Starting phenix.real_space_refine on Wed Sep 25 21:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/09_2024/3j6j_5925.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/09_2024/3j6j_5925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/09_2024/3j6j_5925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/09_2024/3j6j_5925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/09_2024/3j6j_5925.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/09_2024/3j6j_5925.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6344 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4040 2.51 5 N 1088 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6344 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "I" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Time building chain proxies: 5.19, per 1000 atoms: 0.82 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=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 866.8 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.052A pdb=" N PHE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 15 through 20' Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.686A pdb=" N HIS A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 3.651A pdb=" N TYR A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.903A pdb=" N CYS B 20 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.101A pdb=" N ASP B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.529A pdb=" N TRP B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.660A pdb=" N TYR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.673A pdb=" N SER B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.705A pdb=" N ASP C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.660A pdb=" N HIS C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.600A pdb=" N TYR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.667A pdb=" N PHE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 20' Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 35 through 50 removed outlier: 4.090A pdb=" N ASP D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 removed outlier: 3.502A pdb=" N TRP D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.953A pdb=" N PHE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 20' Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 35 through 50 removed outlier: 4.123A pdb=" N ASP E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 removed outlier: 3.865A pdb=" N TRP E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.836A pdb=" N TYR E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 15 through 20 removed outlier: 3.834A pdb=" N PHE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 15 through 20' Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 35 through 50 removed outlier: 3.985A pdb=" N ASP G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 63 removed outlier: 3.666A pdb=" N TRP G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 removed outlier: 3.537A pdb=" N TYR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.613A pdb=" N TYR G 95 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 15 through 20 removed outlier: 3.668A pdb=" N PHE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS I 20 " --> pdb=" O PHE I 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 15 through 20' Processing helix chain 'I' and resid 23 through 28 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 35 through 50 removed outlier: 3.889A pdb=" N ASP I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 63 removed outlier: 3.992A pdb=" N TRP I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 removed outlier: 3.655A pdb=" N TYR I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 94 Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 15 through 20 removed outlier: 3.564A pdb=" N PHE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS L 20 " --> pdb=" O PHE L 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 15 through 20' Processing helix chain 'L' and resid 23 through 28 Processing helix chain 'L' and resid 35 through 50 removed outlier: 3.997A pdb=" N ASP L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 63 removed outlier: 3.570A pdb=" N TRP L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 79 removed outlier: 3.710A pdb=" N TYR L 71 " --> pdb=" O GLY L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 94 396 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.85 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: 27 2.24 - 2.91: 2828 2.91 - 3.57: 10142 3.57 - 4.24: 15508 4.24 - 4.90: 26180 Nonbonded interactions: 54685 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=" NH2 ARG B 43 " pdb=" CH2 TRP C 56 " model vdw 1.838 3.420 nonbonded pdb=" OE1 GLN C 39 " pdb=" CZ2 TRP G 56 " model vdw 1.889 3.340 nonbonded pdb=" NH2 ARG B 43 " pdb=" CZ3 TRP C 56 " model vdw 1.926 3.420 ... (remaining 54680 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- 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 : 0.007 0.083 6496 Z= 0.452 Angle : 1.414 21.017 8840 Z= 0.997 Chirality : 0.058 0.343 968 Planarity : 0.005 0.036 1144 Dihedral : 15.900 84.850 2352 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 0.92 % Allowed : 4.08 % Favored : 95.00 % Rotamer: Outliers : 6.10 % Allowed : 9.16 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.26), residues: 760 helix: -0.53 (0.19), residues: 536 sheet: None (None), residues: 0 loop : -1.78 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 56 HIS 0.019 0.003 HIS G 57 PHE 0.021 0.002 PHE I 72 TYR 0.026 0.003 TYR G 30 ARG 0.012 0.001 ARG L 64 *********************** 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 fitting. rotamer outliers: 42 poor density : 516 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.9289 (mmtt) cc_final: 0.9074 (mmtm) REVERT: A 66 PRO cc_start: 0.9215 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: A 77 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8379 (mtp85) REVERT: A 82 VAL cc_start: 0.9016 (t) cc_final: 0.8698 (p) REVERT: B 14 ARG cc_start: 0.9034 (ttp-110) cc_final: 0.8738 (mtm-85) REVERT: B 24 VAL cc_start: 0.9299 (t) cc_final: 0.8624 (t) REVERT: B 35 THR cc_start: 0.9204 (m) cc_final: 0.8680 (m) REVERT: B 38 ASP cc_start: 0.9603 (t0) cc_final: 0.9261 (m-30) REVERT: B 77 ARG cc_start: 0.8949 (mtt-85) cc_final: 0.8473 (mmt90) REVERT: B 83 ASP cc_start: 0.9129 (m-30) cc_final: 0.8784 (m-30) REVERT: B 95 TYR cc_start: 0.8993 (m-80) cc_final: 0.8391 (m-80) REVERT: B 96 GLN cc_start: 0.7958 (mt0) cc_final: 0.7754 (mm-40) REVERT: C 3 PHE cc_start: 0.7767 (t80) cc_final: 0.7242 (t80) REVERT: C 21 ASN cc_start: 0.9164 (m110) cc_final: 0.8558 (m-40) REVERT: C 31 LEU cc_start: 0.9161 (mt) cc_final: 0.8903 (mt) REVERT: C 41 ARG cc_start: 0.9284 (ttt180) cc_final: 0.8894 (tpp80) REVERT: C 53 ASP cc_start: 0.9613 (m-30) cc_final: 0.9190 (m-30) REVERT: D 3 PHE cc_start: 0.8490 (t80) cc_final: 0.7684 (t80) REVERT: D 14 ARG cc_start: 0.8780 (ttp-110) cc_final: 0.8449 (mtm-85) REVERT: D 21 ASN cc_start: 0.9174 (m110) cc_final: 0.8873 (m-40) REVERT: D 35 THR cc_start: 0.8773 (m) cc_final: 0.8411 (p) REVERT: D 40 ASP cc_start: 0.8091 (m-30) cc_final: 0.7796 (m-30) REVERT: D 54 THR cc_start: 0.9471 (m) cc_final: 0.9148 (p) REVERT: E 9 TYR cc_start: 0.9417 (t80) cc_final: 0.9077 (t80) REVERT: E 23 ASP cc_start: 0.9264 (t70) cc_final: 0.9057 (t0) REVERT: E 35 THR cc_start: 0.8651 (m) cc_final: 0.8180 (p) REVERT: E 60 ASN cc_start: 0.9546 (t0) cc_final: 0.9279 (m110) REVERT: E 87 GLU cc_start: 0.8960 (tt0) cc_final: 0.8664 (tp30) REVERT: E 90 SER cc_start: 0.9179 (t) cc_final: 0.8827 (p) REVERT: G 5 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7779 (mt-10) REVERT: G 24 VAL cc_start: 0.9330 (t) cc_final: 0.9022 (m) REVERT: G 28 LEU cc_start: 0.9350 (mt) cc_final: 0.9050 (mt) REVERT: G 35 THR cc_start: 0.8615 (m) cc_final: 0.8237 (p) REVERT: G 76 LEU cc_start: 0.9456 (mt) cc_final: 0.9015 (mt) REVERT: I 14 ARG cc_start: 0.9140 (ttp-110) cc_final: 0.8839 (mtm-85) REVERT: I 24 VAL cc_start: 0.9488 (t) cc_final: 0.9102 (m) REVERT: I 53 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: I 60 ASN cc_start: 0.9562 (t0) cc_final: 0.9317 (m110) REVERT: I 72 PHE cc_start: 0.9444 (t80) cc_final: 0.9172 (t80) REVERT: I 90 SER cc_start: 0.8871 (t) cc_final: 0.8571 (p) REVERT: L 21 ASN cc_start: 0.8869 (m110) cc_final: 0.8508 (m-40) REVERT: L 28 LEU cc_start: 0.8607 (mt) cc_final: 0.8371 (mt) REVERT: L 31 LEU cc_start: 0.9130 (mt) cc_final: 0.8905 (mt) REVERT: L 40 ASP cc_start: 0.8676 (m-30) cc_final: 0.8423 (m-30) REVERT: L 41 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8294 (ttm170) outliers start: 42 outliers final: 3 residues processed: 524 average time/residue: 0.2215 time to fit residues: 142.7949 Evaluate side-chains 467 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 462 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain L residue 41 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 57 HIS A 63 GLN A 96 GLN B 21 ASN B 60 ASN C 21 ASN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 21 ASN D 96 GLN E 39 GLN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS L 21 ASN L 39 GLN L 51 ASN L 60 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6496 Z= 0.243 Angle : 0.749 9.550 8840 Z= 0.393 Chirality : 0.044 0.197 968 Planarity : 0.007 0.055 1144 Dihedral : 6.295 58.837 896 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.71 % Favored : 98.03 % Rotamer: Outliers : 7.99 % Allowed : 24.27 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.28), residues: 760 helix: 0.95 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 1.16 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 56 HIS 0.002 0.001 HIS I 57 PHE 0.036 0.003 PHE G 59 TYR 0.024 0.002 TYR L 92 ARG 0.008 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 515 time to evaluate : 0.751 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 37 ARG cc_start: 0.8420 (ttp80) cc_final: 0.7456 (ttp80) REVERT: A 51 ASN cc_start: 0.8462 (p0) cc_final: 0.7926 (t0) REVERT: A 55 LEU cc_start: 0.9216 (mt) cc_final: 0.8888 (mt) REVERT: A 64 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8611 (tpp80) REVERT: A 96 GLN cc_start: 0.7716 (mt0) cc_final: 0.7494 (mm-40) REVERT: B 9 TYR cc_start: 0.8991 (t80) cc_final: 0.8688 (t80) REVERT: B 43 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.9075 (mtt90) REVERT: B 51 ASN cc_start: 0.8289 (p0) cc_final: 0.7488 (t0) REVERT: B 77 ARG cc_start: 0.9023 (mtt-85) cc_final: 0.8696 (mmt-90) REVERT: B 82 VAL cc_start: 0.8808 (m) cc_final: 0.8275 (t) REVERT: B 86 ASP cc_start: 0.9101 (m-30) cc_final: 0.8743 (m-30) REVERT: C 9 TYR cc_start: 0.8990 (t80) cc_final: 0.8742 (t80) REVERT: C 15 ASN cc_start: 0.9487 (m110) cc_final: 0.9188 (m110) REVERT: C 35 THR cc_start: 0.8969 (m) cc_final: 0.8702 (p) REVERT: C 41 ARG cc_start: 0.9428 (ttt180) cc_final: 0.9034 (ttp-170) REVERT: C 43 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.9077 (mtt180) REVERT: C 95 TYR cc_start: 0.9064 (m-80) cc_final: 0.8668 (m-80) REVERT: D 6 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8970 (p0) REVERT: D 16 PHE cc_start: 0.8798 (t80) cc_final: 0.8492 (t80) REVERT: D 57 HIS cc_start: 0.9798 (m-70) cc_final: 0.9556 (m-70) REVERT: E 3 PHE cc_start: 0.8955 (t80) cc_final: 0.8563 (t80) REVERT: E 5 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8705 (mt-10) REVERT: E 7 LYS cc_start: 0.9373 (mmtt) cc_final: 0.9091 (mmtm) REVERT: E 16 PHE cc_start: 0.9305 (t80) cc_final: 0.9046 (t80) REVERT: E 35 THR cc_start: 0.8703 (m) cc_final: 0.8289 (p) REVERT: E 42 LEU cc_start: 0.9364 (mt) cc_final: 0.9071 (mm) REVERT: E 51 ASN cc_start: 0.8840 (p0) cc_final: 0.8299 (t0) REVERT: E 60 ASN cc_start: 0.9701 (t0) cc_final: 0.9486 (m110) REVERT: E 77 ARG cc_start: 0.9051 (ttm110) cc_final: 0.8661 (mmt90) REVERT: E 95 TYR cc_start: 0.9119 (m-80) cc_final: 0.8887 (m-80) REVERT: G 5 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7767 (mt-10) REVERT: G 8 THR cc_start: 0.9362 (m) cc_final: 0.9075 (p) REVERT: G 9 TYR cc_start: 0.9171 (t80) cc_final: 0.8837 (t80) REVERT: G 24 VAL cc_start: 0.9462 (t) cc_final: 0.9225 (m) REVERT: G 28 LEU cc_start: 0.9521 (mt) cc_final: 0.9166 (mt) REVERT: G 31 LEU cc_start: 0.9129 (mt) cc_final: 0.8871 (mm) REVERT: G 59 PHE cc_start: 0.9475 (m-80) cc_final: 0.9080 (m-80) REVERT: G 60 ASN cc_start: 0.9423 (t0) cc_final: 0.9183 (m110) REVERT: G 66 PRO cc_start: 0.9338 (Cg_exo) cc_final: 0.9083 (Cg_endo) REVERT: G 71 TYR cc_start: 0.9446 (m-80) cc_final: 0.9107 (m-80) REVERT: G 76 LEU cc_start: 0.9638 (mt) cc_final: 0.9379 (mt) REVERT: G 77 ARG cc_start: 0.9329 (tpp80) cc_final: 0.8848 (mmt90) REVERT: I 5 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8678 (mt-10) REVERT: I 9 TYR cc_start: 0.9402 (t80) cc_final: 0.9178 (t80) REVERT: I 14 ARG cc_start: 0.9227 (ttp-110) cc_final: 0.8983 (mtm-85) REVERT: I 37 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8412 (ptm-80) REVERT: I 38 ASP cc_start: 0.9361 (m-30) cc_final: 0.8981 (p0) REVERT: I 77 ARG cc_start: 0.9237 (ttm110) cc_final: 0.8777 (mmt90) REVERT: I 90 SER cc_start: 0.9339 (t) cc_final: 0.9057 (p) REVERT: I 96 GLN cc_start: 0.8378 (mt0) cc_final: 0.7602 (tp40) REVERT: L 5 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8413 (mt-10) REVERT: L 14 ARG cc_start: 0.8871 (ttp-110) cc_final: 0.7803 (mtp-110) REVERT: L 26 GLU cc_start: 0.9168 (mp0) cc_final: 0.8862 (mp0) REVERT: L 41 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8129 (ttm110) REVERT: L 53 ASP cc_start: 0.9229 (m-30) cc_final: 0.8894 (m-30) REVERT: L 54 THR cc_start: 0.9437 (m) cc_final: 0.9133 (p) REVERT: L 59 PHE cc_start: 0.9549 (m-80) cc_final: 0.9051 (m-80) REVERT: L 64 ARG cc_start: 0.9366 (mmt90) cc_final: 0.9139 (mmm-85) outliers start: 55 outliers final: 26 residues processed: 525 average time/residue: 0.2180 time to fit residues: 141.3919 Evaluate side-chains 516 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 485 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 CYS 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 43 ARG Chi-restraints excluded: chain D residue 6 ASP 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 46 CYS Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 90 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 21 ASN B 96 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 63 GLN D 51 ASN D 63 GLN G 18 ASN G 39 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN L 51 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.7610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6496 Z= 0.274 Angle : 0.713 7.837 8840 Z= 0.375 Chirality : 0.044 0.188 968 Planarity : 0.006 0.061 1144 Dihedral : 5.536 51.430 892 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.18 % Favored : 98.68 % Rotamer: Outliers : 10.47 % Allowed : 27.03 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 760 helix: 0.76 (0.19), residues: 600 sheet: None (None), residues: 0 loop : 2.09 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 56 HIS 0.002 0.001 HIS A 57 PHE 0.029 0.003 PHE G 59 TYR 0.021 0.002 TYR I 92 ARG 0.007 0.001 ARG C 14 *********************** 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 570 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 498 time to evaluate : 0.710 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 14 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8721 (mtm-85) REVERT: A 43 ARG cc_start: 0.9592 (OUTLIER) cc_final: 0.9380 (mtt90) REVERT: A 51 ASN cc_start: 0.8397 (p0) cc_final: 0.8110 (t0) REVERT: A 52 ARG cc_start: 0.8980 (ptp-110) cc_final: 0.8561 (ptp-110) REVERT: A 55 LEU cc_start: 0.9102 (mt) cc_final: 0.8769 (mt) REVERT: A 64 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8596 (tpp80) REVERT: A 77 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: A 96 GLN cc_start: 0.7595 (mt0) cc_final: 0.7321 (mm110) REVERT: B 14 ARG cc_start: 0.9220 (ttp-110) cc_final: 0.8841 (mtm-85) REVERT: B 16 PHE cc_start: 0.9138 (t80) cc_final: 0.8893 (t80) REVERT: B 38 ASP cc_start: 0.9356 (m-30) cc_final: 0.9105 (m-30) REVERT: B 43 ARG cc_start: 0.9406 (OUTLIER) cc_final: 0.8941 (mtt90) REVERT: B 51 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8104 (p0) REVERT: B 77 ARG cc_start: 0.9199 (mtt-85) cc_final: 0.8933 (mmt-90) REVERT: B 82 VAL cc_start: 0.8879 (m) cc_final: 0.8357 (t) REVERT: B 86 ASP cc_start: 0.9092 (m-30) cc_final: 0.8691 (m-30) REVERT: C 9 TYR cc_start: 0.9207 (t80) cc_final: 0.8901 (t80) REVERT: C 35 THR cc_start: 0.8953 (m) cc_final: 0.8738 (p) REVERT: C 41 ARG cc_start: 0.9378 (ttt180) cc_final: 0.9046 (ttp-170) REVERT: C 54 THR cc_start: 0.9745 (t) cc_final: 0.9418 (m) REVERT: C 86 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.9151 (p0) REVERT: C 88 VAL cc_start: 0.9518 (t) cc_final: 0.9275 (p) REVERT: D 37 ARG cc_start: 0.8755 (ttt180) cc_final: 0.8251 (tmm-80) REVERT: D 41 ARG cc_start: 0.8971 (ttp-170) cc_final: 0.8268 (ttm110) REVERT: D 57 HIS cc_start: 0.9775 (m-70) cc_final: 0.9562 (m-70) REVERT: D 59 PHE cc_start: 0.9319 (m-10) cc_final: 0.9096 (m-10) REVERT: E 3 PHE cc_start: 0.9032 (t80) cc_final: 0.8670 (t80) REVERT: E 7 LYS cc_start: 0.9326 (mmtt) cc_final: 0.8941 (mmtm) REVERT: E 16 PHE cc_start: 0.9515 (t80) cc_final: 0.9312 (t80) REVERT: E 35 THR cc_start: 0.8991 (m) cc_final: 0.8721 (p) REVERT: E 51 ASN cc_start: 0.9062 (p0) cc_final: 0.8766 (p0) REVERT: E 77 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8740 (mmt-90) REVERT: E 95 TYR cc_start: 0.9223 (m-80) cc_final: 0.8473 (m-80) REVERT: G 24 VAL cc_start: 0.9695 (t) cc_final: 0.9403 (p) REVERT: G 71 TYR cc_start: 0.9408 (m-80) cc_final: 0.9099 (m-80) REVERT: G 72 PHE cc_start: 0.9656 (t80) cc_final: 0.9365 (t80) REVERT: G 76 LEU cc_start: 0.9724 (mt) cc_final: 0.9432 (mt) REVERT: G 77 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8962 (mmt90) REVERT: I 9 TYR cc_start: 0.9302 (t80) cc_final: 0.8937 (t80) REVERT: I 24 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9186 (p) REVERT: I 38 ASP cc_start: 0.9418 (m-30) cc_final: 0.8800 (p0) REVERT: I 60 ASN cc_start: 0.9719 (t0) cc_final: 0.9489 (m110) REVERT: I 77 ARG cc_start: 0.9274 (ttm110) cc_final: 0.8984 (mmt180) REVERT: I 96 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8175 (tp40) REVERT: L 37 ARG cc_start: 0.8798 (tmt170) cc_final: 0.7705 (tmt170) REVERT: L 41 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8162 (ttp-110) REVERT: L 53 ASP cc_start: 0.9198 (m-30) cc_final: 0.8975 (m-30) REVERT: L 55 LEU cc_start: 0.9532 (tp) cc_final: 0.9305 (tp) REVERT: L 59 PHE cc_start: 0.9540 (m-80) cc_final: 0.9249 (m-80) REVERT: L 64 ARG cc_start: 0.9387 (mmt90) cc_final: 0.9173 (mmm-85) REVERT: L 77 ARG cc_start: 0.9156 (mmt90) cc_final: 0.8786 (mmt180) REVERT: L 82 VAL cc_start: 0.8959 (p) cc_final: 0.8746 (t) REVERT: L 87 GLU cc_start: 0.9352 (tp30) cc_final: 0.9096 (tp30) REVERT: L 92 TYR cc_start: 0.9318 (t80) cc_final: 0.9114 (t80) outliers start: 72 outliers final: 42 residues processed: 515 average time/residue: 0.2168 time to fit residues: 137.5417 Evaluate side-chains 528 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 479 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 ASN Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 65 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 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 G residue 91 VAL Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS C 39 GLN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS D 51 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.8204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6496 Z= 0.243 Angle : 0.683 7.823 8840 Z= 0.361 Chirality : 0.044 0.188 968 Planarity : 0.005 0.051 1144 Dihedral : 5.372 52.530 892 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.45 % Favored : 98.42 % Rotamer: Outliers : 7.99 % Allowed : 32.56 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 760 helix: 0.57 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.53 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 56 HIS 0.000 0.000 HIS C 57 PHE 0.024 0.003 PHE D 16 TYR 0.019 0.002 TYR D 9 ARG 0.005 0.001 ARG I 41 *********************** 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 541 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 486 time to evaluate : 0.678 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 14 ARG cc_start: 0.9022 (mtm-85) cc_final: 0.8581 (mtm-85) REVERT: A 51 ASN cc_start: 0.8437 (p0) cc_final: 0.8056 (t0) REVERT: A 52 ARG cc_start: 0.8857 (ptp-110) cc_final: 0.8434 (ptp-110) REVERT: A 55 LEU cc_start: 0.9097 (mt) cc_final: 0.8760 (mt) REVERT: A 77 ARG cc_start: 0.9000 (mmt-90) cc_final: 0.8722 (mmt-90) REVERT: B 9 TYR cc_start: 0.9052 (t80) cc_final: 0.8545 (t80) REVERT: B 14 ARG cc_start: 0.9224 (ttp-110) cc_final: 0.8821 (mtm-85) REVERT: B 38 ASP cc_start: 0.9214 (m-30) cc_final: 0.8800 (m-30) REVERT: B 41 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7739 (ptp-170) REVERT: B 51 ASN cc_start: 0.8383 (p0) cc_final: 0.7952 (p0) REVERT: B 54 THR cc_start: 0.9484 (m) cc_final: 0.9218 (p) REVERT: B 55 LEU cc_start: 0.9405 (mt) cc_final: 0.9133 (mt) REVERT: B 77 ARG cc_start: 0.9259 (mtt-85) cc_final: 0.8953 (mmt-90) REVERT: B 82 VAL cc_start: 0.8844 (m) cc_final: 0.8525 (t) REVERT: C 9 TYR cc_start: 0.9280 (t80) cc_final: 0.9069 (t80) REVERT: C 14 ARG cc_start: 0.9030 (mtm-85) cc_final: 0.8551 (mtm-85) REVERT: C 35 THR cc_start: 0.8937 (m) cc_final: 0.8582 (p) REVERT: C 38 ASP cc_start: 0.9555 (m-30) cc_final: 0.9290 (m-30) REVERT: C 41 ARG cc_start: 0.9375 (ttt180) cc_final: 0.9116 (ttp-170) REVERT: C 54 THR cc_start: 0.9760 (t) cc_final: 0.9402 (m) REVERT: C 86 ASP cc_start: 0.9479 (OUTLIER) cc_final: 0.9179 (p0) REVERT: D 14 ARG cc_start: 0.9059 (mtm-85) cc_final: 0.8680 (mtm-85) REVERT: D 37 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8270 (tmm-80) REVERT: D 41 ARG cc_start: 0.9145 (ttp-170) cc_final: 0.8695 (ttp-110) REVERT: D 57 HIS cc_start: 0.9793 (m-70) cc_final: 0.9583 (m-70) REVERT: D 77 ARG cc_start: 0.9324 (ttm110) cc_final: 0.9052 (mmt90) REVERT: E 3 PHE cc_start: 0.9042 (t80) cc_final: 0.8779 (t80) REVERT: E 23 ASP cc_start: 0.8806 (t0) cc_final: 0.8344 (t0) REVERT: E 35 THR cc_start: 0.8951 (m) cc_final: 0.8732 (p) REVERT: E 71 TYR cc_start: 0.9527 (m-80) cc_final: 0.9190 (m-80) REVERT: G 9 TYR cc_start: 0.9322 (t80) cc_final: 0.9079 (t80) REVERT: G 24 VAL cc_start: 0.9662 (t) cc_final: 0.9201 (p) REVERT: G 28 LEU cc_start: 0.9575 (mt) cc_final: 0.9262 (mt) REVERT: G 60 ASN cc_start: 0.9454 (m-40) cc_final: 0.9183 (m110) REVERT: G 72 PHE cc_start: 0.9673 (t80) cc_final: 0.9297 (t80) REVERT: G 76 LEU cc_start: 0.9751 (mt) cc_final: 0.9400 (mt) REVERT: G 77 ARG cc_start: 0.9382 (tpp80) cc_final: 0.8972 (mmt90) REVERT: I 9 TYR cc_start: 0.9349 (t80) cc_final: 0.9059 (t80) REVERT: I 14 ARG cc_start: 0.9216 (mtm-85) cc_final: 0.8721 (mtm-85) REVERT: I 30 TYR cc_start: 0.8969 (m-10) cc_final: 0.8710 (m-10) REVERT: I 37 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8588 (ptm-80) REVERT: I 96 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8086 (tp40) REVERT: L 27 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8410 (tp) REVERT: L 64 ARG cc_start: 0.9404 (mmt90) cc_final: 0.9183 (mmm-85) outliers start: 55 outliers final: 34 residues processed: 500 average time/residue: 0.2157 time to fit residues: 134.1534 Evaluate side-chains 511 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 473 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 ARG 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 D residue 27 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain 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 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ILE 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 57 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS C 21 ASN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 63 GLN C 96 GLN E 39 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 ASN L 51 ASN L 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.8801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6496 Z= 0.280 Angle : 0.699 7.472 8840 Z= 0.374 Chirality : 0.046 0.191 968 Planarity : 0.005 0.058 1144 Dihedral : 4.852 37.368 884 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 7.70 % Allowed : 36.19 % Favored : 56.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 760 helix: 0.43 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.82 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 56 HIS 0.001 0.000 HIS D 57 PHE 0.018 0.002 PHE A 16 TYR 0.032 0.002 TYR L 92 ARG 0.006 0.001 ARG L 77 *********************** 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 fitting. rotamer outliers: 53 poor density : 493 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.9065 (mtm-85) cc_final: 0.8737 (mtm-85) REVERT: A 51 ASN cc_start: 0.8485 (p0) cc_final: 0.8065 (t0) REVERT: A 55 LEU cc_start: 0.9066 (mt) cc_final: 0.8698 (mt) REVERT: A 77 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8740 (mmt-90) REVERT: B 9 TYR cc_start: 0.9102 (t80) cc_final: 0.8796 (t80) REVERT: B 14 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8787 (mtm-85) REVERT: B 38 ASP cc_start: 0.9217 (m-30) cc_final: 0.8861 (m-30) REVERT: B 41 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7814 (ptp-170) REVERT: B 51 ASN cc_start: 0.8640 (p0) cc_final: 0.8157 (p0) REVERT: B 54 THR cc_start: 0.9503 (m) cc_final: 0.9176 (p) REVERT: B 55 LEU cc_start: 0.9290 (mt) cc_final: 0.9047 (mt) REVERT: B 77 ARG cc_start: 0.9276 (mtt-85) cc_final: 0.8912 (mmt-90) REVERT: B 82 VAL cc_start: 0.8884 (m) cc_final: 0.8262 (t) REVERT: B 86 ASP cc_start: 0.9174 (m-30) cc_final: 0.8729 (m-30) REVERT: B 87 GLU cc_start: 0.9443 (tp30) cc_final: 0.9156 (tp30) REVERT: C 9 TYR cc_start: 0.9387 (t80) cc_final: 0.9098 (t80) REVERT: C 21 ASN cc_start: 0.9150 (m-40) cc_final: 0.8751 (t0) REVERT: C 35 THR cc_start: 0.9075 (m) cc_final: 0.8688 (p) REVERT: C 38 ASP cc_start: 0.9498 (m-30) cc_final: 0.9204 (m-30) REVERT: C 41 ARG cc_start: 0.9395 (ttt180) cc_final: 0.9089 (ttp-170) REVERT: C 54 THR cc_start: 0.9706 (t) cc_final: 0.9327 (m) REVERT: C 86 ASP cc_start: 0.9514 (OUTLIER) cc_final: 0.9307 (p0) REVERT: C 88 VAL cc_start: 0.9615 (t) cc_final: 0.9397 (p) REVERT: D 14 ARG cc_start: 0.9106 (mtm-85) cc_final: 0.8792 (mtm-85) REVERT: D 37 ARG cc_start: 0.8696 (ttt180) cc_final: 0.8349 (tmm-80) REVERT: D 41 ARG cc_start: 0.9186 (ttp-170) cc_final: 0.8788 (ttp-110) REVERT: D 57 HIS cc_start: 0.9796 (m-70) cc_final: 0.9568 (m-70) REVERT: D 77 ARG cc_start: 0.9356 (ttm110) cc_final: 0.8904 (mmt90) REVERT: D 87 GLU cc_start: 0.9608 (tp30) cc_final: 0.9371 (tp30) REVERT: E 3 PHE cc_start: 0.9090 (t80) cc_final: 0.8878 (t80) REVERT: E 23 ASP cc_start: 0.8712 (t0) cc_final: 0.7939 (t0) REVERT: E 26 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8992 (mp0) REVERT: E 52 ARG cc_start: 0.9413 (ttm-80) cc_final: 0.9077 (tpp80) REVERT: E 60 ASN cc_start: 0.9603 (t0) cc_final: 0.9362 (m110) REVERT: G 1 MET cc_start: 0.8034 (ttm) cc_final: 0.7630 (ttm) REVERT: G 60 ASN cc_start: 0.9471 (t0) cc_final: 0.9183 (m110) REVERT: G 72 PHE cc_start: 0.9687 (t80) cc_final: 0.9263 (t80) REVERT: G 76 LEU cc_start: 0.9782 (mt) cc_final: 0.9422 (mt) REVERT: G 77 ARG cc_start: 0.9404 (tpp80) cc_final: 0.8908 (mmt90) REVERT: I 1 MET cc_start: 0.7973 (tpp) cc_final: 0.7633 (mmt) REVERT: I 3 PHE cc_start: 0.8716 (t80) cc_final: 0.8426 (t80) REVERT: I 14 ARG cc_start: 0.9220 (mtm-85) cc_final: 0.8786 (mtm-85) REVERT: I 46 CYS cc_start: 0.9732 (t) cc_final: 0.9521 (t) REVERT: I 77 ARG cc_start: 0.9264 (mmt90) cc_final: 0.9018 (mmt180) REVERT: I 87 GLU cc_start: 0.9345 (tt0) cc_final: 0.9111 (tp30) REVERT: I 95 TYR cc_start: 0.9253 (m-80) cc_final: 0.8528 (m-80) REVERT: L 14 ARG cc_start: 0.9066 (mtm-85) cc_final: 0.8844 (mtm-85) REVERT: L 64 ARG cc_start: 0.9389 (mmt90) cc_final: 0.9124 (mmm-85) outliers start: 53 outliers final: 33 residues processed: 502 average time/residue: 0.2233 time to fit residues: 138.5665 Evaluate side-chains 514 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 479 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 43 ARG 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 D residue 27 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN I 39 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.9198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6496 Z= 0.244 Angle : 0.741 11.972 8840 Z= 0.386 Chirality : 0.044 0.189 968 Planarity : 0.006 0.099 1144 Dihedral : 4.525 21.635 880 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.11 % Favored : 97.76 % Rotamer: Outliers : 7.41 % Allowed : 38.37 % Favored : 54.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.30), residues: 760 helix: 0.27 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.82 (0.56), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 56 HIS 0.001 0.000 HIS C 57 PHE 0.027 0.002 PHE D 16 TYR 0.032 0.003 TYR G 9 ARG 0.006 0.001 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 493 time to evaluate : 0.696 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 14 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8626 (mtm-85) REVERT: A 51 ASN cc_start: 0.8417 (p0) cc_final: 0.7949 (t0) REVERT: A 52 ARG cc_start: 0.8964 (ptp-110) cc_final: 0.8460 (ptp-110) REVERT: A 55 LEU cc_start: 0.9075 (mt) cc_final: 0.8673 (mt) REVERT: A 77 ARG cc_start: 0.9008 (mmt-90) cc_final: 0.8762 (mmt-90) REVERT: B 14 ARG cc_start: 0.9206 (ttp-110) cc_final: 0.8784 (mtm-85) REVERT: B 38 ASP cc_start: 0.9215 (m-30) cc_final: 0.8855 (m-30) REVERT: B 41 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7828 (ptp-170) REVERT: B 51 ASN cc_start: 0.8591 (p0) cc_final: 0.8092 (p0) REVERT: B 53 ASP cc_start: 0.9158 (m-30) cc_final: 0.8488 (m-30) REVERT: B 54 THR cc_start: 0.9507 (m) cc_final: 0.9177 (p) REVERT: C 9 TYR cc_start: 0.9389 (t80) cc_final: 0.9124 (t80) REVERT: C 21 ASN cc_start: 0.9066 (m-40) cc_final: 0.8687 (t0) REVERT: C 35 THR cc_start: 0.8936 (m) cc_final: 0.8563 (p) REVERT: C 38 ASP cc_start: 0.9455 (m-30) cc_final: 0.9125 (m-30) REVERT: C 41 ARG cc_start: 0.9387 (ttt180) cc_final: 0.9039 (ttp-170) REVERT: C 54 THR cc_start: 0.9686 (t) cc_final: 0.9328 (m) REVERT: C 86 ASP cc_start: 0.9520 (OUTLIER) cc_final: 0.9217 (p0) REVERT: C 88 VAL cc_start: 0.9611 (t) cc_final: 0.9383 (p) REVERT: D 37 ARG cc_start: 0.8704 (ttt180) cc_final: 0.8317 (tmm-80) REVERT: D 39 GLN cc_start: 0.9555 (pt0) cc_final: 0.9301 (pt0) REVERT: D 41 ARG cc_start: 0.9250 (ttp-170) cc_final: 0.8799 (ttp-110) REVERT: D 87 GLU cc_start: 0.9598 (tp30) cc_final: 0.9353 (tp30) REVERT: D 91 VAL cc_start: 0.9248 (t) cc_final: 0.8944 (p) REVERT: E 3 PHE cc_start: 0.9106 (t80) cc_final: 0.8868 (t80) REVERT: E 23 ASP cc_start: 0.8712 (t0) cc_final: 0.8457 (t70) REVERT: E 37 ARG cc_start: 0.8759 (tmm-80) cc_final: 0.8538 (tmm-80) REVERT: E 52 ARG cc_start: 0.9422 (ttm-80) cc_final: 0.9129 (tpp80) REVERT: E 60 ASN cc_start: 0.9590 (t0) cc_final: 0.9322 (m110) REVERT: G 1 MET cc_start: 0.8005 (ttm) cc_final: 0.7592 (ttm) REVERT: G 3 PHE cc_start: 0.9089 (t80) cc_final: 0.8847 (t80) REVERT: G 60 ASN cc_start: 0.9391 (t0) cc_final: 0.9161 (m110) REVERT: G 72 PHE cc_start: 0.9686 (t80) cc_final: 0.9478 (t80) REVERT: G 76 LEU cc_start: 0.9761 (mt) cc_final: 0.9468 (mt) REVERT: G 77 ARG cc_start: 0.9387 (tpp80) cc_final: 0.9023 (mmt90) REVERT: I 1 MET cc_start: 0.7982 (tpp) cc_final: 0.7697 (mmp) REVERT: I 3 PHE cc_start: 0.8661 (t80) cc_final: 0.8386 (t80) REVERT: I 9 TYR cc_start: 0.9232 (t80) cc_final: 0.9000 (t80) REVERT: I 24 VAL cc_start: 0.9432 (m) cc_final: 0.9037 (p) REVERT: I 46 CYS cc_start: 0.9697 (t) cc_final: 0.9483 (t) REVERT: I 77 ARG cc_start: 0.9245 (mmt90) cc_final: 0.8948 (mmt-90) REVERT: I 95 TYR cc_start: 0.9237 (m-80) cc_final: 0.8658 (m-80) REVERT: I 96 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8151 (mm-40) REVERT: L 9 TYR cc_start: 0.9384 (t80) cc_final: 0.9142 (t80) REVERT: L 14 ARG cc_start: 0.9103 (mtm-85) cc_final: 0.8871 (mtm110) REVERT: L 23 ASP cc_start: 0.9149 (t70) cc_final: 0.8842 (t70) REVERT: L 40 ASP cc_start: 0.9370 (t0) cc_final: 0.9160 (t0) REVERT: L 64 ARG cc_start: 0.9361 (mmt90) cc_final: 0.9108 (mmm-85) REVERT: L 91 VAL cc_start: 0.9264 (t) cc_final: 0.9041 (p) outliers start: 51 outliers final: 35 residues processed: 505 average time/residue: 0.2121 time to fit residues: 132.7565 Evaluate side-chains 517 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 480 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 35 THR Chi-restraints excluded: chain A residue 48 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 C residue 6 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 43 ARG 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 D residue 51 ASN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 60 ASN A 96 GLN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN L 18 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.9450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6496 Z= 0.275 Angle : 0.758 9.118 8840 Z= 0.398 Chirality : 0.045 0.185 968 Planarity : 0.006 0.076 1144 Dihedral : 4.572 22.480 880 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.37 % Favored : 97.50 % Rotamer: Outliers : 7.56 % Allowed : 39.97 % Favored : 52.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.30), residues: 760 helix: 0.21 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.59 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.001 0.000 HIS C 57 PHE 0.023 0.002 PHE E 16 TYR 0.031 0.003 TYR G 9 ARG 0.013 0.001 ARG E 37 *********************** 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 532 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 480 time to evaluate : 0.700 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: A 14 ARG cc_start: 0.9114 (mtm-85) cc_final: 0.8668 (mtm-85) REVERT: A 51 ASN cc_start: 0.8453 (p0) cc_final: 0.7901 (t0) REVERT: A 52 ARG cc_start: 0.8959 (ptp-110) cc_final: 0.8652 (ptp-110) REVERT: A 55 LEU cc_start: 0.9138 (mt) cc_final: 0.8732 (mt) REVERT: A 77 ARG cc_start: 0.8958 (mmt-90) cc_final: 0.8719 (mmt-90) REVERT: A 95 TYR cc_start: 0.8845 (m-10) cc_final: 0.8645 (m-10) REVERT: B 9 TYR cc_start: 0.8905 (t80) cc_final: 0.8418 (t80) REVERT: B 14 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8968 (mtp-110) REVERT: B 22 VAL cc_start: 0.9247 (t) cc_final: 0.8832 (m) REVERT: B 38 ASP cc_start: 0.9205 (m-30) cc_final: 0.8696 (m-30) REVERT: B 41 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7693 (ptp-170) REVERT: B 53 ASP cc_start: 0.9216 (m-30) cc_final: 0.8701 (m-30) REVERT: C 9 TYR cc_start: 0.9439 (t80) cc_final: 0.9064 (t80) REVERT: C 14 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.8799 (mtm-85) REVERT: C 20 CYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8857 (t) REVERT: C 21 ASN cc_start: 0.9052 (m-40) cc_final: 0.8506 (t0) REVERT: C 35 THR cc_start: 0.8945 (m) cc_final: 0.8595 (p) REVERT: C 38 ASP cc_start: 0.9446 (m-30) cc_final: 0.9146 (m-30) REVERT: C 41 ARG cc_start: 0.9380 (ttt180) cc_final: 0.9051 (ttp-170) REVERT: C 86 ASP cc_start: 0.9539 (OUTLIER) cc_final: 0.9298 (p0) REVERT: C 88 VAL cc_start: 0.9608 (t) cc_final: 0.9396 (p) REVERT: D 37 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8373 (tmm-80) REVERT: D 41 ARG cc_start: 0.9268 (ttp-170) cc_final: 0.8847 (ttp-110) REVERT: D 77 ARG cc_start: 0.9314 (mmt90) cc_final: 0.9098 (mmt90) REVERT: D 91 VAL cc_start: 0.9315 (t) cc_final: 0.9042 (p) REVERT: E 3 PHE cc_start: 0.9152 (t80) cc_final: 0.8920 (t80) REVERT: E 14 ARG cc_start: 0.8993 (mtp-110) cc_final: 0.8780 (mtm-85) REVERT: E 23 ASP cc_start: 0.8686 (t0) cc_final: 0.8132 (t0) REVERT: E 26 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9012 (mm-30) REVERT: E 52 ARG cc_start: 0.9455 (ttm-80) cc_final: 0.9188 (tpp80) REVERT: E 60 ASN cc_start: 0.9637 (t0) cc_final: 0.9396 (m110) REVERT: E 77 ARG cc_start: 0.9296 (mmt90) cc_final: 0.8878 (mmt180) REVERT: E 87 GLU cc_start: 0.9423 (tt0) cc_final: 0.9189 (tp30) REVERT: G 1 MET cc_start: 0.8010 (ttm) cc_final: 0.7702 (ttm) REVERT: G 59 PHE cc_start: 0.9570 (m-80) cc_final: 0.9298 (m-80) REVERT: G 60 ASN cc_start: 0.9439 (t0) cc_final: 0.9198 (m110) REVERT: G 77 ARG cc_start: 0.9403 (tpp80) cc_final: 0.9028 (mmt90) REVERT: I 1 MET cc_start: 0.7967 (tpp) cc_final: 0.7682 (mmp) REVERT: I 3 PHE cc_start: 0.8682 (t80) cc_final: 0.8414 (t80) REVERT: I 24 VAL cc_start: 0.9421 (m) cc_final: 0.9017 (p) REVERT: I 46 CYS cc_start: 0.9688 (t) cc_final: 0.9456 (t) REVERT: I 87 GLU cc_start: 0.9384 (tt0) cc_final: 0.9128 (tp30) REVERT: I 95 TYR cc_start: 0.9260 (m-80) cc_final: 0.8721 (m-80) REVERT: I 96 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8151 (mm-40) REVERT: L 40 ASP cc_start: 0.9463 (t0) cc_final: 0.9255 (t0) REVERT: L 54 THR cc_start: 0.9720 (t) cc_final: 0.9451 (p) REVERT: L 64 ARG cc_start: 0.9363 (mmt90) cc_final: 0.9132 (mmm-85) outliers start: 52 outliers final: 37 residues processed: 493 average time/residue: 0.2101 time to fit residues: 128.9049 Evaluate side-chains 504 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 463 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 48 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 42 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 82 VAL Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 27 ILE 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 20 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS C 63 GLN E 39 GLN E 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN I 39 GLN I 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.9632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6496 Z= 0.241 Angle : 0.794 9.774 8840 Z= 0.407 Chirality : 0.045 0.188 968 Planarity : 0.006 0.136 1144 Dihedral : 4.534 21.957 880 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.37 % Favored : 97.50 % Rotamer: Outliers : 7.27 % Allowed : 41.13 % Favored : 51.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.30), residues: 760 helix: 0.19 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.43 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 56 HIS 0.001 0.000 HIS B 57 PHE 0.027 0.002 PHE D 16 TYR 0.036 0.002 TYR G 9 ARG 0.015 0.001 ARG E 37 *********************** 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 532 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 482 time to evaluate : 0.793 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 51 ASN cc_start: 0.8462 (p0) cc_final: 0.7891 (t0) REVERT: A 52 ARG cc_start: 0.8971 (ptp-110) cc_final: 0.8674 (ptp-110) REVERT: A 55 LEU cc_start: 0.9113 (mt) cc_final: 0.8691 (mt) REVERT: A 77 ARG cc_start: 0.8992 (mmt-90) cc_final: 0.8765 (mmt-90) REVERT: B 9 TYR cc_start: 0.8903 (t80) cc_final: 0.8392 (t80) REVERT: B 14 ARG cc_start: 0.9227 (ttp-110) cc_final: 0.8957 (mtp-110) REVERT: B 22 VAL cc_start: 0.9257 (t) cc_final: 0.8797 (m) REVERT: B 38 ASP cc_start: 0.9164 (m-30) cc_final: 0.8795 (m-30) REVERT: B 41 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7813 (ptp-170) REVERT: B 53 ASP cc_start: 0.9163 (m-30) cc_final: 0.8588 (m-30) REVERT: C 3 PHE cc_start: 0.8672 (t80) cc_final: 0.8115 (t80) REVERT: C 7 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8873 (mtmm) REVERT: C 9 TYR cc_start: 0.9420 (t80) cc_final: 0.9006 (t80) REVERT: C 20 CYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8867 (t) REVERT: C 21 ASN cc_start: 0.9081 (m-40) cc_final: 0.8446 (t0) REVERT: C 35 THR cc_start: 0.8842 (m) cc_final: 0.8515 (p) REVERT: C 38 ASP cc_start: 0.9424 (m-30) cc_final: 0.9120 (m-30) REVERT: C 41 ARG cc_start: 0.9415 (ttt180) cc_final: 0.9051 (ttp-170) REVERT: C 77 ARG cc_start: 0.9186 (mmt90) cc_final: 0.8786 (mmt180) REVERT: C 86 ASP cc_start: 0.9607 (OUTLIER) cc_final: 0.9396 (p0) REVERT: C 88 VAL cc_start: 0.9603 (t) cc_final: 0.9401 (p) REVERT: D 9 TYR cc_start: 0.9354 (t80) cc_final: 0.9113 (t80) REVERT: D 37 ARG cc_start: 0.8711 (ttt180) cc_final: 0.8382 (tmm-80) REVERT: D 41 ARG cc_start: 0.9263 (ttp-170) cc_final: 0.8860 (ttp-110) REVERT: E 3 PHE cc_start: 0.9088 (t80) cc_final: 0.8868 (t80) REVERT: E 9 TYR cc_start: 0.9279 (t80) cc_final: 0.8888 (t80) REVERT: E 14 ARG cc_start: 0.9000 (mtp-110) cc_final: 0.8761 (mtm-85) REVERT: E 23 ASP cc_start: 0.8667 (t0) cc_final: 0.8059 (t0) REVERT: E 26 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8954 (mm-30) REVERT: E 52 ARG cc_start: 0.9432 (ttm-80) cc_final: 0.9182 (tpp80) REVERT: E 60 ASN cc_start: 0.9602 (t0) cc_final: 0.9396 (m110) REVERT: E 87 GLU cc_start: 0.9398 (tt0) cc_final: 0.9177 (tp30) REVERT: G 1 MET cc_start: 0.8126 (ttm) cc_final: 0.7719 (ttm) REVERT: G 10 LYS cc_start: 0.9536 (ttpp) cc_final: 0.9299 (ttpp) REVERT: G 14 ARG cc_start: 0.9297 (mtp-110) cc_final: 0.8928 (mtm-85) REVERT: G 19 PHE cc_start: 0.9336 (m-80) cc_final: 0.9103 (m-80) REVERT: G 59 PHE cc_start: 0.9531 (m-80) cc_final: 0.9272 (m-80) REVERT: G 60 ASN cc_start: 0.9450 (t0) cc_final: 0.9212 (m110) REVERT: G 76 LEU cc_start: 0.9637 (mt) cc_final: 0.9381 (mt) REVERT: G 77 ARG cc_start: 0.9351 (tpp80) cc_final: 0.9074 (mmt90) REVERT: I 1 MET cc_start: 0.7940 (tpp) cc_final: 0.7593 (mmp) REVERT: I 3 PHE cc_start: 0.8583 (t80) cc_final: 0.8302 (t80) REVERT: I 14 ARG cc_start: 0.9223 (mtm110) cc_final: 0.8997 (mtm110) REVERT: I 87 GLU cc_start: 0.9372 (tt0) cc_final: 0.9098 (tp30) REVERT: I 95 TYR cc_start: 0.9212 (m-80) cc_final: 0.8726 (m-80) REVERT: I 96 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8110 (mm-40) REVERT: L 40 ASP cc_start: 0.9461 (t0) cc_final: 0.9260 (t0) REVERT: L 41 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8776 (ttm110) REVERT: L 54 THR cc_start: 0.9701 (t) cc_final: 0.9464 (p) REVERT: L 64 ARG cc_start: 0.9391 (mmt90) cc_final: 0.9146 (mmm-85) outliers start: 50 outliers final: 39 residues processed: 497 average time/residue: 0.2140 time to fit residues: 131.7758 Evaluate side-chains 514 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 472 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 35 THR Chi-restraints excluded: chain A residue 48 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 B residue 91 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 43 ARG 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 86 ASP Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 42 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 82 VAL Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 CYS 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 66 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS C 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN I 39 GLN ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.9770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6496 Z= 0.291 Angle : 0.836 9.434 8840 Z= 0.432 Chirality : 0.046 0.187 968 Planarity : 0.007 0.166 1144 Dihedral : 4.606 21.336 880 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.63 % Favored : 97.24 % Rotamer: Outliers : 6.10 % Allowed : 42.30 % Favored : 51.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.30), residues: 760 helix: 0.19 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.39 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.002 0.000 HIS C 57 PHE 0.022 0.002 PHE G 16 TYR 0.035 0.002 TYR G 9 ARG 0.013 0.001 ARG D 14 *********************** 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 528 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 486 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8376 (ttp80) REVERT: A 51 ASN cc_start: 0.8489 (p0) cc_final: 0.7924 (t0) REVERT: A 52 ARG cc_start: 0.8965 (ptp-110) cc_final: 0.8664 (ptp-110) REVERT: A 55 LEU cc_start: 0.9165 (mt) cc_final: 0.8763 (mt) REVERT: A 77 ARG cc_start: 0.8965 (mmt-90) cc_final: 0.8722 (mmt-90) REVERT: B 9 TYR cc_start: 0.8918 (t80) cc_final: 0.8447 (t80) REVERT: B 14 ARG cc_start: 0.9219 (ttp-110) cc_final: 0.8960 (mtp-110) REVERT: B 22 VAL cc_start: 0.9289 (t) cc_final: 0.8843 (m) REVERT: B 41 ARG cc_start: 0.8265 (ttm110) cc_final: 0.7522 (ptp-170) REVERT: B 53 ASP cc_start: 0.9185 (m-30) cc_final: 0.8523 (m-30) REVERT: B 71 TYR cc_start: 0.9425 (m-80) cc_final: 0.9128 (m-80) REVERT: C 3 PHE cc_start: 0.8698 (t80) cc_final: 0.8177 (t80) REVERT: C 7 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8904 (mtmm) REVERT: C 9 TYR cc_start: 0.9449 (t80) cc_final: 0.9065 (t80) REVERT: C 14 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8742 (mtm-85) REVERT: C 20 CYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8867 (t) REVERT: C 21 ASN cc_start: 0.9086 (m-40) cc_final: 0.8581 (t0) REVERT: C 35 THR cc_start: 0.8847 (m) cc_final: 0.8528 (p) REVERT: C 38 ASP cc_start: 0.9419 (m-30) cc_final: 0.9110 (m-30) REVERT: C 41 ARG cc_start: 0.9399 (ttt180) cc_final: 0.9061 (ttp-170) REVERT: C 77 ARG cc_start: 0.9213 (mmt90) cc_final: 0.8893 (mmt-90) REVERT: C 86 ASP cc_start: 0.9610 (OUTLIER) cc_final: 0.9399 (p0) REVERT: C 88 VAL cc_start: 0.9620 (t) cc_final: 0.9396 (p) REVERT: D 37 ARG cc_start: 0.8666 (ttt180) cc_final: 0.8295 (tmm-80) REVERT: D 41 ARG cc_start: 0.9293 (ttp-170) cc_final: 0.8862 (ttp-110) REVERT: E 3 PHE cc_start: 0.9131 (t80) cc_final: 0.8903 (t80) REVERT: E 9 TYR cc_start: 0.9334 (t80) cc_final: 0.8991 (t80) REVERT: E 14 ARG cc_start: 0.9022 (mtp-110) cc_final: 0.8789 (mtm-85) REVERT: E 23 ASP cc_start: 0.8653 (t0) cc_final: 0.7975 (t0) REVERT: E 26 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8921 (mm-30) REVERT: E 52 ARG cc_start: 0.9447 (ttm-80) cc_final: 0.9202 (tpp80) REVERT: E 60 ASN cc_start: 0.9686 (t0) cc_final: 0.9438 (m110) REVERT: E 87 GLU cc_start: 0.9406 (tt0) cc_final: 0.9196 (tp30) REVERT: G 1 MET cc_start: 0.8149 (ttm) cc_final: 0.7831 (ttm) REVERT: G 10 LYS cc_start: 0.9549 (ttpp) cc_final: 0.9342 (ttpp) REVERT: G 14 ARG cc_start: 0.9305 (mtp-110) cc_final: 0.8937 (mtm-85) REVERT: G 19 PHE cc_start: 0.9328 (m-80) cc_final: 0.9079 (m-80) REVERT: G 37 ARG cc_start: 0.8848 (tmt170) cc_final: 0.7947 (tmt170) REVERT: G 41 ARG cc_start: 0.9437 (ttp80) cc_final: 0.9129 (ttp80) REVERT: G 59 PHE cc_start: 0.9566 (m-80) cc_final: 0.9309 (m-80) REVERT: G 60 ASN cc_start: 0.9481 (t0) cc_final: 0.9222 (m110) REVERT: G 76 LEU cc_start: 0.9642 (mt) cc_final: 0.9388 (mt) REVERT: G 77 ARG cc_start: 0.9368 (tpp80) cc_final: 0.9065 (mmt90) REVERT: I 3 PHE cc_start: 0.8662 (t80) cc_final: 0.8459 (t80) REVERT: I 14 ARG cc_start: 0.9236 (mtm110) cc_final: 0.9018 (mtm110) REVERT: I 77 ARG cc_start: 0.9365 (mmt90) cc_final: 0.8926 (mmt-90) REVERT: I 87 GLU cc_start: 0.9380 (tt0) cc_final: 0.9145 (tp30) REVERT: I 95 TYR cc_start: 0.9249 (m-80) cc_final: 0.8739 (m-80) REVERT: I 96 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8124 (mm-40) REVERT: L 39 GLN cc_start: 0.9231 (pt0) cc_final: 0.8862 (pp30) REVERT: L 43 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.8726 (mtt90) REVERT: L 54 THR cc_start: 0.9720 (t) cc_final: 0.9480 (p) outliers start: 42 outliers final: 34 residues processed: 499 average time/residue: 0.2189 time to fit residues: 134.7721 Evaluate side-chains 518 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 480 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 35 THR Chi-restraints excluded: chain A residue 48 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 B residue 91 VAL Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 43 ARG 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 D residue 51 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 39 GLN 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 27 ILE Chi-restraints excluded: chain L residue 43 ARG Chi-restraints excluded: chain L residue 46 CYS 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 32 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 0.0570 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 57 HIS C 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 1.0006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6496 Z= 0.250 Angle : 0.877 10.886 8840 Z= 0.444 Chirality : 0.045 0.194 968 Planarity : 0.007 0.137 1144 Dihedral : 4.602 21.463 880 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.63 % Favored : 97.24 % Rotamer: Outliers : 4.65 % Allowed : 45.06 % Favored : 50.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 760 helix: -0.01 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.06 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 56 HIS 0.001 0.000 HIS C 57 PHE 0.028 0.002 PHE L 59 TYR 0.038 0.002 TYR G 9 ARG 0.014 0.001 ARG D 14 ********************** 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 527 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 495 time to evaluate : 0.799 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: 0.9093 (mt-10) cc_final: 0.8867 (tt0) REVERT: A 14 ARG cc_start: 0.9070 (mtp-110) cc_final: 0.8662 (mtm-85) REVERT: A 22 VAL cc_start: 0.9626 (m) cc_final: 0.9418 (m) REVERT: A 37 ARG cc_start: 0.8926 (ttp80) cc_final: 0.8041 (ttp80) REVERT: A 39 GLN cc_start: 0.9209 (pt0) cc_final: 0.8830 (pp30) REVERT: A 41 ARG cc_start: 0.9344 (ttp80) cc_final: 0.8773 (ttm110) REVERT: A 51 ASN cc_start: 0.8352 (p0) cc_final: 0.7743 (t0) REVERT: A 52 ARG cc_start: 0.8853 (ptp-110) cc_final: 0.8583 (ptp-110) REVERT: A 55 LEU cc_start: 0.9081 (mt) cc_final: 0.8667 (mt) REVERT: A 77 ARG cc_start: 0.8993 (mmt-90) cc_final: 0.8684 (mmt180) REVERT: B 14 ARG cc_start: 0.9213 (ttp-110) cc_final: 0.8954 (mtp-110) REVERT: B 38 ASP cc_start: 0.9039 (m-30) cc_final: 0.8645 (m-30) REVERT: B 41 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7826 (ptp-170) REVERT: B 53 ASP cc_start: 0.9079 (m-30) cc_final: 0.8512 (m-30) REVERT: B 63 GLN cc_start: 0.9435 (pp30) cc_final: 0.8758 (pt0) REVERT: B 77 ARG cc_start: 0.9449 (mmt-90) cc_final: 0.9175 (mmt180) REVERT: B 86 ASP cc_start: 0.9337 (p0) cc_final: 0.8920 (p0) REVERT: C 3 PHE cc_start: 0.8513 (t80) cc_final: 0.8212 (t80) REVERT: C 9 TYR cc_start: 0.9387 (t80) cc_final: 0.8972 (t80) REVERT: C 21 ASN cc_start: 0.8929 (m-40) cc_final: 0.8424 (t0) REVERT: C 35 THR cc_start: 0.8698 (m) cc_final: 0.8425 (p) REVERT: C 38 ASP cc_start: 0.9396 (m-30) cc_final: 0.9088 (m-30) REVERT: C 41 ARG cc_start: 0.9415 (ttt180) cc_final: 0.9064 (ttp-170) REVERT: C 77 ARG cc_start: 0.9260 (mmt90) cc_final: 0.8943 (mmt180) REVERT: C 86 ASP cc_start: 0.9588 (OUTLIER) cc_final: 0.9377 (p0) REVERT: D 10 LYS cc_start: 0.9566 (ptpt) cc_final: 0.9354 (ttpp) REVERT: D 37 ARG cc_start: 0.8694 (ttt180) cc_final: 0.8316 (tmm-80) REVERT: D 41 ARG cc_start: 0.9287 (ttp-170) cc_final: 0.8893 (ttp-170) REVERT: D 77 ARG cc_start: 0.9227 (mmt90) cc_final: 0.9017 (mmt90) REVERT: E 3 PHE cc_start: 0.9033 (t80) cc_final: 0.8759 (t80) REVERT: E 9 TYR cc_start: 0.9251 (t80) cc_final: 0.8616 (t80) REVERT: E 14 ARG cc_start: 0.8985 (mtp-110) cc_final: 0.8747 (mtm110) REVERT: E 23 ASP cc_start: 0.8674 (t0) cc_final: 0.8065 (t0) REVERT: E 26 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8880 (mm-30) REVERT: E 52 ARG cc_start: 0.9354 (ttm-80) cc_final: 0.9117 (tpp80) REVERT: E 60 ASN cc_start: 0.9672 (t0) cc_final: 0.9471 (m110) REVERT: E 91 VAL cc_start: 0.9262 (t) cc_final: 0.8872 (p) REVERT: G 1 MET cc_start: 0.8041 (ttm) cc_final: 0.7610 (ttm) REVERT: G 14 ARG cc_start: 0.9288 (mtp-110) cc_final: 0.8965 (mtm110) REVERT: G 59 PHE cc_start: 0.9514 (m-80) cc_final: 0.9204 (m-80) REVERT: G 60 ASN cc_start: 0.9422 (t0) cc_final: 0.9213 (m110) REVERT: G 91 VAL cc_start: 0.9351 (t) cc_final: 0.9149 (p) REVERT: I 1 MET cc_start: 0.7659 (tpp) cc_final: 0.7434 (mmp) REVERT: I 3 PHE cc_start: 0.8468 (t80) cc_final: 0.8210 (t80) REVERT: I 11 TYR cc_start: 0.9433 (t80) cc_final: 0.9126 (t80) REVERT: I 14 ARG cc_start: 0.9195 (mtm110) cc_final: 0.8874 (mtm110) REVERT: I 77 ARG cc_start: 0.9384 (mmt90) cc_final: 0.9094 (mmt180) REVERT: I 87 GLU cc_start: 0.9355 (tt0) cc_final: 0.9088 (tp30) REVERT: I 95 TYR cc_start: 0.9131 (m-80) cc_final: 0.8761 (m-80) REVERT: I 96 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8123 (mm-40) REVERT: L 39 GLN cc_start: 0.9140 (pt0) cc_final: 0.8879 (pp30) REVERT: L 41 ARG cc_start: 0.8989 (ttm110) cc_final: 0.8716 (ttm110) REVERT: L 43 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.9047 (mtt-85) outliers start: 32 outliers final: 25 residues processed: 506 average time/residue: 0.2259 time to fit residues: 140.6499 Evaluate side-chains 511 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 483 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 43 ARG 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 D residue 51 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 43 ARG 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 52 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.064823 restraints weight = 22166.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066905 restraints weight = 11768.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.068332 restraints weight = 7422.392| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 1.0056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.194 6496 Z= 0.504 Angle : 1.311 59.200 8840 Z= 0.735 Chirality : 0.054 0.938 968 Planarity : 0.010 0.172 1144 Dihedral : 4.597 21.506 880 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.76 % Favored : 97.11 % Rotamer: Outliers : 4.51 % Allowed : 45.93 % Favored : 49.56 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 760 helix: -0.04 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.06 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 56 HIS 0.001 0.000 HIS C 57 PHE 0.024 0.002 PHE E 16 TYR 0.056 0.003 TYR E 95 ARG 0.029 0.001 ARG L 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.66 seconds wall clock time: 41 minutes 7.63 seconds (2467.63 seconds total)