Starting phenix.real_space_refine on Wed Jun 11 22:08:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwz_35069/06_2025/8hwz_35069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwz_35069/06_2025/8hwz_35069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwz_35069/06_2025/8hwz_35069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwz_35069/06_2025/8hwz_35069.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwz_35069/06_2025/8hwz_35069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwz_35069/06_2025/8hwz_35069.cif" } resolution = 3.56 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= 0.003 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 8453 2.51 5 N 2432 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13625 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "B" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "C" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1131 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "D" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "G" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "H" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "J" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.34, per 1000 atoms: 0.61 Number of scatterers: 13625 At special positions: 0 Unit cell: (103.04, 103.04, 102.12, 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 12 16.00 O 2728 8.00 N 2432 7.00 C 8453 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: 3.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 16 through 44 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 103 through 133 removed outlier: 4.001A pdb=" N ASP A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 156 Processing helix chain 'B' and resid 17 through 44 Processing helix chain 'B' and resid 48 through 77 removed outlier: 3.914A pdb=" N LEU B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 Processing helix chain 'B' and resid 103 through 131 removed outlier: 4.464A pdb=" N ASP B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 156 Processing helix chain 'C' and resid 18 through 44 Processing helix chain 'C' and resid 48 through 77 Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'C' and resid 103 through 133 removed outlier: 4.348A pdb=" N ASP C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 156 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'D' and resid 17 through 44 removed outlier: 3.554A pdb=" N VAL D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 77 removed outlier: 3.858A pdb=" N LEU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 92 Processing helix chain 'D' and resid 103 through 133 removed outlier: 4.064A pdb=" N ASP D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 156 Processing helix chain 'E' and resid 17 through 44 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 84 through 92 Processing helix chain 'E' and resid 103 through 133 removed outlier: 4.058A pdb=" N ASP E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 156 Processing helix chain 'G' and resid 17 through 44 Processing helix chain 'G' and resid 48 through 77 removed outlier: 3.911A pdb=" N LEU G 52 " --> pdb=" O ASN G 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP G 57 " --> pdb=" O HIS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 92 Processing helix chain 'G' and resid 103 through 131 removed outlier: 4.413A pdb=" N ASP G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 159 removed outlier: 4.079A pdb=" N GLU G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 44 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 84 through 92 Processing helix chain 'I' and resid 103 through 133 removed outlier: 4.489A pdb=" N ASP I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 156 Processing helix chain 'K' and resid 17 through 43 Processing helix chain 'K' and resid 48 through 77 removed outlier: 3.873A pdb=" N LEU K 52 " --> pdb=" O ASN K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 92 Processing helix chain 'K' and resid 103 through 133 removed outlier: 4.219A pdb=" N ASP K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 156 Processing helix chain 'F' and resid 17 through 44 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 84 through 92 Processing helix chain 'F' and resid 103 through 133 removed outlier: 4.040A pdb=" N ASP F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 156 Processing helix chain 'H' and resid 17 through 44 Processing helix chain 'H' and resid 48 through 77 removed outlier: 4.003A pdb=" N LEU H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP H 57 " --> pdb=" O HIS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 92 Processing helix chain 'H' and resid 103 through 131 removed outlier: 4.615A pdb=" N ASP H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA H 128 " --> pdb=" O ARG H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 156 Processing helix chain 'J' and resid 17 through 44 Processing helix chain 'J' and resid 48 through 77 Processing helix chain 'J' and resid 84 through 92 Processing helix chain 'J' and resid 103 through 133 removed outlier: 4.529A pdb=" N ASP J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ALA J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 156 Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'L' and resid 17 through 44 Processing helix chain 'L' and resid 48 through 77 removed outlier: 3.848A pdb=" N LEU L 52 " --> pdb=" O ASN L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 92 Processing helix chain 'L' and resid 103 through 133 removed outlier: 4.170A pdb=" N ASP L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 159 removed outlier: 4.114A pdb=" N GLU L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN L 158 " --> pdb=" O ILE L 154 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3555 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: 3.86 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4833 1.34 - 1.45: 1063 1.45 - 1.57: 7909 1.57 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 13829 Sorted by residual: bond pdb=" CB PRO F 98 " pdb=" CG PRO F 98 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.08e+00 bond pdb=" CB MET C 74 " pdb=" CG MET C 74 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.20e-01 bond pdb=" CB GLN D 36 " pdb=" CG GLN D 36 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.55e-01 bond pdb=" C VAL A 125 " pdb=" O VAL A 125 " ideal model delta sigma weight residual 1.236 1.249 -0.012 1.35e-02 5.49e+03 8.01e-01 bond pdb=" CA THR F 16 " pdb=" C THR F 16 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.10e-02 2.27e+03 7.99e-01 ... (remaining 13824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 18464 1.99 - 3.97: 340 3.97 - 5.96: 21 5.96 - 7.94: 0 7.94 - 9.93: 1 Bond angle restraints: 18826 Sorted by residual: angle pdb=" N GLY B 46 " pdb=" CA GLY B 46 " pdb=" C GLY B 46 " ideal model delta sigma weight residual 110.43 114.48 -4.05 1.35e+00 5.49e-01 9.00e+00 angle pdb=" N ARG H 124 " pdb=" CA ARG H 124 " pdb=" CB ARG H 124 " ideal model delta sigma weight residual 110.01 114.17 -4.16 1.45e+00 4.76e-01 8.24e+00 angle pdb=" N HIS B 126 " pdb=" CA HIS B 126 " pdb=" C HIS B 126 " ideal model delta sigma weight residual 111.07 114.08 -3.01 1.07e+00 8.73e-01 7.91e+00 angle pdb=" N HIS G 126 " pdb=" CA HIS G 126 " pdb=" C HIS G 126 " ideal model delta sigma weight residual 111.28 114.19 -2.91 1.09e+00 8.42e-01 7.11e+00 angle pdb=" N VAL I 80 " pdb=" CA VAL I 80 " pdb=" C VAL I 80 " ideal model delta sigma weight residual 107.89 110.79 -2.90 1.09e+00 8.42e-01 7.08e+00 ... (remaining 18821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7545 17.92 - 35.83: 663 35.83 - 53.75: 118 53.75 - 71.67: 27 71.67 - 89.58: 22 Dihedral angle restraints: 8375 sinusoidal: 3326 harmonic: 5049 Sorted by residual: dihedral pdb=" CA TRP I 42 " pdb=" C TRP I 42 " pdb=" N ASN I 43 " pdb=" CA ASN I 43 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TRP C 42 " pdb=" C TRP C 42 " pdb=" N ASN C 43 " pdb=" CA ASN C 43 " ideal model delta harmonic sigma weight residual -180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP K 86 " pdb=" CB ASP K 86 " pdb=" CG ASP K 86 " pdb=" OD1 ASP K 86 " ideal model delta sinusoidal sigma weight residual -30.00 -89.46 59.46 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 8372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1316 0.026 - 0.051: 586 0.051 - 0.077: 245 0.077 - 0.102: 67 0.102 - 0.128: 28 Chirality restraints: 2242 Sorted by residual: chirality pdb=" CA VAL F 45 " pdb=" N VAL F 45 " pdb=" C VAL F 45 " pdb=" CB VAL F 45 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CB VAL B 125 " pdb=" CA VAL B 125 " pdb=" CG1 VAL B 125 " pdb=" CG2 VAL B 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ASP A 145 " pdb=" N ASP A 145 " pdb=" C ASP A 145 " pdb=" CB ASP A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 2239 not shown) Planarity restraints: 2503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 97 " -0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO B 98 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 97 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO F 98 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 98 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 98 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 97 " -0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO G 98 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 98 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 98 " -0.038 5.00e-02 4.00e+02 ... (remaining 2500 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 167 2.66 - 3.22: 14222 3.22 - 3.78: 22863 3.78 - 4.34: 27347 4.34 - 4.90: 47587 Nonbonded interactions: 112186 Sorted by model distance: nonbonded pdb=" OE1 GLN K 39 " pdb=" ND2 ASN K 43 " model vdw 2.103 3.120 nonbonded pdb=" OD2 ASP H 120 " pdb=" NH1 ARG H 124 " model vdw 2.138 3.120 nonbonded pdb=" OD2 ASP B 133 " pdb=" OG SER B 135 " model vdw 2.141 3.040 nonbonded pdb=" O GLU A 18 " pdb=" ND2 ASN A 22 " model vdw 2.213 3.120 nonbonded pdb=" OD2 ASP C 68 " pdb=" NZ LYS D 38 " model vdw 2.241 3.120 ... (remaining 112181 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'B' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'C' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'D' and resid 17 through 161) selection = (chain 'E' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'F' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'G' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'H' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'I' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'J' and (resid 17 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'K' and resid 17 through 161) selection = (chain 'L' and resid 17 through 161) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.410 Find NCS groups from input model: 0.700 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: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.003 0.052 13829 Z= 0.152 Angle : 0.620 9.930 18826 Z= 0.365 Chirality : 0.036 0.128 2242 Planarity : 0.005 0.097 2503 Dihedral : 14.516 89.585 5065 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.47 (0.20), residues: 1727 helix: 3.41 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : 0.52 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 152 HIS 0.005 0.001 HIS C 53 PHE 0.024 0.002 PHE I 49 ARG 0.008 0.001 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.09094 ( 1185) hydrogen bonds : angle 3.69380 ( 3555) covalent geometry : bond 0.00319 (13829) covalent geometry : angle 0.61970 (18826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.681 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7579 (mp0) cc_final: 0.7375 (tt0) REVERT: B 24 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8391 (tp40) REVERT: C 32 GLU cc_start: 0.8494 (tp30) cc_final: 0.8045 (tp30) REVERT: C 55 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8467 (tp-100) REVERT: D 157 GLU cc_start: 0.8809 (tp30) cc_final: 0.8474 (tp30) REVERT: E 157 GLU cc_start: 0.8713 (tp30) cc_final: 0.8436 (tp30) REVERT: K 22 ASN cc_start: 0.8764 (m110) cc_final: 0.8394 (m110) REVERT: K 103 SER cc_start: 0.8739 (t) cc_final: 0.8444 (p) REVERT: K 148 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8270 (mm-30) REVERT: F 32 GLU cc_start: 0.8313 (tp30) cc_final: 0.8093 (tp30) REVERT: H 55 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8121 (tp-100) REVERT: J 32 GLU cc_start: 0.8546 (tp30) cc_final: 0.8178 (tp30) REVERT: J 43 ASN cc_start: 0.8704 (t0) cc_final: 0.8484 (t0) REVERT: L 120 ASP cc_start: 0.8126 (t70) cc_final: 0.7909 (t0) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.2148 time to fit residues: 116.8307 Evaluate side-chains 253 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 ASN B 41 HIS ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 36 GLN ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 36 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 HIS I 43 ASN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.092058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080063 restraints weight = 31153.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083193 restraints weight = 15401.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.085231 restraints weight = 9143.480| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13829 Z= 0.130 Angle : 0.522 8.892 18826 Z= 0.281 Chirality : 0.036 0.153 2242 Planarity : 0.005 0.072 2503 Dihedral : 4.452 60.933 1883 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.51 % Allowed : 8.31 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.50 (0.20), residues: 1727 helix: 3.44 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : 0.53 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 152 HIS 0.006 0.002 HIS K 53 PHE 0.021 0.002 PHE A 19 ARG 0.007 0.000 ARG J 155 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 1185) hydrogen bonds : angle 3.36149 ( 3555) covalent geometry : bond 0.00285 (13829) covalent geometry : angle 0.52242 (18826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7969 (mp0) cc_final: 0.7691 (tt0) REVERT: A 121 THR cc_start: 0.8098 (m) cc_final: 0.7867 (p) REVERT: A 157 GLU cc_start: 0.8704 (tp30) cc_final: 0.8207 (tp30) REVERT: B 24 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8163 (tp40) REVERT: C 18 GLU cc_start: 0.7536 (mp0) cc_final: 0.7312 (tt0) REVERT: C 32 GLU cc_start: 0.8304 (tp30) cc_final: 0.7835 (tp30) REVERT: D 18 GLU cc_start: 0.7877 (pm20) cc_final: 0.7485 (tt0) REVERT: D 133 ASP cc_start: 0.6848 (t0) cc_final: 0.6617 (t0) REVERT: E 32 GLU cc_start: 0.8645 (tp30) cc_final: 0.8392 (tp30) REVERT: E 72 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7662 (mm-30) REVERT: G 133 ASP cc_start: 0.7433 (t0) cc_final: 0.7037 (t0) REVERT: I 32 GLU cc_start: 0.8371 (tp30) cc_final: 0.7941 (tp30) REVERT: K 103 SER cc_start: 0.8374 (t) cc_final: 0.8004 (p) REVERT: K 133 ASP cc_start: 0.6919 (t0) cc_final: 0.6658 (t0) REVERT: F 32 GLU cc_start: 0.8346 (tp30) cc_final: 0.8039 (tp30) REVERT: H 18 GLU cc_start: 0.8024 (mp0) cc_final: 0.7747 (tt0) REVERT: H 55 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8219 (tp-100) REVERT: H 125 VAL cc_start: 0.9153 (p) cc_final: 0.8931 (p) REVERT: J 43 ASN cc_start: 0.8629 (t0) cc_final: 0.8402 (t0) REVERT: J 133 ASP cc_start: 0.6852 (t0) cc_final: 0.6534 (t0) REVERT: L 18 GLU cc_start: 0.8026 (pm20) cc_final: 0.7755 (tt0) REVERT: L 148 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8115 (mm-30) outliers start: 52 outliers final: 35 residues processed: 319 average time/residue: 0.2087 time to fit residues: 104.5739 Evaluate side-chains 291 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 158 ASN Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 GLN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.085925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073787 restraints weight = 32312.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076797 restraints weight = 16221.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078879 restraints weight = 9837.759| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13829 Z= 0.188 Angle : 0.574 10.246 18826 Z= 0.305 Chirality : 0.037 0.155 2242 Planarity : 0.005 0.066 2503 Dihedral : 4.605 60.634 1883 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.65 % Allowed : 12.69 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.20), residues: 1727 helix: 3.24 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.42 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 152 HIS 0.006 0.002 HIS K 41 PHE 0.027 0.002 PHE I 49 ARG 0.005 0.001 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 1185) hydrogen bonds : angle 3.48979 ( 3555) covalent geometry : bond 0.00435 (13829) covalent geometry : angle 0.57377 (18826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 266 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7954 (m-80) cc_final: 0.7590 (m-80) REVERT: A 157 GLU cc_start: 0.8812 (tp30) cc_final: 0.8402 (tp30) REVERT: C 18 GLU cc_start: 0.7647 (mp0) cc_final: 0.7385 (tt0) REVERT: C 135 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8587 (p) REVERT: D 32 GLU cc_start: 0.8390 (tp30) cc_final: 0.8162 (tp30) REVERT: E 32 GLU cc_start: 0.8748 (tp30) cc_final: 0.8519 (tp30) REVERT: E 72 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7778 (mm-30) REVERT: G 18 GLU cc_start: 0.8421 (tt0) cc_final: 0.8167 (mp0) REVERT: G 133 ASP cc_start: 0.7501 (t0) cc_final: 0.7177 (t0) REVERT: I 18 GLU cc_start: 0.8567 (tt0) cc_final: 0.8248 (mp0) REVERT: I 32 GLU cc_start: 0.8444 (tp30) cc_final: 0.7916 (tp30) REVERT: I 55 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8536 (tp40) REVERT: K 18 GLU cc_start: 0.7934 (mp0) cc_final: 0.7627 (tt0) REVERT: K 103 SER cc_start: 0.8490 (t) cc_final: 0.8127 (p) REVERT: F 32 GLU cc_start: 0.8397 (tp30) cc_final: 0.7913 (tp30) REVERT: F 43 ASN cc_start: 0.8737 (t0) cc_final: 0.8519 (t0) REVERT: H 103 SER cc_start: 0.8706 (t) cc_final: 0.8364 (p) REVERT: H 124 ARG cc_start: 0.7892 (mpp-170) cc_final: 0.7613 (mtt90) REVERT: J 18 GLU cc_start: 0.8131 (mp0) cc_final: 0.7770 (tt0) REVERT: J 43 ASN cc_start: 0.8694 (t0) cc_final: 0.8380 (t0) REVERT: J 133 ASP cc_start: 0.6860 (t0) cc_final: 0.6619 (t0) outliers start: 54 outliers final: 40 residues processed: 295 average time/residue: 0.2199 time to fit residues: 99.3518 Evaluate side-chains 289 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 103 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 47 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077110 restraints weight = 31640.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080031 restraints weight = 15902.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081956 restraints weight = 9629.078| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13829 Z= 0.146 Angle : 0.531 9.986 18826 Z= 0.281 Chirality : 0.036 0.154 2242 Planarity : 0.005 0.059 2503 Dihedral : 4.570 61.304 1883 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.12 % Allowed : 14.38 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.20), residues: 1727 helix: 3.28 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : 0.44 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 152 HIS 0.006 0.002 HIS D 41 PHE 0.022 0.002 PHE J 49 ARG 0.004 0.000 ARG K 114 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 1185) hydrogen bonds : angle 3.36004 ( 3555) covalent geometry : bond 0.00330 (13829) covalent geometry : angle 0.53089 (18826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7837 (mp0) cc_final: 0.7524 (tt0) REVERT: A 55 GLN cc_start: 0.8860 (tp40) cc_final: 0.8621 (tp40) REVERT: A 100 PHE cc_start: 0.7917 (m-80) cc_final: 0.7531 (m-80) REVERT: A 157 GLU cc_start: 0.8691 (tp30) cc_final: 0.8337 (tp30) REVERT: C 32 GLU cc_start: 0.8059 (tp30) cc_final: 0.7840 (tp30) REVERT: C 135 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8531 (p) REVERT: E 72 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7796 (mm-30) REVERT: G 133 ASP cc_start: 0.7486 (t0) cc_final: 0.7213 (t0) REVERT: I 18 GLU cc_start: 0.8465 (tt0) cc_final: 0.8232 (mp0) REVERT: I 32 GLU cc_start: 0.8459 (tp30) cc_final: 0.7974 (tp30) REVERT: K 103 SER cc_start: 0.8595 (t) cc_final: 0.8241 (p) REVERT: H 103 SER cc_start: 0.8797 (t) cc_final: 0.8476 (p) REVERT: J 43 ASN cc_start: 0.8590 (t0) cc_final: 0.8289 (t0) REVERT: L 18 GLU cc_start: 0.7764 (mp0) cc_final: 0.7413 (tt0) outliers start: 61 outliers final: 48 residues processed: 310 average time/residue: 0.2058 time to fit residues: 99.0682 Evaluate side-chains 293 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 158 ASN Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 43 ASN F 22 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079240 restraints weight = 31517.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.082224 restraints weight = 15801.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084292 restraints weight = 9473.040| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13829 Z= 0.123 Angle : 0.512 9.957 18826 Z= 0.269 Chirality : 0.035 0.151 2242 Planarity : 0.004 0.055 2503 Dihedral : 4.507 62.852 1883 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.17 % Allowed : 16.48 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.38 (0.20), residues: 1727 helix: 3.35 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.56 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 152 HIS 0.006 0.002 HIS K 41 PHE 0.016 0.002 PHE I 49 ARG 0.004 0.000 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 1185) hydrogen bonds : angle 3.26037 ( 3555) covalent geometry : bond 0.00271 (13829) covalent geometry : angle 0.51219 (18826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7676 (mp0) cc_final: 0.7410 (tt0) REVERT: A 55 GLN cc_start: 0.8891 (tp40) cc_final: 0.8605 (tp40) REVERT: A 100 PHE cc_start: 0.7831 (m-80) cc_final: 0.7454 (m-80) REVERT: A 157 GLU cc_start: 0.8659 (tp30) cc_final: 0.8242 (tp30) REVERT: B 24 GLN cc_start: 0.8745 (tm-30) cc_final: 0.7996 (tp40) REVERT: B 65 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8707 (mm-30) REVERT: C 32 GLU cc_start: 0.8004 (tp30) cc_final: 0.7776 (tp30) REVERT: C 135 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8525 (p) REVERT: E 24 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8064 (tp40) REVERT: E 72 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7793 (mm-30) REVERT: G 32 GLU cc_start: 0.8686 (tp30) cc_final: 0.8483 (tp30) REVERT: G 133 ASP cc_start: 0.7364 (t0) cc_final: 0.7102 (t0) REVERT: I 32 GLU cc_start: 0.8394 (tp30) cc_final: 0.7955 (tp30) REVERT: I 153 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8933 (tt) REVERT: K 103 SER cc_start: 0.8569 (t) cc_final: 0.8216 (p) REVERT: F 32 GLU cc_start: 0.8427 (tp30) cc_final: 0.8118 (tp30) REVERT: F 55 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8501 (tp-100) REVERT: F 157 GLU cc_start: 0.8826 (tp30) cc_final: 0.8541 (tp30) REVERT: H 103 SER cc_start: 0.8724 (t) cc_final: 0.8395 (p) REVERT: J 120 ASP cc_start: 0.8270 (t0) cc_final: 0.7749 (t70) REVERT: L 148 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8214 (mm-30) outliers start: 47 outliers final: 43 residues processed: 310 average time/residue: 0.1961 time to fit residues: 95.3006 Evaluate side-chains 292 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076931 restraints weight = 32302.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080053 restraints weight = 16404.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082006 restraints weight = 9913.700| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13829 Z= 0.129 Angle : 0.520 10.063 18826 Z= 0.273 Chirality : 0.035 0.151 2242 Planarity : 0.004 0.054 2503 Dihedral : 4.500 64.268 1883 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.39 % Allowed : 16.95 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.20), residues: 1727 helix: 3.35 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.61 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 152 HIS 0.006 0.002 HIS K 41 PHE 0.016 0.002 PHE I 49 ARG 0.010 0.000 ARG J 124 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 1185) hydrogen bonds : angle 3.24779 ( 3555) covalent geometry : bond 0.00290 (13829) covalent geometry : angle 0.52028 (18826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7877 (mp0) cc_final: 0.7482 (tt0) REVERT: A 55 GLN cc_start: 0.8856 (tp40) cc_final: 0.8554 (tp40) REVERT: A 100 PHE cc_start: 0.7916 (m-80) cc_final: 0.7524 (m-80) REVERT: A 157 GLU cc_start: 0.8639 (tp30) cc_final: 0.8304 (tp30) REVERT: B 24 GLN cc_start: 0.8695 (tm-30) cc_final: 0.7932 (tp40) REVERT: B 65 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8723 (mm-30) REVERT: C 32 GLU cc_start: 0.7963 (tp30) cc_final: 0.7751 (tp30) REVERT: C 55 GLN cc_start: 0.8991 (tp40) cc_final: 0.8344 (tp-100) REVERT: C 135 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8628 (p) REVERT: E 24 GLN cc_start: 0.8829 (tm-30) cc_final: 0.7959 (tp40) REVERT: E 72 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7766 (mm-30) REVERT: G 18 GLU cc_start: 0.8493 (tt0) cc_final: 0.8221 (mp0) REVERT: G 24 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8429 (tm-30) REVERT: G 133 ASP cc_start: 0.7318 (t0) cc_final: 0.6994 (t0) REVERT: I 18 GLU cc_start: 0.7881 (mp0) cc_final: 0.7648 (tt0) REVERT: I 32 GLU cc_start: 0.8419 (tp30) cc_final: 0.7959 (tp30) REVERT: I 153 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8861 (tt) REVERT: K 43 ASN cc_start: 0.8303 (m-40) cc_final: 0.8101 (m110) REVERT: K 103 SER cc_start: 0.8414 (t) cc_final: 0.8047 (p) REVERT: H 103 SER cc_start: 0.8615 (t) cc_final: 0.8263 (p) REVERT: J 18 GLU cc_start: 0.8057 (mp0) cc_final: 0.7711 (tt0) REVERT: L 148 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8142 (mm-30) outliers start: 65 outliers final: 54 residues processed: 307 average time/residue: 0.2120 time to fit residues: 101.2133 Evaluate side-chains 305 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 103 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 5 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.084425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072175 restraints weight = 32812.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.075164 restraints weight = 16706.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077112 restraints weight = 10181.309| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13829 Z= 0.195 Angle : 0.595 10.529 18826 Z= 0.310 Chirality : 0.037 0.154 2242 Planarity : 0.005 0.058 2503 Dihedral : 4.686 64.773 1883 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.25 % Allowed : 17.69 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.20), residues: 1727 helix: 3.14 (0.13), residues: 1427 sheet: None (None), residues: 0 loop : 0.15 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 152 HIS 0.006 0.001 HIS K 41 PHE 0.031 0.002 PHE I 49 ARG 0.004 0.000 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.04964 ( 1185) hydrogen bonds : angle 3.47079 ( 3555) covalent geometry : bond 0.00453 (13829) covalent geometry : angle 0.59453 (18826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 1.818 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7936 (mp0) cc_final: 0.7530 (tt0) REVERT: A 55 GLN cc_start: 0.8931 (tp40) cc_final: 0.8644 (tp40) REVERT: A 100 PHE cc_start: 0.8072 (m-80) cc_final: 0.7824 (m-80) REVERT: A 157 GLU cc_start: 0.8766 (tp30) cc_final: 0.8563 (tp30) REVERT: C 49 PHE cc_start: 0.8595 (t80) cc_final: 0.8374 (t80) REVERT: C 55 GLN cc_start: 0.9073 (tp40) cc_final: 0.8454 (tp-100) REVERT: C 133 ASP cc_start: 0.7322 (t0) cc_final: 0.6931 (t0) REVERT: E 32 GLU cc_start: 0.8408 (tp30) cc_final: 0.8154 (tp30) REVERT: G 18 GLU cc_start: 0.8583 (tt0) cc_final: 0.8293 (mp0) REVERT: G 133 ASP cc_start: 0.7559 (t0) cc_final: 0.7220 (t0) REVERT: I 133 ASP cc_start: 0.7061 (t0) cc_final: 0.6734 (t0) REVERT: K 43 ASN cc_start: 0.8369 (m-40) cc_final: 0.8152 (m110) REVERT: K 103 SER cc_start: 0.8552 (t) cc_final: 0.8199 (p) REVERT: K 133 ASP cc_start: 0.6938 (t0) cc_final: 0.6707 (t0) REVERT: F 48 ASN cc_start: 0.8868 (m-40) cc_final: 0.8667 (m-40) REVERT: F 55 GLN cc_start: 0.8845 (tp40) cc_final: 0.8615 (tp-100) REVERT: H 103 SER cc_start: 0.8773 (t) cc_final: 0.8456 (p) REVERT: H 157 GLU cc_start: 0.9074 (tp30) cc_final: 0.8830 (tp30) REVERT: J 18 GLU cc_start: 0.8106 (mp0) cc_final: 0.7799 (tt0) REVERT: J 74 MET cc_start: 0.9172 (ttp) cc_final: 0.8937 (ptt) outliers start: 63 outliers final: 54 residues processed: 286 average time/residue: 0.2265 time to fit residues: 102.3914 Evaluate side-chains 290 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 103 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN K 48 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.086160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073873 restraints weight = 32588.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076894 restraints weight = 16588.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078901 restraints weight = 10127.617| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13829 Z= 0.152 Angle : 0.562 10.427 18826 Z= 0.292 Chirality : 0.036 0.151 2242 Planarity : 0.004 0.057 2503 Dihedral : 4.648 65.191 1883 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.19 % Allowed : 18.03 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.20), residues: 1727 helix: 3.25 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.44 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 152 HIS 0.006 0.002 HIS K 41 PHE 0.023 0.002 PHE I 49 ARG 0.004 0.000 ARG K 114 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 1185) hydrogen bonds : angle 3.34984 ( 3555) covalent geometry : bond 0.00347 (13829) covalent geometry : angle 0.56194 (18826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7886 (mp0) cc_final: 0.7536 (tt0) REVERT: A 32 GLU cc_start: 0.8394 (tp30) cc_final: 0.7401 (tp30) REVERT: A 36 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.6785 (mp10) REVERT: A 55 GLN cc_start: 0.8893 (tp40) cc_final: 0.8637 (tp40) REVERT: A 74 MET cc_start: 0.9092 (ttp) cc_final: 0.8883 (ptt) REVERT: A 100 PHE cc_start: 0.8136 (m-80) cc_final: 0.7869 (m-80) REVERT: A 157 GLU cc_start: 0.8706 (tp30) cc_final: 0.8497 (tp30) REVERT: C 55 GLN cc_start: 0.9074 (tp40) cc_final: 0.8397 (tp-100) REVERT: C 133 ASP cc_start: 0.7042 (t0) cc_final: 0.6761 (t0) REVERT: E 72 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7729 (mm-30) REVERT: G 18 GLU cc_start: 0.8513 (tt0) cc_final: 0.8243 (mp0) REVERT: G 133 ASP cc_start: 0.7465 (t0) cc_final: 0.7129 (t0) REVERT: I 32 GLU cc_start: 0.8721 (tp30) cc_final: 0.8498 (tp30) REVERT: K 43 ASN cc_start: 0.8280 (m-40) cc_final: 0.8035 (m110) REVERT: K 103 SER cc_start: 0.8505 (t) cc_final: 0.8152 (p) REVERT: K 133 ASP cc_start: 0.6890 (t0) cc_final: 0.6670 (t0) REVERT: F 55 GLN cc_start: 0.8809 (tp40) cc_final: 0.8576 (tp-100) REVERT: H 103 SER cc_start: 0.8747 (t) cc_final: 0.8437 (p) REVERT: H 157 GLU cc_start: 0.9057 (tp30) cc_final: 0.8788 (tp30) REVERT: J 18 GLU cc_start: 0.8068 (mp0) cc_final: 0.7724 (tt0) outliers start: 62 outliers final: 57 residues processed: 295 average time/residue: 0.2063 time to fit residues: 95.3774 Evaluate side-chains 297 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 154 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN K 48 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.087079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075041 restraints weight = 32212.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078061 restraints weight = 16382.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080036 restraints weight = 9894.582| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13829 Z= 0.138 Angle : 0.555 10.404 18826 Z= 0.288 Chirality : 0.035 0.149 2242 Planarity : 0.004 0.057 2503 Dihedral : 4.634 66.562 1883 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.25 % Allowed : 18.03 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.20), residues: 1727 helix: 3.28 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.44 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 152 HIS 0.005 0.002 HIS K 41 PHE 0.016 0.001 PHE C 49 ARG 0.004 0.000 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 1185) hydrogen bonds : angle 3.28355 ( 3555) covalent geometry : bond 0.00310 (13829) covalent geometry : angle 0.55463 (18826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 257 time to evaluate : 1.565 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7846 (mp0) cc_final: 0.7492 (tt0) REVERT: A 32 GLU cc_start: 0.8272 (tp30) cc_final: 0.7328 (tp30) REVERT: A 36 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: A 55 GLN cc_start: 0.8865 (tp40) cc_final: 0.8534 (tp40) REVERT: A 100 PHE cc_start: 0.8132 (m-80) cc_final: 0.7854 (m-80) REVERT: A 157 GLU cc_start: 0.8741 (tp30) cc_final: 0.8525 (tp30) REVERT: C 55 GLN cc_start: 0.9065 (tp40) cc_final: 0.8374 (tp-100) REVERT: E 32 GLU cc_start: 0.8285 (tp30) cc_final: 0.8064 (tp30) REVERT: E 72 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7659 (mm-30) REVERT: G 18 GLU cc_start: 0.8515 (tt0) cc_final: 0.8281 (mp0) REVERT: G 133 ASP cc_start: 0.7399 (t0) cc_final: 0.7071 (t0) REVERT: I 32 GLU cc_start: 0.8708 (tp30) cc_final: 0.8481 (tp30) REVERT: K 43 ASN cc_start: 0.8144 (m-40) cc_final: 0.7901 (m110) REVERT: K 103 SER cc_start: 0.8475 (t) cc_final: 0.8116 (p) REVERT: F 55 GLN cc_start: 0.8805 (tp40) cc_final: 0.8557 (tp-100) REVERT: H 103 SER cc_start: 0.8706 (t) cc_final: 0.8409 (p) REVERT: H 157 GLU cc_start: 0.9011 (tp30) cc_final: 0.8768 (tp30) REVERT: J 18 GLU cc_start: 0.8031 (mp0) cc_final: 0.7694 (tt0) REVERT: J 124 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7828 (mtm110) REVERT: L 148 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8156 (mm-30) outliers start: 63 outliers final: 56 residues processed: 298 average time/residue: 0.2085 time to fit residues: 97.0400 Evaluate side-chains 307 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN K 48 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.090592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078411 restraints weight = 31816.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.081526 restraints weight = 16129.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083345 restraints weight = 9728.966| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13829 Z= 0.123 Angle : 0.542 9.975 18826 Z= 0.280 Chirality : 0.034 0.152 2242 Planarity : 0.004 0.056 2503 Dihedral : 4.573 70.582 1883 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.58 % Allowed : 18.91 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.20), residues: 1727 helix: 3.36 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : 0.52 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 152 HIS 0.005 0.002 HIS L 41 PHE 0.013 0.001 PHE C 49 ARG 0.004 0.000 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1185) hydrogen bonds : angle 3.21478 ( 3555) covalent geometry : bond 0.00271 (13829) covalent geometry : angle 0.54226 (18826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7750 (mp0) cc_final: 0.7343 (tt0) REVERT: A 32 GLU cc_start: 0.8262 (tp30) cc_final: 0.7355 (tp30) REVERT: A 36 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: A 55 GLN cc_start: 0.8842 (tp40) cc_final: 0.8536 (tp40) REVERT: A 100 PHE cc_start: 0.8115 (m-80) cc_final: 0.7822 (m-80) REVERT: B 24 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8224 (tp40) REVERT: C 49 PHE cc_start: 0.8190 (t80) cc_final: 0.7840 (t80) REVERT: C 55 GLN cc_start: 0.9006 (tp40) cc_final: 0.8341 (tp-100) REVERT: D 157 GLU cc_start: 0.8784 (tp30) cc_final: 0.8527 (tp30) REVERT: E 24 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8022 (tp40) REVERT: E 32 GLU cc_start: 0.8256 (tp30) cc_final: 0.7986 (tp30) REVERT: E 72 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7794 (mm-30) REVERT: G 18 GLU cc_start: 0.8484 (tt0) cc_final: 0.8280 (mp0) REVERT: G 133 ASP cc_start: 0.7237 (t0) cc_final: 0.6937 (t0) REVERT: I 32 GLU cc_start: 0.8597 (tp30) cc_final: 0.8380 (tp30) REVERT: K 24 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8303 (tp40) REVERT: K 103 SER cc_start: 0.8388 (t) cc_final: 0.8022 (p) REVERT: H 18 GLU cc_start: 0.7836 (mp0) cc_final: 0.7623 (tt0) REVERT: H 96 GLU cc_start: 0.8715 (pm20) cc_final: 0.8412 (pm20) REVERT: H 103 SER cc_start: 0.8582 (t) cc_final: 0.8251 (p) REVERT: H 157 GLU cc_start: 0.8937 (tp30) cc_final: 0.8707 (tp30) REVERT: J 18 GLU cc_start: 0.7887 (mp0) cc_final: 0.7615 (tt0) REVERT: J 124 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7879 (mtm110) REVERT: L 148 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8244 (mm-30) outliers start: 53 outliers final: 48 residues processed: 323 average time/residue: 0.2602 time to fit residues: 132.6686 Evaluate side-chains 319 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.090502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.078230 restraints weight = 32075.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081360 restraints weight = 16279.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.083563 restraints weight = 9749.408| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13829 Z= 0.166 Angle : 0.816 59.200 18826 Z= 0.479 Chirality : 0.035 0.163 2242 Planarity : 0.004 0.056 2503 Dihedral : 4.579 70.571 1883 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.24 % Allowed : 19.99 % Favored : 76.77 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.20), residues: 1727 helix: 3.35 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : 0.47 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 42 HIS 0.006 0.002 HIS J 53 PHE 0.013 0.001 PHE I 49 ARG 0.004 0.000 ARG E 114 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1185) hydrogen bonds : angle 3.21495 ( 3555) covalent geometry : bond 0.00351 (13829) covalent geometry : angle 0.81599 (18826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4736.71 seconds wall clock time: 86 minutes 1.40 seconds (5161.40 seconds total)