ttm-80) cc_final: 0.9008 (tpp80) REVERT: E 61 THR cc_start: 0.9482 (m) cc_final: 0.9223 (p) REVERT: E 77 ARG cc_start: 0.9267 (mmt180) cc_final: 0.8730 (mmt180) REVERT: G 1 MET cc_start: 0.7983 (ttm) cc_final: 0.7680 (ttm) REVERT: G 5 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7854 (tt0) REVERT: G 9 TYR cc_start: 0.9343 (t80) cc_final: 0.9041 (t80) REVERT: G 14 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8229 (mtp-110) REVERT: G 70 GLU cc_start: 0.8359 (pp20) cc_final: 0.7881 (pp20) REVERT: G 71 TYR cc_start: 0.9331 (m-80) cc_final: 0.8938 (m-80) REVERT: I 1 MET cc_start: 0.8395 (tpp) cc_final: 0.7966 (mmp) REVERT: I 15 ASN cc_start: 0.9269 (m110) cc_final: 0.8906 (m110) REVERT: I 38 ASP cc_start: 0.9007 (m-30) cc_final: 0.8757 (m-30) REVERT: I 70 GLU cc_start: 0.8583 (pp20) cc_final: 0.8121 (pp20) REVERT: I 71 TYR cc_start: 0.9381 (m-80) cc_final: 0.8981 (m-80) REVERT: I 77 ARG cc_start: 0.9168 (mmt-90) cc_final: 0.8852 (mmt180) REVERT: L 9 TYR cc_start: 0.9328 (t80) cc_final: 0.9010 (t80) REVERT: L 43 ARG cc_start: 0.8992 (mtt90) cc_final: 0.8713 (mtt180) REVERT: L 52 ARG cc_start: 0.9453 (mtp85) cc_final: 0.9105 (tpp80) REVERT: L 64 ARG cc_start: 0.9088 (mmm-85) cc_final: 0.8696 (mmm-85) REVERT: L 77 ARG cc_start: 0.8999 (mmt90) cc_final: 0.8538 (mmt180) outliers start: 38 outliers final: 32 residues processed: 490 average time/residue: 0.1055 time to fit residues: 64.4027 Evaluate side-chains 500 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 466 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP 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 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 C residue 7 LYS 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 D residue 22 VAL Chi-restraints excluded: chain D residue 27 ILE 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 39 GLN Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 48 LEU 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 63 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 71 optimal weight: 0.0980 chunk 8 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 39 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN G 51 ASN I 39 GLN ** I 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 = 0.3141 r_free = 0.3141 target = 0.071890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.062835 restraints weight = 22793.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064879 restraints weight = 12413.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066284 restraints weight = 7955.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067337 restraints weight = 5596.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067961 restraints weight = 4200.334| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 1.0162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6497 Z= 0.180 Angle : 0.908 10.672 8840 Z= 0.459 Chirality : 0.047 0.191 968 Planarity : 0.006 0.081 1144 Dihedral : 4.692 24.393 880 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.24 % Favored : 97.63 % Rotamer: Outliers : 5.38 % Allowed : 44.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.30), residues: 760 helix: 0.18 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.24 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 14 TYR 0.025 0.002 TYR E 9 PHE 0.035 0.002 PHE I 59 TRP 0.025 0.002 TRP I 56 HIS 0.001 0.000 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6496) covalent geometry : angle 0.90759 ( 8840) hydrogen bonds : bond 0.04391 ( 396) hydrogen bonds : angle 4.84837 ( 1185) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1427.94 seconds wall clock time: 25 minutes 19.70 seconds (1519.70 seconds total)