Starting phenix.real_space_refine on Sun Nov 17 08:16:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwz_35069/11_2024/8hwz_35069.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwz_35069/11_2024/8hwz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwz_35069/11_2024/8hwz_35069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwz_35069/11_2024/8hwz_35069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwz_35069/11_2024/8hwz_35069.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwz_35069/11_2024/8hwz_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-5513/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: 8.36, 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: 3.58 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: 1.14 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: 4.13 Time building geometry restraints manager: 4.15 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: 0.580 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 32.380 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.360 ------------------------------------------------------------------------------- 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= 0.208 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 *********************** 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 : 1.720 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: 0.2210 time to fit residues: 119.9155 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 : 1.615 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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= 0.186 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 *********************** 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 : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 THR cc_start: 0.8240 (m) cc_final: 0.8018 (p) REVERT: A 157 GLU cc_start: 0.8547 (tp30) cc_final: 0.8069 (tp30) REVERT: B 24 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8333 (tp40) REVERT: C 32 GLU cc_start: 0.8331 (tp30) cc_final: 0.7877 (tp30) REVERT: D 18 GLU cc_start: 0.7352 (pm20) cc_final: 0.7120 (tt0) REVERT: E 32 GLU cc_start: 0.8709 (tp30) cc_final: 0.8506 (tp30) REVERT: E 72 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7679 (mm-30) REVERT: I 32 GLU cc_start: 0.8370 (tp30) cc_final: 0.7957 (tp30) REVERT: K 103 SER cc_start: 0.8635 (t) cc_final: 0.8327 (p) REVERT: F 32 GLU cc_start: 0.8307 (tp30) cc_final: 0.8062 (tp30) REVERT: H 55 GLN cc_start: 0.8534 (tp-100) cc_final: 0.8228 (tp-100) REVERT: H 125 VAL cc_start: 0.9350 (p) cc_final: 0.9125 (p) REVERT: J 133 ASP cc_start: 0.6958 (t0) cc_final: 0.6748 (t0) REVERT: L 148 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8126 (mm-30) outliers start: 52 outliers final: 35 residues processed: 319 average time/residue: 0.2060 time to fit residues: 102.8268 Evaluate side-chains 287 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 84 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13829 Z= 0.314 Angle : 0.600 10.575 18826 Z= 0.319 Chirality : 0.038 0.158 2242 Planarity : 0.005 0.067 2503 Dihedral : 4.676 60.974 1883 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.92 % Allowed : 12.76 % Favored : 83.32 % 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: 4.08 (0.20), residues: 1727 helix: 3.15 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.38 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 42 HIS 0.007 0.002 HIS K 41 PHE 0.031 0.003 PHE I 49 ARG 0.005 0.001 ARG A 114 *********************** 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 319 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7841 (m-80) cc_final: 0.7558 (m-80) REVERT: A 157 GLU cc_start: 0.8720 (tp30) cc_final: 0.8255 (tp30) REVERT: C 133 ASP cc_start: 0.7181 (t0) cc_final: 0.6978 (t0) REVERT: D 32 GLU cc_start: 0.8465 (tp30) cc_final: 0.8245 (tp30) REVERT: E 72 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7757 (mm-30) REVERT: G 133 ASP cc_start: 0.7473 (t0) cc_final: 0.7239 (t0) REVERT: I 32 GLU cc_start: 0.8557 (tp30) cc_final: 0.8105 (tp30) REVERT: I 55 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8532 (tp40) REVERT: K 103 SER cc_start: 0.8771 (t) cc_final: 0.8473 (p) REVERT: K 148 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8349 (mm-30) REVERT: F 32 GLU cc_start: 0.8392 (tp30) cc_final: 0.8149 (tp30) REVERT: H 103 SER cc_start: 0.8922 (t) cc_final: 0.8674 (p) REVERT: H 120 ASP cc_start: 0.8154 (t0) cc_final: 0.6973 (t0) REVERT: H 121 THR cc_start: 0.8717 (p) cc_final: 0.7665 (t) REVERT: H 124 ARG cc_start: 0.7856 (mpp-170) cc_final: 0.7215 (mtm110) outliers start: 58 outliers final: 40 residues processed: 294 average time/residue: 0.2298 time to fit residues: 103.9378 Evaluate side-chains 280 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 156 SER 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 154 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 103 SER 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 E residue 154 ILE 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 154 ILE Chi-restraints excluded: chain L residue 34 SER 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 151 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 ** 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** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13829 Z= 0.234 Angle : 0.546 10.235 18826 Z= 0.289 Chirality : 0.036 0.154 2242 Planarity : 0.005 0.060 2503 Dihedral : 4.628 61.514 1883 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.19 % Allowed : 14.31 % 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: 4.17 (0.20), residues: 1727 helix: 3.22 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.41 (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 D 41 PHE 0.022 0.002 PHE J 49 ARG 0.005 0.000 ARG K 114 *********************** 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 322 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8894 (tp40) cc_final: 0.8678 (tp40) REVERT: A 100 PHE cc_start: 0.7845 (m-80) cc_final: 0.7512 (m-80) REVERT: A 157 GLU cc_start: 0.8591 (tp30) cc_final: 0.8290 (tp30) REVERT: C 32 GLU cc_start: 0.8468 (tp30) cc_final: 0.8255 (tp30) REVERT: D 157 GLU cc_start: 0.8930 (tp30) cc_final: 0.8513 (tp30) REVERT: E 72 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7805 (mm-30) REVERT: I 32 GLU cc_start: 0.8405 (tp30) cc_final: 0.7951 (tp30) REVERT: K 39 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8818 (tp40) REVERT: K 103 SER cc_start: 0.8754 (t) cc_final: 0.8457 (p) REVERT: K 148 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8315 (mm-30) REVERT: H 103 SER cc_start: 0.8888 (t) cc_final: 0.8679 (p) REVERT: J 43 ASN cc_start: 0.8480 (t0) cc_final: 0.8213 (t0) REVERT: L 148 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8117 (mm-30) outliers start: 62 outliers final: 50 residues processed: 305 average time/residue: 0.2101 time to fit residues: 99.8661 Evaluate side-chains 288 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 125 VAL 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 103 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 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 156 SER 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 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 158 ASN 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 J residue 154 ILE Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** ** 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** ** 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** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN ** J 41 HIS ** 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 22 ASN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13829 Z= 0.278 Angle : 0.576 10.857 18826 Z= 0.302 Chirality : 0.037 0.155 2242 Planarity : 0.005 0.057 2503 Dihedral : 4.663 61.130 1883 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.66 % Allowed : 14.65 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.07 (0.20), residues: 1727 helix: 3.15 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.34 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 152 HIS 0.006 0.002 HIS K 41 PHE 0.015 0.002 PHE J 49 ARG 0.004 0.000 ARG H 114 *********************** 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 312 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 243 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8938 (tp40) cc_final: 0.8708 (tp40) REVERT: A 100 PHE cc_start: 0.7812 (m-80) cc_final: 0.7536 (m-80) REVERT: C 32 GLU cc_start: 0.8161 (tp30) cc_final: 0.7744 (tp30) REVERT: E 72 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7785 (mm-30) REVERT: I 32 GLU cc_start: 0.8419 (tp30) cc_final: 0.7954 (tp30) REVERT: I 153 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9046 (tt) REVERT: K 39 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8433 (tp-100) REVERT: K 103 SER cc_start: 0.8813 (t) cc_final: 0.8533 (p) REVERT: K 148 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8290 (mm-30) REVERT: H 103 SER cc_start: 0.8937 (t) cc_final: 0.8722 (p) outliers start: 69 outliers final: 56 residues processed: 288 average time/residue: 0.2249 time to fit residues: 101.1462 Evaluate side-chains 288 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 125 VAL 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 103 SER Chi-restraints excluded: chain C residue 107 VAL 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 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 153 LEU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 156 SER 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 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 158 ASN 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 J residue 154 ILE Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 154 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN F 22 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** J 41 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13829 Z= 0.184 Angle : 0.530 10.551 18826 Z= 0.276 Chirality : 0.035 0.149 2242 Planarity : 0.004 0.054 2503 Dihedral : 4.553 62.206 1883 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.05 % Allowed : 16.14 % Favored : 79.81 % 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: 4.28 (0.20), residues: 1727 helix: 3.28 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.49 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 152 HIS 0.005 0.002 HIS K 41 PHE 0.013 0.001 PHE A 19 ARG 0.004 0.000 ARG E 114 *********************** 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 334 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8289 (tp30) cc_final: 0.7293 (tp30) REVERT: A 36 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.6756 (mp10) REVERT: A 55 GLN cc_start: 0.8877 (tp40) cc_final: 0.8619 (tp40) REVERT: A 100 PHE cc_start: 0.7824 (m-80) cc_final: 0.7518 (m-80) REVERT: A 157 GLU cc_start: 0.8611 (tp30) cc_final: 0.8208 (tp30) REVERT: C 55 GLN cc_start: 0.9062 (tp40) cc_final: 0.8837 (tp40) REVERT: D 157 GLU cc_start: 0.8937 (tp30) cc_final: 0.8553 (tp30) REVERT: E 157 GLU cc_start: 0.8928 (tp30) cc_final: 0.8648 (tp30) REVERT: I 32 GLU cc_start: 0.8385 (tp30) cc_final: 0.7960 (tp30) REVERT: K 39 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8480 (tp-100) REVERT: K 103 SER cc_start: 0.8708 (t) cc_final: 0.8400 (p) REVERT: H 103 SER cc_start: 0.8865 (t) cc_final: 0.8648 (p) REVERT: J 120 ASP cc_start: 0.8181 (t0) cc_final: 0.7640 (t70) REVERT: L 24 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8391 (tm-30) REVERT: L 148 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8215 (mm-30) REVERT: L 153 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8777 (tt) outliers start: 60 outliers final: 47 residues processed: 314 average time/residue: 0.2070 time to fit residues: 101.6545 Evaluate side-chains 296 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 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 154 ILE 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 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 122 ILE Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 158 ASN 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 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 153 LEU Chi-restraints excluded: chain L residue 154 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** 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** I 48 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** 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 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13829 Z= 0.356 Angle : 0.645 11.109 18826 Z= 0.334 Chirality : 0.039 0.176 2242 Planarity : 0.005 0.060 2503 Dihedral : 4.734 60.788 1883 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.79 % Allowed : 17.08 % Favored : 78.12 % 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: 3.88 (0.20), residues: 1727 helix: 3.02 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : 0.29 (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 0.022 0.002 PHE E 49 ARG 0.014 0.001 ARG J 124 *********************** 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 309 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 1.829 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8972 (tp40) cc_final: 0.8722 (tp40) REVERT: A 133 ASP cc_start: 0.7287 (t0) cc_final: 0.7079 (t0) REVERT: B 65 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8638 (mm-30) REVERT: D 157 GLU cc_start: 0.8985 (tp30) cc_final: 0.8583 (tp30) REVERT: E 72 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7768 (mm-30) REVERT: K 39 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8679 (tp-100) REVERT: K 148 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8330 (mm-30) REVERT: J 74 MET cc_start: 0.9104 (ttp) cc_final: 0.8902 (ptt) REVERT: L 153 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8909 (tt) outliers start: 71 outliers final: 58 residues processed: 286 average time/residue: 0.2259 time to fit residues: 103.1773 Evaluate side-chains 287 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 228 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 158 ASN 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 70 ILE 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 158 ASN 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 103 SER 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 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 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 K residue 158 ASN 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 154 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 31 ILE 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 103 SER Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** I 48 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN ** 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 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13829 Z= 0.183 Angle : 0.546 10.007 18826 Z= 0.286 Chirality : 0.035 0.178 2242 Planarity : 0.004 0.055 2503 Dihedral : 4.608 61.421 1883 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.58 % Allowed : 19.11 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.20), residues: 1727 helix: 3.25 (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 0.012 0.001 TRP H 152 HIS 0.007 0.002 HIS I 53 PHE 0.018 0.001 PHE I 49 ARG 0.006 0.000 ARG J 124 *********************** 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 326 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8254 (tp30) cc_final: 0.7250 (tp30) REVERT: A 36 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.6744 (mp10) REVERT: A 55 GLN cc_start: 0.8851 (tp40) cc_final: 0.8559 (tp40) REVERT: B 120 ASP cc_start: 0.8177 (t0) cc_final: 0.7480 (t70) REVERT: C 32 GLU cc_start: 0.8538 (tp30) cc_final: 0.8328 (tp30) REVERT: E 72 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7676 (mm-30) REVERT: G 32 GLU cc_start: 0.8670 (tp30) cc_final: 0.8322 (tp30) REVERT: K 148 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8181 (mm-30) REVERT: L 24 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8350 (tm-30) REVERT: L 148 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8219 (mm-30) outliers start: 53 outliers final: 45 residues processed: 311 average time/residue: 0.2105 time to fit residues: 102.8809 Evaluate side-chains 297 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 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 156 SER Chi-restraints excluded: chain C residue 158 ASN 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 119 VAL 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 153 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 80 VAL 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 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 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 48 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN E 43 ASN I 48 ASN ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 43 ASN K 48 ASN ** 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 ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13829 Z= 0.184 Angle : 0.561 10.249 18826 Z= 0.288 Chirality : 0.035 0.167 2242 Planarity : 0.004 0.057 2503 Dihedral : 4.583 62.787 1883 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.44 % Allowed : 20.12 % Favored : 76.43 % 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: 4.12 (0.20), residues: 1727 helix: 3.18 (0.13), residues: 1427 sheet: None (None), residues: 0 loop : 0.27 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 152 HIS 0.006 0.002 HIS J 53 PHE 0.019 0.001 PHE F 49 ARG 0.011 0.000 ARG B 124 *********************** 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 325 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8846 (tp40) cc_final: 0.8587 (tp40) REVERT: A 157 GLU cc_start: 0.8731 (tp30) cc_final: 0.8265 (tp30) REVERT: B 24 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8041 (tp40) REVERT: C 32 GLU cc_start: 0.8429 (tp30) cc_final: 0.8199 (tp30) REVERT: D 22 ASN cc_start: 0.8855 (m-40) cc_final: 0.8509 (m110) REVERT: D 32 GLU cc_start: 0.8387 (tp30) cc_final: 0.8131 (tp30) REVERT: E 65 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8609 (mm-30) REVERT: E 72 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7643 (mm-30) REVERT: E 157 GLU cc_start: 0.8925 (tp30) cc_final: 0.8592 (tp30) REVERT: K 148 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8188 (mm-30) REVERT: J 55 GLN cc_start: 0.8294 (tp-100) cc_final: 0.8022 (tp-100) REVERT: L 24 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8353 (tm-30) REVERT: L 148 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8209 (mm-30) outliers start: 51 outliers final: 44 residues processed: 306 average time/residue: 0.2075 time to fit residues: 99.4871 Evaluate side-chains 304 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 103 SER 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 158 ASN Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 34 SER 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 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 122 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 F residue 34 SER Chi-restraints excluded: chain F residue 52 LEU 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 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 48 ASN Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 103 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 0.0060 chunk 105 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 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 I 48 ASN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN ** 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 ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13829 Z= 0.185 Angle : 0.561 10.101 18826 Z= 0.290 Chirality : 0.035 0.147 2242 Planarity : 0.004 0.059 2503 Dihedral : 4.624 63.874 1883 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.04 % Allowed : 20.53 % Favored : 76.43 % 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: 4.15 (0.20), residues: 1727 helix: 3.20 (0.13), residues: 1427 sheet: None (None), residues: 0 loop : 0.26 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 152 HIS 0.006 0.002 HIS J 53 PHE 0.040 0.002 PHE J 49 ARG 0.006 0.000 ARG B 124 ********************** 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 311 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8851 (tp40) cc_final: 0.8589 (tp40) REVERT: A 74 MET cc_start: 0.8932 (ttp) cc_final: 0.8713 (ptt) REVERT: A 157 GLU cc_start: 0.8714 (tp30) cc_final: 0.8250 (tp30) REVERT: B 24 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8069 (tp40) REVERT: C 32 GLU cc_start: 0.8426 (tp30) cc_final: 0.8190 (tp30) REVERT: D 22 ASN cc_start: 0.8833 (m-40) cc_final: 0.8503 (m110) REVERT: E 65 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8577 (mm-30) REVERT: E 72 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7640 (mm-30) REVERT: I 32 GLU cc_start: 0.8628 (tp30) cc_final: 0.8374 (tp30) REVERT: K 103 SER cc_start: 0.8718 (t) cc_final: 0.8489 (p) REVERT: K 148 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8158 (mm-30) REVERT: H 96 GLU cc_start: 0.8446 (pm20) cc_final: 0.8174 (pm20) REVERT: J 55 GLN cc_start: 0.8324 (tp-100) cc_final: 0.7999 (tp-100) REVERT: J 74 MET cc_start: 0.8811 (ttp) cc_final: 0.8546 (ptt) REVERT: L 24 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8389 (tm-30) REVERT: L 32 GLU cc_start: 0.8722 (tp30) cc_final: 0.8350 (tp30) REVERT: L 148 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8168 (mm-30) outliers start: 45 outliers final: 43 residues processed: 291 average time/residue: 0.2030 time to fit residues: 93.1334 Evaluate side-chains 301 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER 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 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 158 ASN Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 34 SER 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 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 122 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 F residue 34 SER Chi-restraints excluded: chain F residue 74 MET 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 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 48 ASN Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 103 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN G 24 GLN I 48 ASN ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 48 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079429 restraints weight = 31428.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.082425 restraints weight = 15810.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084331 restraints weight = 9621.796| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13829 Z= 0.182 Angle : 0.556 10.257 18826 Z= 0.287 Chirality : 0.035 0.148 2242 Planarity : 0.004 0.056 2503 Dihedral : 4.628 65.143 1883 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.38 % Allowed : 20.19 % Favored : 76.43 % 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: 4.17 (0.20), residues: 1727 helix: 3.22 (0.13), residues: 1427 sheet: None (None), residues: 0 loop : 0.23 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 42 HIS 0.005 0.002 HIS D 41 PHE 0.030 0.002 PHE J 49 ARG 0.007 0.000 ARG B 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2588.35 seconds wall clock time: 48 minutes 10.93 seconds (2890.93 seconds total)