Starting phenix.real_space_refine on Mon Dec 30 07:28:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dhx_27437/12_2024/8dhx_27437_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dhx_27437/12_2024/8dhx_27437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dhx_27437/12_2024/8dhx_27437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dhx_27437/12_2024/8dhx_27437.map" model { file = "/net/cci-nas-00/data/ceres_data/8dhx_27437/12_2024/8dhx_27437_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dhx_27437/12_2024/8dhx_27437_neut.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 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 33936 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 120 5.16 5 C 21504 2.51 5 N 5976 2.21 5 O 6600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 34200 Number of models: 1 Model: "" Number of chains: 1 Chain: "1" Number of atoms: 1425 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1436 Restraints were copied for chains: 2, 4, 6, A, B, E, G, F, I, H, K, M, O, Q, P, S, U, W, Y, X, a, e, r Time building chain proxies: 7.84, per 1000 atoms: 0.23 Number of scatterers: 34200 At special positions: 0 Unit cell: (137.16, 137.16, 137.16, 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 120 16.00 O 6600 8.00 N 5976 7.00 C 21504 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: 6.24 Conformation dependent library (CDL) restraints added in 6.0 seconds 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain '1' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE 1 20 " --> pdb=" O SER 1 16 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 76 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS 1 130 " --> pdb=" O ASP 1 126 " (cutoff:3.500A) Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 162 through 174 Processing helix chain '2' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE 2 20 " --> pdb=" O SER 2 16 " (cutoff:3.500A) Processing helix chain '2' and resid 48 through 76 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS 2 130 " --> pdb=" O ASP 2 126 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 162 through 174 Processing helix chain '4' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE 4 20 " --> pdb=" O SER 4 16 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 76 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS 4 130 " --> pdb=" O ASP 4 126 " (cutoff:3.500A) Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 162 through 174 Processing helix chain '6' and resid 13 through 42 removed outlier: 3.510A pdb=" N ILE 6 20 " --> pdb=" O SER 6 16 " (cutoff:3.500A) Processing helix chain '6' and resid 48 through 76 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS 6 130 " --> pdb=" O ASP 6 126 " (cutoff:3.500A) Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 162 through 174 Processing helix chain 'A' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'B' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'E' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'F' and resid 13 through 42 removed outlier: 3.510A pdb=" N ILE F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 13 through 42 removed outlier: 3.510A pdb=" N ILE G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 162 through 174 Processing helix chain 'H' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS H 130 " --> pdb=" O ASP H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 162 through 174 Processing helix chain 'I' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS I 130 " --> pdb=" O ASP I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 162 through 174 Processing helix chain 'K' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE K 20 " --> pdb=" O SER K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 162 through 174 Processing helix chain 'M' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE M 20 " --> pdb=" O SER M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS M 130 " --> pdb=" O ASP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 162 through 174 Processing helix chain 'O' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE O 20 " --> pdb=" O SER O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS O 130 " --> pdb=" O ASP O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 162 through 174 Processing helix chain 'P' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE P 20 " --> pdb=" O SER P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS P 130 " --> pdb=" O ASP P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 162 through 174 Processing helix chain 'Q' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE Q 20 " --> pdb=" O SER Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS Q 130 " --> pdb=" O ASP Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 162 through 174 Processing helix chain 'S' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE S 20 " --> pdb=" O SER S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 removed outlier: 3.515A pdb=" N CYS S 130 " --> pdb=" O ASP S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 162 through 174 Processing helix chain 'U' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE U 20 " --> pdb=" O SER U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS U 130 " --> pdb=" O ASP U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 162 through 174 Processing helix chain 'W' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE W 20 " --> pdb=" O SER W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS W 130 " --> pdb=" O ASP W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 162 through 174 Processing helix chain 'X' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE X 20 " --> pdb=" O SER X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 removed outlier: 3.515A pdb=" N CYS X 130 " --> pdb=" O ASP X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 162 through 174 Processing helix chain 'Y' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE Y 20 " --> pdb=" O SER Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 76 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS Y 130 " --> pdb=" O ASP Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 162 through 174 Processing helix chain 'a' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE a 20 " --> pdb=" O SER a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 76 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS a 130 " --> pdb=" O ASP a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 162 through 174 Processing helix chain 'e' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 76 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'r' and resid 13 through 42 removed outlier: 3.509A pdb=" N ILE r 20 " --> pdb=" O SER r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 76 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 removed outlier: 3.514A pdb=" N CYS r 130 " --> pdb=" O ASP r 126 " (cutoff:3.500A) Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 162 through 174 2664 hydrogen bonds defined for protein. 7944 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: 8.58 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6748 1.32 - 1.45: 8650 1.45 - 1.57: 19330 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 34944 Sorted by residual: bond pdb=" C SER F 163 " pdb=" O SER F 163 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.17e-02 7.31e+03 7.87e+00 bond pdb=" C SER O 163 " pdb=" O SER O 163 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.17e-02 7.31e+03 7.84e+00 bond pdb=" C SER 4 163 " pdb=" O SER 4 163 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.17e-02 7.31e+03 7.84e+00 bond pdb=" C SER M 163 " pdb=" O SER M 163 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.51e+00 bond pdb=" C SER W 163 " pdb=" O SER W 163 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.51e+00 ... (remaining 34939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 46024 2.25 - 4.50: 896 4.50 - 6.75: 192 6.75 - 9.00: 24 9.00 - 11.25: 24 Bond angle restraints: 47160 Sorted by residual: angle pdb=" C GLN A 14 " pdb=" N ASP A 15 " pdb=" CA ASP A 15 " ideal model delta sigma weight residual 120.44 131.69 -11.25 1.30e+00 5.92e-01 7.49e+01 angle pdb=" C GLN Y 14 " pdb=" N ASP Y 15 " pdb=" CA ASP Y 15 " ideal model delta sigma weight residual 120.44 131.68 -11.24 1.30e+00 5.92e-01 7.48e+01 angle pdb=" C GLN X 14 " pdb=" N ASP X 15 " pdb=" CA ASP X 15 " ideal model delta sigma weight residual 120.44 131.66 -11.22 1.30e+00 5.92e-01 7.45e+01 angle pdb=" C GLN Q 14 " pdb=" N ASP Q 15 " pdb=" CA ASP Q 15 " ideal model delta sigma weight residual 120.44 131.65 -11.21 1.30e+00 5.92e-01 7.44e+01 angle pdb=" C GLN I 14 " pdb=" N ASP I 15 " pdb=" CA ASP I 15 " ideal model delta sigma weight residual 120.44 131.65 -11.21 1.30e+00 5.92e-01 7.44e+01 ... (remaining 47155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 18236 17.41 - 34.83: 2092 34.83 - 52.24: 648 52.24 - 69.65: 168 69.65 - 87.06: 96 Dihedral angle restraints: 21240 sinusoidal: 8736 harmonic: 12504 Sorted by residual: dihedral pdb=" CA TYR r 39 " pdb=" C TYR r 39 " pdb=" N TYR r 40 " pdb=" CA TYR r 40 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TYR A 39 " pdb=" C TYR A 39 " pdb=" N TYR A 40 " pdb=" CA TYR A 40 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TYR S 39 " pdb=" C TYR S 39 " pdb=" N TYR S 40 " pdb=" CA TYR S 40 " ideal model delta harmonic sigma weight residual 180.00 164.14 15.86 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 21237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4234 0.047 - 0.094: 421 0.094 - 0.141: 268 0.141 - 0.188: 45 0.188 - 0.234: 24 Chirality restraints: 4992 Sorted by residual: chirality pdb=" CG LEU W 97 " pdb=" CB LEU W 97 " pdb=" CD1 LEU W 97 " pdb=" CD2 LEU W 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU I 97 " pdb=" CB LEU I 97 " pdb=" CD1 LEU I 97 " pdb=" CD2 LEU I 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU Y 97 " pdb=" CB LEU Y 97 " pdb=" CD1 LEU Y 97 " pdb=" CD2 LEU Y 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 4989 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 95 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C SER M 95 " -0.018 2.00e-02 2.50e+03 pdb=" O SER M 95 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY M 96 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 95 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C SER F 95 " -0.018 2.00e-02 2.50e+03 pdb=" O SER F 95 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY F 96 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER U 95 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C SER U 95 " 0.018 2.00e-02 2.50e+03 pdb=" O SER U 95 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY U 96 " -0.006 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4885 2.75 - 3.29: 33685 3.29 - 3.83: 58947 3.83 - 4.36: 69949 4.36 - 4.90: 120726 Nonbonded interactions: 288192 Sorted by model distance: nonbonded pdb=" ND2 ASN X 50 " pdb=" OD1 ASP X 171 " model vdw 2.218 3.120 nonbonded pdb=" ND2 ASN I 50 " pdb=" OD1 ASP I 171 " model vdw 2.218 3.120 nonbonded pdb=" ND2 ASN F 50 " pdb=" OD1 ASP F 171 " model vdw 2.218 3.120 nonbonded pdb=" ND2 ASN H 50 " pdb=" OD1 ASP H 171 " model vdw 2.218 3.120 nonbonded pdb=" ND2 ASN E 50 " pdb=" OD1 ASP E 171 " model vdw 2.219 3.120 ... (remaining 288187 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 '1' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain '2' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain '4' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain '6' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'A' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'B' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'E' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'F' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'G' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'H' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'I' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'K' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'M' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'O' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'P' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'Q' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'S' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'U' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'W' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'X' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'Y' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'a' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'e' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) selection = (chain 'r' and (resid 4 through 112 or resid 114 through 132 or resid 134 throug \ h 176)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.400 Construct map_model_manager: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.260 Set scattering table: 0.350 Process input model: 51.440 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2119 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 : 0.004 0.033 34944 Z= 0.254 Angle : 0.819 11.251 47160 Z= 0.517 Chirality : 0.043 0.234 4992 Planarity : 0.003 0.016 6216 Dihedral : 17.606 87.065 13176 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.58 % Allowed : 1.75 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 19.48 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.13), residues: 4152 helix: 3.21 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.37 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 2 93 HIS 0.007 0.001 HIS U 13 PHE 0.011 0.001 PHE O 132 TYR 0.012 0.002 TYR Q 137 ARG 0.002 0.000 ARG F 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 639 time to evaluate : 3.264 Fit side-chains REVERT: 2 153 THR cc_start: 0.3586 (OUTLIER) cc_final: 0.3232 (t) REVERT: 4 153 THR cc_start: 0.3585 (OUTLIER) cc_final: 0.3227 (t) REVERT: 6 153 THR cc_start: 0.3584 (OUTLIER) cc_final: 0.3184 (t) REVERT: F 153 THR cc_start: 0.3578 (OUTLIER) cc_final: 0.3209 (t) REVERT: H 153 THR cc_start: 0.3579 (OUTLIER) cc_final: 0.3181 (t) REVERT: I 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3224 (t) REVERT: M 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3225 (t) REVERT: O 153 THR cc_start: 0.3582 (OUTLIER) cc_final: 0.3223 (t) REVERT: P 153 THR cc_start: 0.3605 (OUTLIER) cc_final: 0.3210 (t) REVERT: Q 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3226 (t) REVERT: S 153 THR cc_start: 0.3586 (OUTLIER) cc_final: 0.3230 (t) REVERT: U 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3228 (t) REVERT: W 153 THR cc_start: 0.3585 (OUTLIER) cc_final: 0.3224 (t) REVERT: X 153 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3223 (t) REVERT: Y 153 THR cc_start: 0.3587 (OUTLIER) cc_final: 0.3230 (t) outliers start: 72 outliers final: 24 residues processed: 687 average time/residue: 1.2212 time to fit residues: 1002.4110 Evaluate side-chains 580 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 541 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 89 ASP Chi-restraints excluded: chain 2 residue 89 ASP Chi-restraints excluded: chain 2 residue 153 THR Chi-restraints excluded: chain 4 residue 89 ASP Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 6 residue 89 ASP Chi-restraints excluded: chain 6 residue 153 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 153 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 153 THR Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 153 THR Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 153 THR Chi-restraints excluded: chain Y residue 89 ASP Chi-restraints excluded: chain Y residue 153 THR Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain e residue 89 ASP Chi-restraints excluded: chain r residue 89 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2128 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 34944 Z= 0.296 Angle : 0.645 7.542 47160 Z= 0.331 Chirality : 0.039 0.123 4992 Planarity : 0.003 0.022 6216 Dihedral : 5.916 58.569 4671 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.03 % Allowed : 20.59 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.13), residues: 4152 helix: 3.67 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -1.33 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP S 93 HIS 0.004 0.001 HIS F 151 PHE 0.018 0.002 PHE 1 41 TYR 0.027 0.002 TYR G 39 ARG 0.005 0.001 ARG a 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 610 time to evaluate : 2.901 Fit side-chains outliers start: 149 outliers final: 40 residues processed: 681 average time/residue: 1.1986 time to fit residues: 974.1755 Evaluate side-chains 616 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 576 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 153 THR Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 153 THR Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 153 THR Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 153 THR Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 153 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 153 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 153 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 153 THR Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 153 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain r residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 371 optimal weight: 0.9990 chunk 400 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 297 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2132 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34944 Z= 0.191 Angle : 0.565 8.554 47160 Z= 0.292 Chirality : 0.035 0.119 4992 Planarity : 0.002 0.020 6216 Dihedral : 4.280 19.504 4623 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.76 % Allowed : 22.13 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.11 (0.13), residues: 4152 helix: 4.22 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.77 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 1 93 HIS 0.003 0.001 HIS H 151 PHE 0.013 0.001 PHE A 132 TYR 0.024 0.002 TYR W 39 ARG 0.007 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 591 time to evaluate : 2.933 Fit side-chains outliers start: 102 outliers final: 46 residues processed: 624 average time/residue: 1.2291 time to fit residues: 908.0571 Evaluate side-chains 636 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 590 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 64 GLU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain r residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 192 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 372 optimal weight: 0.9980 chunk 394 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2133 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34944 Z= 0.182 Angle : 0.544 7.226 47160 Z= 0.284 Chirality : 0.035 0.120 4992 Planarity : 0.003 0.023 6216 Dihedral : 4.127 19.569 4608 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.11 % Allowed : 21.70 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.28 (0.13), residues: 4152 helix: 4.30 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.50 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 2 93 HIS 0.003 0.000 HIS 6 151 PHE 0.013 0.002 PHE e 132 TYR 0.023 0.002 TYR S 39 ARG 0.007 0.001 ARG K 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 581 time to evaluate : 3.014 Fit side-chains outliers start: 152 outliers final: 67 residues processed: 663 average time/residue: 1.1823 time to fit residues: 932.0119 Evaluate side-chains 648 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 581 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 64 GLU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 64 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 293 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 336 optimal weight: 7.9990 chunk 272 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 353 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2133 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34944 Z= 0.253 Angle : 0.581 6.916 47160 Z= 0.305 Chirality : 0.037 0.119 4992 Planarity : 0.003 0.022 6216 Dihedral : 4.228 19.833 4608 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.71 % Allowed : 21.29 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.08 (0.13), residues: 4152 helix: 4.13 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.43 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 93 HIS 0.004 0.001 HIS I 151 PHE 0.015 0.002 PHE B 132 TYR 0.028 0.002 TYR A 39 ARG 0.006 0.001 ARG r 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 607 time to evaluate : 2.908 Fit side-chains outliers start: 174 outliers final: 73 residues processed: 692 average time/residue: 1.1346 time to fit residues: 943.2848 Evaluate side-chains 666 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 593 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 59 SER Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 64 GLU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 59 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 59 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2130 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34944 Z= 0.200 Angle : 0.591 9.886 47160 Z= 0.302 Chirality : 0.035 0.123 4992 Planarity : 0.003 0.031 6216 Dihedral : 4.189 20.628 4608 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.60 % Allowed : 21.02 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.35 (0.13), residues: 4152 helix: 4.35 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.47 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 93 HIS 0.003 0.000 HIS M 151 PHE 0.013 0.002 PHE e 132 TYR 0.029 0.002 TYR A 39 ARG 0.008 0.001 ARG F 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 565 time to evaluate : 2.908 Fit side-chains outliers start: 170 outliers final: 91 residues processed: 649 average time/residue: 1.1835 time to fit residues: 913.1287 Evaluate side-chains 658 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 567 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 59 SER Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 59 SER Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 64 GLU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 59 SER Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 59 SER Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 59 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 64 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2135 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34944 Z= 0.223 Angle : 0.596 9.664 47160 Z= 0.306 Chirality : 0.036 0.134 4992 Planarity : 0.003 0.026 6216 Dihedral : 4.199 20.939 4608 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.63 % Allowed : 23.13 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.24 (0.13), residues: 4152 helix: 4.28 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.52 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP r 93 HIS 0.003 0.000 HIS O 151 PHE 0.014 0.002 PHE K 132 TYR 0.024 0.002 TYR W 39 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 565 time to evaluate : 2.888 Fit side-chains outliers start: 134 outliers final: 96 residues processed: 638 average time/residue: 1.1815 time to fit residues: 896.9824 Evaluate side-chains 661 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 565 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 59 SER Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 59 SER Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 59 SER Chi-restraints excluded: chain 4 residue 64 GLU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 59 SER Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 59 SER Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 59 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 64 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.0870 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2133 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34944 Z= 0.173 Angle : 0.578 8.776 47160 Z= 0.295 Chirality : 0.034 0.131 4992 Planarity : 0.003 0.030 6216 Dihedral : 4.122 21.323 4608 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.98 % Allowed : 23.94 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.48 (0.13), residues: 4152 helix: 4.44 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.41 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 93 HIS 0.003 0.000 HIS Q 151 PHE 0.012 0.001 PHE 1 132 TYR 0.028 0.002 TYR M 29 ARG 0.006 0.000 ARG F 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 567 time to evaluate : 4.006 Fit side-chains outliers start: 110 outliers final: 55 residues processed: 623 average time/residue: 1.1551 time to fit residues: 859.7805 Evaluate side-chains 621 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 566 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 59 SER Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 59 SER Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 59 SER Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 59 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain r residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 4.9990 chunk 366 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 365 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2134 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34944 Z= 0.185 Angle : 0.572 8.538 47160 Z= 0.294 Chirality : 0.034 0.133 4992 Planarity : 0.003 0.030 6216 Dihedral : 4.114 20.237 4608 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.35 % Allowed : 25.11 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.45 (0.13), residues: 4152 helix: 4.41 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.37 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 93 HIS 0.003 0.000 HIS P 151 PHE 0.013 0.001 PHE 1 132 TYR 0.026 0.002 TYR 6 29 ARG 0.006 0.000 ARG H 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 571 time to evaluate : 3.191 Fit side-chains REVERT: 4 158 MET cc_start: -0.0440 (mmm) cc_final: -0.0646 (mtm) REVERT: U 158 MET cc_start: -0.0450 (mmm) cc_final: -0.0656 (mtm) outliers start: 87 outliers final: 66 residues processed: 613 average time/residue: 1.1202 time to fit residues: 832.9167 Evaluate side-chains 637 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 571 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 59 SER Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 59 SER Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 59 SER Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 59 SER Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 59 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 59 SER Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 406 optimal weight: 0.9990 chunk 374 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 250 optimal weight: 0.0570 chunk 198 optimal weight: 8.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2138 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34944 Z= 0.215 Angle : 0.600 8.332 47160 Z= 0.306 Chirality : 0.035 0.134 4992 Planarity : 0.003 0.033 6216 Dihedral : 4.151 20.604 4608 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.19 % Allowed : 25.35 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.31 (0.13), residues: 4152 helix: 4.30 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.38 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 6 93 HIS 0.004 0.001 HIS Q 151 PHE 0.013 0.002 PHE K 132 TYR 0.026 0.002 TYR M 29 ARG 0.004 0.000 ARG B 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8304 Ramachandran restraints generated. 4152 Oldfield, 0 Emsley, 4152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 566 time to evaluate : 2.961 Fit side-chains outliers start: 81 outliers final: 73 residues processed: 615 average time/residue: 1.0912 time to fit residues: 809.1620 Evaluate side-chains 641 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 568 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 59 SER Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 SER Chi-restraints excluded: chain 2 residue 59 SER Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 59 SER Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 6 SER Chi-restraints excluded: chain 6 residue 59 SER Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 59 SER Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 SER Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 59 SER Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 59 SER Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 6 SER Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 SER Chi-restraints excluded: chain r residue 59 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 332 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122602 restraints weight = 182962.035| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.44 r_work: 0.3447 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34944 Z= 0.162 Angle : 0.580 10.463 47160 Z= 0.295 Chirality : 0.034 0.144 4992 Planarity : 0.003 0.032 6216 Dihedral : 4.114 21.100 4608 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.81 % Allowed : 25.73 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.52 (0.13), residues: 4152 helix: 4.44 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.27 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP r 93 HIS 0.003 0.000 HIS O 151 PHE 0.012 0.001 PHE e 132 TYR 0.027 0.001 TYR X 29 ARG 0.005 0.000 ARG W 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12982.27 seconds wall clock time: 224 minutes 48.67 seconds (13488.67 seconds total)