Starting phenix.real_space_refine on Tue Mar 3 14:52:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1l_62748/03_2026/9l1l_62748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1l_62748/03_2026/9l1l_62748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l1l_62748/03_2026/9l1l_62748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1l_62748/03_2026/9l1l_62748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l1l_62748/03_2026/9l1l_62748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1l_62748/03_2026/9l1l_62748.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.084 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 22 5.16 5 C 3913 2.51 5 N 1030 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6155 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1429 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 166} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1620 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 14, 'TRANS': 203} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1564 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 201} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "P" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 129 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Time building chain proxies: 1.41, per 1000 atoms: 0.23 Number of scatterers: 6155 At special positions: 0 Unit cell: (95.04, 71.28, 135.63, 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 22 16.00 O 1190 8.00 N 1030 7.00 C 3913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 193 " distance=2.03 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: 0.52 Conformation dependent library (CDL) restraints added in 386.8 milliseconds 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 17 sheets defined 12.3% alpha, 43.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 59 through 81 removed outlier: 4.135A pdb=" N GLY A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 54 through 65 removed outlier: 4.087A pdb=" N GLU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.959A pdb=" N LEU B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.648A pdb=" N GLN B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 182 through 188 removed outlier: 3.648A pdb=" N HIS D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 removed outlier: 10.144A pdb=" N GLY A 24 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASP A 39 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 26 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR A 37 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 28 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 44 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.792A pdb=" N LEU B 26 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP B 41 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 28 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 39 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR B 30 " --> pdb=" O TYR B 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 97 removed outlier: 5.871A pdb=" N PHE A 149 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS A 150 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE A 141 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU A 152 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 102 removed outlier: 5.558A pdb=" N PHE B 154 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.504A pdb=" N TYR B 170 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.978A pdb=" N TYR C 33 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG C 53 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP C 35 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR C 51 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 132 removed outlier: 5.985A pdb=" N TYR C 183 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER C 170 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 132 removed outlier: 5.985A pdb=" N TYR C 183 " --> pdb=" O GLY C 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 5 removed outlier: 5.280A pdb=" N ASP D 17 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASN D 77 " --> pdb=" O ASP D 17 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.850A pdb=" N MET D 11 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 52 through 54 removed outlier: 3.807A pdb=" N SER D 52 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG D 54 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU D 47 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D 90 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 96 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 113 through 117 removed outlier: 5.455A pdb=" N SER D 130 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU D 180 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL D 132 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU D 178 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE D 134 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N SER D 176 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN D 136 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET D 174 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 152 through 153 removed outlier: 5.530A pdb=" N HIS D 197 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N SER D 202 " --> pdb=" O HIS D 197 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1119 1.33 - 1.45: 1753 1.45 - 1.57: 3414 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 6316 Sorted by residual: bond pdb=" CA SER D 92 " pdb=" CB SER D 92 " ideal model delta sigma weight residual 1.529 1.483 0.046 1.55e-02 4.16e+03 8.82e+00 bond pdb=" N VAL D 33 " pdb=" CA VAL D 33 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.08e+00 bond pdb=" C GLN D 90 " pdb=" O GLN D 90 " ideal model delta sigma weight residual 1.235 1.204 0.032 1.22e-02 6.72e+03 6.83e+00 bond pdb=" C GLN D 89 " pdb=" N GLN D 90 " ideal model delta sigma weight residual 1.331 1.297 0.034 1.38e-02 5.25e+03 5.90e+00 bond pdb=" N THR D 31 " pdb=" CA THR D 31 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.22e-02 6.72e+03 4.95e+00 ... (remaining 6311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 8277 1.44 - 2.89: 272 2.89 - 4.33: 61 4.33 - 5.78: 9 5.78 - 7.22: 5 Bond angle restraints: 8624 Sorted by residual: angle pdb=" N TYR D 91 " pdb=" CA TYR D 91 " pdb=" C TYR D 91 " ideal model delta sigma weight residual 113.02 107.19 5.83 1.20e+00 6.94e-01 2.36e+01 angle pdb=" CA TYR D 91 " pdb=" CB TYR D 91 " pdb=" CG TYR D 91 " ideal model delta sigma weight residual 113.90 121.12 -7.22 1.80e+00 3.09e-01 1.61e+01 angle pdb=" CA THR D 32 " pdb=" C THR D 32 " pdb=" O THR D 32 " ideal model delta sigma weight residual 122.41 118.03 4.38 1.21e+00 6.83e-01 1.31e+01 angle pdb=" N THR D 32 " pdb=" CA THR D 32 " pdb=" CB THR D 32 " ideal model delta sigma weight residual 110.58 105.44 5.14 1.44e+00 4.82e-01 1.28e+01 angle pdb=" CA ARG D 93 " pdb=" C ARG D 93 " pdb=" O ARG D 93 " ideal model delta sigma weight residual 121.11 117.06 4.05 1.17e+00 7.31e-01 1.20e+01 ... (remaining 8619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 3445 14.55 - 29.11: 201 29.11 - 43.66: 54 43.66 - 58.22: 9 58.22 - 72.77: 5 Dihedral angle restraints: 3714 sinusoidal: 1389 harmonic: 2325 Sorted by residual: dihedral pdb=" CA SER C 31 " pdb=" C SER C 31 " pdb=" N ALA C 32 " pdb=" CA ALA C 32 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CB CYS A 111 " pdb=" SG CYS A 111 " pdb=" SG CYS A 167 " pdb=" CB CYS A 167 " ideal model delta sinusoidal sigma weight residual 93.00 54.20 38.80 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA TYR C 106 " pdb=" C TYR C 106 " pdb=" N ALA C 107 " pdb=" CA ALA C 107 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 3711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 722 0.048 - 0.096: 160 0.096 - 0.143: 66 0.143 - 0.191: 11 0.191 - 0.239: 3 Chirality restraints: 962 Sorted by residual: chirality pdb=" CA LYS A 79 " pdb=" N LYS A 79 " pdb=" C LYS A 79 " pdb=" CB LYS A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLN D 90 " pdb=" N GLN D 90 " pdb=" C GLN D 90 " pdb=" CB GLN D 90 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE A 14 " pdb=" N ILE A 14 " pdb=" C ILE A 14 " pdb=" CB ILE A 14 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 959 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 89 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C GLN D 89 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN D 89 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN D 90 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 79 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C LYS A 79 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS A 79 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 80 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 91 " -0.025 2.00e-02 2.50e+03 1.65e-02 5.42e+00 pdb=" CG TYR D 91 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR D 91 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 91 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 91 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 91 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 91 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 91 " -0.006 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 323 2.72 - 3.26: 6409 3.26 - 3.81: 10504 3.81 - 4.35: 13652 4.35 - 4.90: 23119 Nonbonded interactions: 54007 Sorted by model distance: nonbonded pdb=" O SER A 81 " pdb=" OG1 THR A 84 " model vdw 2.169 3.040 nonbonded pdb=" NZ LYS A 79 " pdb=" OH TYR D 94 " model vdw 2.238 3.120 nonbonded pdb=" OG SER B 103 " pdb=" OG1 THR B 113 " model vdw 2.302 3.040 nonbonded pdb=" O VAL B 8 " pdb=" O TYR B 32 " model vdw 2.309 3.040 nonbonded pdb=" N TRP D 50 " pdb=" OH TYR D 91 " model vdw 2.354 3.120 ... (remaining 54002 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.690 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 : 0.005 0.050 6322 Z= 0.266 Angle : 0.657 7.220 8636 Z= 0.390 Chirality : 0.051 0.239 962 Planarity : 0.004 0.041 1104 Dihedral : 10.617 72.772 2202 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.66 % Favored : 93.09 % Rotamer: Outliers : 0.46 % Allowed : 7.47 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.29), residues: 781 helix: -0.02 (0.67), residues: 74 sheet: -0.87 (0.27), residues: 319 loop : -1.30 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 98 TYR 0.038 0.002 TYR D 91 PHE 0.014 0.002 PHE C 79 TRP 0.014 0.002 TRP C 111 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 6316) covalent geometry : angle 0.65697 ( 8624) SS BOND : bond 0.00364 ( 6) SS BOND : angle 0.89249 ( 12) hydrogen bonds : bond 0.13545 ( 244) hydrogen bonds : angle 8.09892 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7976 (pm20) REVERT: A 88 ASN cc_start: 0.7763 (m-40) cc_final: 0.7474 (m-40) REVERT: A 89 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5358 (mp0) REVERT: A 147 TYR cc_start: 0.7370 (m-10) cc_final: 0.7030 (m-80) REVERT: B 22 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7583 (tm-30) REVERT: B 74 ASP cc_start: 0.7542 (m-30) cc_final: 0.7309 (p0) REVERT: B 78 ARG cc_start: 0.6872 (ttm-80) cc_final: 0.6646 (ttm-80) REVERT: B 152 TRP cc_start: 0.7350 (m100) cc_final: 0.7092 (m100) REVERT: B 159 MET cc_start: 0.8782 (mtp) cc_final: 0.8304 (mmm) REVERT: B 160 LEU cc_start: 0.9071 (tp) cc_final: 0.8842 (tp) REVERT: C 3 GLN cc_start: 0.7368 (mp10) cc_final: 0.7117 (mp10) REVERT: C 45 LYS cc_start: 0.7828 (mttt) cc_final: 0.7128 (ttpp) REVERT: C 85 SER cc_start: 0.8431 (m) cc_final: 0.8102 (t) REVERT: C 113 GLN cc_start: 0.7141 (pm20) cc_final: 0.6848 (mp10) REVERT: C 174 PHE cc_start: 0.8614 (m-80) cc_final: 0.8413 (m-80) REVERT: D 4 MET cc_start: 0.8218 (mmm) cc_final: 0.7613 (mmm) REVERT: D 32 THR cc_start: 0.9009 (m) cc_final: 0.8465 (p) REVERT: D 67 SER cc_start: 0.8603 (p) cc_final: 0.8179 (t) REVERT: D 83 LEU cc_start: 0.7929 (mt) cc_final: 0.7720 (mt) REVERT: D 90 GLN cc_start: 0.8748 (pp30) cc_final: 0.8041 (pp30) REVERT: D 91 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7731 (p90) REVERT: D 139 TYR cc_start: 0.6502 (t80) cc_final: 0.6275 (t80) REVERT: D 168 LYS cc_start: 0.7696 (ttpp) cc_final: 0.7307 (tptt) outliers start: 3 outliers final: 1 residues processed: 156 average time/residue: 0.0877 time to fit residues: 17.7221 Evaluate side-chains 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS D 8 HIS D 55 HIS D 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.221140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.176156 restraints weight = 6503.447| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.84 r_work: 0.3835 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 6322 Z= 0.339 Angle : 0.744 9.400 8636 Z= 0.408 Chirality : 0.049 0.202 962 Planarity : 0.006 0.050 1104 Dihedral : 6.321 68.865 871 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.62 % Rotamer: Outliers : 1.37 % Allowed : 10.21 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.30), residues: 781 helix: 0.12 (0.65), residues: 72 sheet: -0.72 (0.28), residues: 319 loop : -1.47 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.016 0.003 TYR A 37 PHE 0.018 0.003 PHE C 79 TRP 0.019 0.002 TRP C 111 HIS 0.006 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00804 ( 6316) covalent geometry : angle 0.74133 ( 8624) SS BOND : bond 0.00787 ( 6) SS BOND : angle 1.80212 ( 12) hydrogen bonds : bond 0.04589 ( 244) hydrogen bonds : angle 7.00172 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.7213 (m-40) REVERT: A 146 ASP cc_start: 0.8615 (p0) cc_final: 0.8402 (p0) REVERT: B 153 THR cc_start: 0.8560 (p) cc_final: 0.8235 (p) REVERT: C 6 GLU cc_start: 0.7239 (mp0) cc_final: 0.6986 (mp0) REVERT: C 15 SER cc_start: 0.8290 (t) cc_final: 0.7860 (p) REVERT: D 4 MET cc_start: 0.7479 (mmm) cc_final: 0.7278 (mmm) REVERT: D 67 SER cc_start: 0.8662 (p) cc_final: 0.8318 (t) REVERT: D 80 SER cc_start: 0.8064 (p) cc_final: 0.7861 (m) REVERT: D 106 LYS cc_start: 0.8384 (mmmm) cc_final: 0.8099 (mmmm) outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 0.0996 time to fit residues: 15.9340 Evaluate side-chains 105 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 0.0170 chunk 53 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 40.0000 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN C 3 GLN D 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.224321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.180855 restraints weight = 6456.500| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.86 r_work: 0.3894 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 6322 Z= 0.221 Angle : 0.643 7.442 8636 Z= 0.350 Chirality : 0.047 0.189 962 Planarity : 0.005 0.039 1104 Dihedral : 5.997 64.571 869 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 1.83 % Allowed : 12.50 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.30), residues: 781 helix: 0.60 (0.68), residues: 66 sheet: -0.59 (0.28), residues: 321 loop : -1.25 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.014 0.002 TYR C 51 PHE 0.018 0.002 PHE C 174 TRP 0.014 0.002 TRP C 111 HIS 0.007 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 6316) covalent geometry : angle 0.64217 ( 8624) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.01114 ( 12) hydrogen bonds : bond 0.03881 ( 244) hydrogen bonds : angle 6.59260 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7317 (ttm-80) REVERT: C 3 GLN cc_start: 0.7191 (mp-120) cc_final: 0.6916 (mp10) REVERT: C 6 GLU cc_start: 0.7210 (mp0) cc_final: 0.6906 (mp0) REVERT: C 15 SER cc_start: 0.8265 (t) cc_final: 0.7745 (p) REVERT: D 67 SER cc_start: 0.8606 (p) cc_final: 0.8330 (t) REVERT: D 106 LYS cc_start: 0.8329 (mmmm) cc_final: 0.7997 (mmmm) outliers start: 12 outliers final: 2 residues processed: 110 average time/residue: 0.0855 time to fit residues: 12.4510 Evaluate side-chains 101 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 160 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.227885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.186358 restraints weight = 6469.468| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 1.88 r_work: 0.3924 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6322 Z= 0.175 Angle : 0.617 7.414 8636 Z= 0.332 Chirality : 0.046 0.183 962 Planarity : 0.005 0.038 1104 Dihedral : 5.733 58.527 868 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 0.91 % Allowed : 13.87 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.31), residues: 781 helix: 0.79 (0.66), residues: 66 sheet: -0.54 (0.29), residues: 324 loop : -1.04 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 145 TYR 0.015 0.002 TYR C 104 PHE 0.015 0.002 PHE B 131 TRP 0.012 0.001 TRP C 111 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6316) covalent geometry : angle 0.61633 ( 8624) SS BOND : bond 0.00374 ( 6) SS BOND : angle 0.83883 ( 12) hydrogen bonds : bond 0.03559 ( 244) hydrogen bonds : angle 6.31158 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.8455 (p0) cc_final: 0.8175 (p0) REVERT: A 170 GLU cc_start: 0.7237 (tp30) cc_final: 0.6858 (tm-30) REVERT: B 78 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7446 (ttm110) REVERT: B 153 THR cc_start: 0.8518 (p) cc_final: 0.8184 (p) REVERT: C 6 GLU cc_start: 0.7083 (mp0) cc_final: 0.6715 (mp0) REVERT: C 15 SER cc_start: 0.8229 (t) cc_final: 0.7758 (p) REVERT: C 22 CYS cc_start: 0.5508 (t) cc_final: 0.5095 (t) REVERT: D 4 MET cc_start: 0.7149 (mmm) cc_final: 0.6484 (mmm) REVERT: D 67 SER cc_start: 0.8585 (p) cc_final: 0.8341 (t) REVERT: P 53 TYR cc_start: 0.7630 (m-10) cc_final: 0.7414 (m-10) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.0905 time to fit residues: 13.4102 Evaluate side-chains 108 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 30.0000 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 chunk 71 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 42 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN D 123 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.228634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.183121 restraints weight = 6530.316| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.40 r_work: 0.3916 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6322 Z= 0.155 Angle : 0.587 6.896 8636 Z= 0.316 Chirality : 0.045 0.172 962 Planarity : 0.004 0.039 1104 Dihedral : 5.548 52.046 868 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 1.52 % Allowed : 13.57 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.31), residues: 781 helix: 0.94 (0.67), residues: 66 sheet: -0.39 (0.29), residues: 328 loop : -0.98 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 56 TYR 0.023 0.002 TYR C 33 PHE 0.013 0.002 PHE B 131 TRP 0.015 0.001 TRP C 111 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6316) covalent geometry : angle 0.58643 ( 8624) SS BOND : bond 0.00372 ( 6) SS BOND : angle 0.70473 ( 12) hydrogen bonds : bond 0.03348 ( 244) hydrogen bonds : angle 6.06998 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.5360 (OUTLIER) cc_final: 0.5112 (mt-10) REVERT: A 146 ASP cc_start: 0.8267 (p0) cc_final: 0.7986 (p0) REVERT: A 170 GLU cc_start: 0.7117 (tp30) cc_final: 0.6809 (tm-30) REVERT: B 63 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7265 (mmtt) REVERT: B 78 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7078 (ttp-170) REVERT: B 120 ASP cc_start: 0.8119 (t0) cc_final: 0.7764 (t0) REVERT: B 153 THR cc_start: 0.8397 (p) cc_final: 0.8034 (p) REVERT: C 6 GLU cc_start: 0.6978 (mp0) cc_final: 0.6667 (mp0) REVERT: C 15 SER cc_start: 0.8243 (t) cc_final: 0.7749 (p) REVERT: D 4 MET cc_start: 0.7103 (mmm) cc_final: 0.6423 (mmm) REVERT: D 67 SER cc_start: 0.8480 (p) cc_final: 0.8259 (t) REVERT: P 53 TYR cc_start: 0.7437 (m-10) cc_final: 0.7205 (m-10) outliers start: 10 outliers final: 7 residues processed: 118 average time/residue: 0.0774 time to fit residues: 12.3615 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.224267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.182416 restraints weight = 6476.165| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 1.84 r_work: 0.3933 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6322 Z= 0.227 Angle : 0.648 8.287 8636 Z= 0.350 Chirality : 0.047 0.256 962 Planarity : 0.005 0.041 1104 Dihedral : 5.739 54.182 868 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.02 % Favored : 93.85 % Rotamer: Outliers : 1.68 % Allowed : 14.18 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.31), residues: 781 helix: 0.83 (0.66), residues: 66 sheet: -0.34 (0.29), residues: 324 loop : -1.05 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 56 TYR 0.034 0.002 TYR C 33 PHE 0.016 0.002 PHE C 79 TRP 0.015 0.002 TRP C 111 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 6316) covalent geometry : angle 0.64791 ( 8624) SS BOND : bond 0.00460 ( 6) SS BOND : angle 0.77929 ( 12) hydrogen bonds : bond 0.03781 ( 244) hydrogen bonds : angle 6.27827 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7251 (ttp-110) REVERT: B 120 ASP cc_start: 0.8156 (t0) cc_final: 0.7818 (t0) REVERT: B 153 THR cc_start: 0.8400 (p) cc_final: 0.8069 (p) REVERT: C 6 GLU cc_start: 0.7118 (mp0) cc_final: 0.6863 (mp0) REVERT: C 15 SER cc_start: 0.8258 (t) cc_final: 0.7752 (p) REVERT: C 22 CYS cc_start: 0.5538 (t) cc_final: 0.5186 (t) REVERT: D 4 MET cc_start: 0.7281 (mmm) cc_final: 0.6764 (mmm) REVERT: D 33 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7748 (p) REVERT: D 67 SER cc_start: 0.8583 (p) cc_final: 0.8302 (t) REVERT: D 105 ILE cc_start: 0.7382 (pt) cc_final: 0.7140 (pt) REVERT: D 106 LYS cc_start: 0.8542 (mmmm) cc_final: 0.7982 (mppt) outliers start: 11 outliers final: 9 residues processed: 124 average time/residue: 0.0804 time to fit residues: 13.4013 Evaluate side-chains 117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 42 optimal weight: 0.0070 chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.224207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.179611 restraints weight = 6453.854| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.13 r_work: 0.3925 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6322 Z= 0.168 Angle : 0.611 8.174 8636 Z= 0.330 Chirality : 0.046 0.318 962 Planarity : 0.004 0.041 1104 Dihedral : 5.598 49.731 868 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.15 % Favored : 93.73 % Rotamer: Outliers : 2.44 % Allowed : 14.48 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.31), residues: 781 helix: 0.87 (0.66), residues: 66 sheet: -0.26 (0.29), residues: 324 loop : -1.01 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.026 0.002 TYR C 33 PHE 0.016 0.002 PHE A 28 TRP 0.012 0.001 TRP B 130 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6316) covalent geometry : angle 0.61143 ( 8624) SS BOND : bond 0.00368 ( 6) SS BOND : angle 0.63431 ( 12) hydrogen bonds : bond 0.03544 ( 244) hydrogen bonds : angle 6.07749 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.5357 (OUTLIER) cc_final: 0.5098 (mt-10) REVERT: B 52 GLU cc_start: 0.6459 (pp20) cc_final: 0.6247 (pp20) REVERT: B 63 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7423 (mmtt) REVERT: B 78 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7169 (ttp-170) REVERT: B 120 ASP cc_start: 0.8164 (t0) cc_final: 0.7811 (t0) REVERT: B 153 THR cc_start: 0.8324 (p) cc_final: 0.7994 (p) REVERT: C 6 GLU cc_start: 0.7056 (mp0) cc_final: 0.6689 (mp0) REVERT: C 15 SER cc_start: 0.8272 (t) cc_final: 0.7757 (p) REVERT: C 45 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7762 (tptt) REVERT: D 4 MET cc_start: 0.7311 (mmm) cc_final: 0.6703 (mmm) REVERT: D 33 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7734 (p) REVERT: D 67 SER cc_start: 0.8579 (p) cc_final: 0.8312 (t) REVERT: D 105 ILE cc_start: 0.7479 (pt) cc_final: 0.7228 (pt) REVERT: D 174 MET cc_start: 0.6538 (tpp) cc_final: 0.6263 (tpp) outliers start: 16 outliers final: 11 residues processed: 125 average time/residue: 0.0814 time to fit residues: 13.5448 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.224112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180659 restraints weight = 6529.940| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.12 r_work: 0.3919 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6322 Z= 0.177 Angle : 0.623 7.727 8636 Z= 0.333 Chirality : 0.046 0.182 962 Planarity : 0.004 0.041 1104 Dihedral : 5.577 46.912 868 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.60 % Rotamer: Outliers : 2.44 % Allowed : 14.79 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.31), residues: 781 helix: 0.88 (0.66), residues: 66 sheet: -0.23 (0.29), residues: 323 loop : -0.99 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.022 0.002 TYR C 33 PHE 0.016 0.002 PHE A 28 TRP 0.012 0.001 TRP C 111 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6316) covalent geometry : angle 0.62267 ( 8624) SS BOND : bond 0.00344 ( 6) SS BOND : angle 0.60918 ( 12) hydrogen bonds : bond 0.03399 ( 244) hydrogen bonds : angle 6.03053 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7882 (t0) REVERT: B 52 GLU cc_start: 0.6506 (pp20) cc_final: 0.6303 (pp20) REVERT: B 63 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7453 (mmpt) REVERT: B 78 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7198 (ttp-170) REVERT: B 120 ASP cc_start: 0.8154 (t0) cc_final: 0.7811 (t0) REVERT: B 129 ARG cc_start: 0.5342 (OUTLIER) cc_final: 0.4824 (mtt90) REVERT: B 153 THR cc_start: 0.8374 (p) cc_final: 0.8048 (p) REVERT: B 159 MET cc_start: 0.6535 (mmm) cc_final: 0.6201 (ppp) REVERT: C 6 GLU cc_start: 0.7055 (mp0) cc_final: 0.6811 (mp0) REVERT: C 15 SER cc_start: 0.8274 (t) cc_final: 0.7765 (p) REVERT: C 45 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7780 (tptt) REVERT: D 4 MET cc_start: 0.7271 (mmm) cc_final: 0.6663 (mmm) REVERT: D 33 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7735 (p) REVERT: D 67 SER cc_start: 0.8577 (p) cc_final: 0.8306 (t) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.0874 time to fit residues: 13.7043 Evaluate side-chains 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 30.0000 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.0570 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.241779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.199334 restraints weight = 6652.867| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 2.10 r_work: 0.4053 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6322 Z= 0.183 Angle : 0.623 7.439 8636 Z= 0.332 Chirality : 0.046 0.188 962 Planarity : 0.004 0.042 1104 Dihedral : 5.549 45.755 868 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.59 % Allowed : 15.40 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.31), residues: 781 helix: 0.82 (0.65), residues: 66 sheet: -0.25 (0.29), residues: 322 loop : -1.01 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 98 TYR 0.016 0.002 TYR D 185 PHE 0.015 0.002 PHE A 28 TRP 0.013 0.001 TRP C 111 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 6316) covalent geometry : angle 0.62280 ( 8624) SS BOND : bond 0.00376 ( 6) SS BOND : angle 0.61320 ( 12) hydrogen bonds : bond 0.03415 ( 244) hydrogen bonds : angle 6.02897 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7815 (t0) REVERT: B 63 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7435 (mmtt) REVERT: B 78 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7161 (ttp-170) REVERT: B 120 ASP cc_start: 0.7835 (t0) cc_final: 0.7487 (t0) REVERT: B 153 THR cc_start: 0.8330 (p) cc_final: 0.7985 (p) REVERT: B 159 MET cc_start: 0.6336 (mmm) cc_final: 0.6089 (ppp) REVERT: C 6 GLU cc_start: 0.6891 (mp0) cc_final: 0.6609 (mp0) REVERT: C 15 SER cc_start: 0.8163 (t) cc_final: 0.7665 (p) REVERT: C 45 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7639 (tptt) REVERT: D 4 MET cc_start: 0.7044 (mmm) cc_final: 0.6513 (mmm) REVERT: D 33 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7693 (p) REVERT: D 67 SER cc_start: 0.8479 (p) cc_final: 0.8187 (t) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.0808 time to fit residues: 13.1557 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 28 optimal weight: 0.0010 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.237283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.195671 restraints weight = 6467.295| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 2.47 r_work: 0.4055 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6322 Z= 0.171 Angle : 0.619 7.223 8636 Z= 0.332 Chirality : 0.045 0.189 962 Planarity : 0.004 0.042 1104 Dihedral : 5.526 42.378 868 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.59 % Allowed : 15.70 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.31), residues: 781 helix: 0.86 (0.65), residues: 66 sheet: -0.25 (0.28), residues: 327 loop : -1.02 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 98 TYR 0.027 0.002 TYR C 54 PHE 0.015 0.002 PHE A 28 TRP 0.016 0.001 TRP C 111 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 6316) covalent geometry : angle 0.61900 ( 8624) SS BOND : bond 0.00370 ( 6) SS BOND : angle 0.63134 ( 12) hydrogen bonds : bond 0.03317 ( 244) hydrogen bonds : angle 6.00542 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 89 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.5006 (mt-10) REVERT: B 63 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7432 (mmtt) REVERT: B 78 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7170 (ttp-170) REVERT: B 120 ASP cc_start: 0.7838 (t0) cc_final: 0.7512 (t0) REVERT: B 153 THR cc_start: 0.8340 (p) cc_final: 0.8016 (p) REVERT: B 159 MET cc_start: 0.6571 (mmm) cc_final: 0.6156 (ppp) REVERT: C 6 GLU cc_start: 0.6867 (mp0) cc_final: 0.6592 (mp0) REVERT: C 15 SER cc_start: 0.8154 (t) cc_final: 0.7649 (p) REVERT: C 45 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7628 (tptt) REVERT: D 4 MET cc_start: 0.7046 (mmm) cc_final: 0.6500 (mmm) REVERT: D 33 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7705 (p) REVERT: D 67 SER cc_start: 0.8477 (p) cc_final: 0.8200 (t) REVERT: D 139 TYR cc_start: 0.6053 (t80) cc_final: 0.5746 (t80) outliers start: 17 outliers final: 13 residues processed: 121 average time/residue: 0.0817 time to fit residues: 13.2407 Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 18 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 113 GLN ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.237767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.196896 restraints weight = 6423.838| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 1.75 r_work: 0.4134 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6322 Z= 0.165 Angle : 0.621 9.195 8636 Z= 0.330 Chirality : 0.046 0.184 962 Planarity : 0.004 0.042 1104 Dihedral : 5.440 38.576 868 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.29 % Allowed : 16.31 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.31), residues: 781 helix: 0.91 (0.66), residues: 66 sheet: -0.26 (0.28), residues: 329 loop : -1.00 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 98 TYR 0.031 0.002 TYR C 54 PHE 0.014 0.002 PHE C 79 TRP 0.017 0.001 TRP C 111 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6316) covalent geometry : angle 0.62076 ( 8624) SS BOND : bond 0.00416 ( 6) SS BOND : angle 0.55802 ( 12) hydrogen bonds : bond 0.03313 ( 244) hydrogen bonds : angle 5.93357 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.58 seconds wall clock time: 36 minutes 52.73 seconds (2212.73 seconds total)