Starting phenix.real_space_refine on Tue Mar 3 20:08:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjd_31618/03_2026/7fjd_31618.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjd_31618/03_2026/7fjd_31618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjd_31618/03_2026/7fjd_31618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjd_31618/03_2026/7fjd_31618.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjd_31618/03_2026/7fjd_31618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjd_31618/03_2026/7fjd_31618.cif" } resolution = 3.2 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= 0.006 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 54 5.16 5 C 5341 2.51 5 N 1368 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 8352 Number of models: 1 Model: "" Number of chains: 10 Chain: "a" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 264 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "b" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "f" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "g" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 887 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1923 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2241 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.23 Number of scatterers: 8352 At special positions: 0 Unit cell: (89.1, 99, 144.1, 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 54 16.00 O 1589 8.00 N 1368 7.00 C 5341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.04 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.03 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.04 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.04 Simple disulfide: pdb=" SG CYS m 227 " - pdb=" SG CYS n 264 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 110 " distance=2.04 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " distance=2.04 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: 0.75 Conformation dependent library (CDL) restraints added in 300.8 milliseconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 26.4% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'a' and resid 29 through 54 removed outlier: 4.480A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS a 54 " --> pdb=" O PHE a 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 54 removed outlier: 3.685A pdb=" N ASP b 36 " --> pdb=" O CYS b 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE b 38 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR b 47 " --> pdb=" O GLY b 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 66 No H-bonds generated for 'chain 'd' and resid 64 through 66' Processing helix chain 'd' and resid 76 through 80 Processing helix chain 'd' and resid 102 through 126 removed outlier: 4.076A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE d 125 " --> pdb=" O GLY d 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.830A pdb=" N ASP e 107 " --> pdb=" O LYS e 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 154 removed outlier: 4.180A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.967A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA f 108 " --> pdb=" O PRO f 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 104 through 108' Processing helix chain 'f' and resid 128 through 142 Processing helix chain 'f' and resid 143 through 154 Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 111 through 138 removed outlier: 3.729A pdb=" N ILE g 115 " --> pdb=" O ASN g 111 " (cutoff:3.500A) Processing helix chain 'm' and resid 231 through 235 removed outlier: 3.540A pdb=" N LYS m 234 " --> pdb=" O LEU m 231 " (cutoff:3.500A) Processing helix chain 'm' and resid 240 through 273 removed outlier: 4.008A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER m 273 " --> pdb=" O ARG m 269 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 3.628A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 157 removed outlier: 3.641A pdb=" N ILE n 154 " --> pdb=" O SER n 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 217 through 221 Processing helix chain 'n' and resid 269 through 308 removed outlier: 4.172A pdb=" N GLN n 273 " --> pdb=" O GLU n 269 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS n 308 " --> pdb=" O MET n 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 27 removed outlier: 6.075A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.842A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN e 60 " --> pdb=" O VAL e 97 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE e 66 " --> pdb=" O TRP e 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 40 removed outlier: 3.656A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER e 83 " --> pdb=" O GLY e 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.510A pdb=" N THR f 44 " --> pdb=" O SER f 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU f 47 " --> pdb=" O LEU f 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY f 76 " --> pdb=" O SER f 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 57 through 61 removed outlier: 3.513A pdb=" N LEU f 114 " --> pdb=" O GLY f 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG f 115 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG g 102 " --> pdb=" O ARG f 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE g 53 " --> pdb=" O PHE g 64 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE g 64 " --> pdb=" O ILE g 53 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.616A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.785A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.554A pdb=" N LEU m 33 " --> pdb=" O MET m 127 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE m 55 " --> pdb=" O TYR m 71 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR m 71 " --> pdb=" O PHE m 55 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP m 57 " --> pdb=" O LEU m 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.554A pdb=" N LEU m 33 " --> pdb=" O MET m 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 41 through 46 Processing sheet with id=AB3, first strand: chain 'm' and resid 140 through 143 removed outlier: 4.093A pdb=" N ALA m 140 " --> pdb=" O THR m 158 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 180 through 184 Processing sheet with id=AB5, first strand: chain 'n' and resid 24 through 26 removed outlier: 3.632A pdb=" N MET n 38 " --> pdb=" O LEU n 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN n 84 " --> pdb=" O ARG n 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'n' and resid 29 through 33 removed outlier: 6.856A pdb=" N GLN n 30 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR n 133 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU n 32 " --> pdb=" O THR n 133 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE n 109 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL n 69 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.543A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.543A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 183 through 184 372 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.01 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: 2067 1.33 - 1.46: 2117 1.46 - 1.58: 4275 1.58 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 8535 Sorted by residual: bond pdb=" CG LEU a 27 " pdb=" CD2 LEU a 27 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.90e+00 bond pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.30e-02 5.92e+03 7.41e+00 bond pdb=" N ILE n 253 " pdb=" CA ILE n 253 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.29e-02 6.01e+03 6.39e+00 bond pdb=" N CYS b 32 " pdb=" CA CYS b 32 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.23e+00 bond pdb=" CB ARG e 117 " pdb=" CG ARG e 117 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.12e+00 ... (remaining 8530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 11369 3.60 - 7.20: 185 7.20 - 10.80: 26 10.80 - 14.40: 4 14.40 - 18.00: 2 Bond angle restraints: 11586 Sorted by residual: angle pdb=" C PHE m 160 " pdb=" N ASP m 161 " pdb=" CA ASP m 161 " ideal model delta sigma weight residual 121.54 133.64 -12.10 1.91e+00 2.74e-01 4.02e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 134.79 -12.99 2.44e+00 1.68e-01 2.83e+01 angle pdb=" CA TYR n 50 " pdb=" CB TYR n 50 " pdb=" CG TYR n 50 " ideal model delta sigma weight residual 113.90 123.18 -9.28 1.80e+00 3.09e-01 2.66e+01 angle pdb=" N ASP m 159 " pdb=" CA ASP m 159 " pdb=" C ASP m 159 " ideal model delta sigma weight residual 110.42 117.93 -7.51 1.46e+00 4.69e-01 2.65e+01 angle pdb=" CA LEU m 182 " pdb=" CB LEU m 182 " pdb=" CG LEU m 182 " ideal model delta sigma weight residual 116.30 134.30 -18.00 3.50e+00 8.16e-02 2.65e+01 ... (remaining 11581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4888 17.13 - 34.26: 236 34.26 - 51.39: 70 51.39 - 68.52: 16 68.52 - 85.65: 9 Dihedral angle restraints: 5219 sinusoidal: 2143 harmonic: 3076 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 127.81 52.19 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual 93.00 178.65 -85.65 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CA MET g 103 " pdb=" C MET g 103 " pdb=" N CYS g 104 " pdb=" CA CYS g 104 " ideal model delta harmonic sigma weight residual 180.00 -135.19 -44.81 0 5.00e+00 4.00e-02 8.03e+01 ... (remaining 5216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1113 0.095 - 0.191: 181 0.191 - 0.286: 9 0.286 - 0.382: 1 0.382 - 0.477: 1 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CG LEU f 90 " pdb=" CB LEU f 90 " pdb=" CD1 LEU f 90 " pdb=" CD2 LEU f 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1302 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR n 50 " -0.043 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR n 50 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR n 50 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR n 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR n 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR n 50 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR n 50 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR n 50 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR e 111 " -0.027 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR e 111 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR e 111 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR e 111 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR e 111 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR e 111 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR e 111 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR e 111 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.026 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR d 90 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.002 2.00e-02 2.50e+03 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1302 2.76 - 3.30: 6821 3.30 - 3.83: 12089 3.83 - 4.37: 13423 4.37 - 4.90: 24896 Nonbonded interactions: 58531 Sorted by model distance: nonbonded pdb=" NZ LYS b 30 " pdb=" O1 CLR b 201 " model vdw 2.229 3.120 nonbonded pdb=" N ASP m 159 " pdb=" OD1 ASP m 159 " model vdw 2.305 3.120 nonbonded pdb=" OG SER m 118 " pdb=" OE1 GLN n 116 " model vdw 2.310 3.040 nonbonded pdb=" O TYR m 71 " pdb=" NZ LYS m 78 " model vdw 2.408 3.120 nonbonded pdb=" N ASP g 39 " pdb=" OD1 ASP g 39 " model vdw 2.409 3.120 ... (remaining 58526 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 26 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 54)) selection = (chain 'b' and resid 26 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 77 or (resid 78 and (nam \ e N or name CA or name C or name O or name CB )) or resid 79 through 155)) selection = (chain 'f' and resid 33 through 155) } 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: 1.010 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.660 Find NCS groups from input model: 0.140 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.011 0.120 8548 Z= 0.450 Angle : 1.251 18.002 11612 Z= 0.670 Chirality : 0.068 0.477 1305 Planarity : 0.008 0.073 1466 Dihedral : 11.941 82.404 3206 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.94 % Favored : 90.87 % Rotamer: Outliers : 0.87 % Allowed : 6.19 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.57 (0.22), residues: 1040 helix: -1.03 (0.28), residues: 237 sheet: -1.35 (0.29), residues: 292 loop : -3.79 (0.19), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG d 63 TYR 0.063 0.005 TYR d 90 PHE 0.041 0.005 PHE f 110 TRP 0.029 0.004 TRP e 59 HIS 0.018 0.005 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.01061 ( 8535) covalent geometry : angle 1.24022 (11586) SS BOND : bond 0.00549 ( 13) SS BOND : angle 3.74477 ( 26) hydrogen bonds : bond 0.26212 ( 353) hydrogen bonds : angle 7.52542 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.302 Fit side-chains REVERT: e 41 SER cc_start: 0.9071 (t) cc_final: 0.8756 (p) REVERT: e 57 ILE cc_start: 0.8761 (mp) cc_final: 0.8355 (tt) REVERT: f 117 ARG cc_start: 0.8506 (ttm170) cc_final: 0.8258 (ttm170) REVERT: g 32 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8215 (mptt) REVERT: g 53 ILE cc_start: 0.7888 (mm) cc_final: 0.7685 (mt) REVERT: m 99 ARG cc_start: 0.7189 (ptp90) cc_final: 0.6860 (mtm-85) REVERT: m 173 ASP cc_start: 0.7734 (m-30) cc_final: 0.7082 (p0) REVERT: m 211 ASN cc_start: 0.8609 (t160) cc_final: 0.8401 (t0) REVERT: n 33 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7531 (ptmt) REVERT: n 92 ASP cc_start: 0.7574 (m-30) cc_final: 0.6680 (t70) REVERT: n 96 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7403 (mtt90) REVERT: n 113 ARG cc_start: 0.6255 (mtp180) cc_final: 0.5994 (mtm180) REVERT: n 121 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6581 (mp0) REVERT: n 183 LYS cc_start: 0.7914 (mttt) cc_final: 0.7421 (mtpp) outliers start: 8 outliers final: 1 residues processed: 202 average time/residue: 0.1117 time to fit residues: 29.2035 Evaluate side-chains 135 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 ASN m 136 ASN m 168 GLN n 25 GLN n 47 ASN n 122 GLN n 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114440 restraints weight = 10141.423| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.11 r_work: 0.2948 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8548 Z= 0.159 Angle : 0.668 9.273 11612 Z= 0.355 Chirality : 0.044 0.223 1305 Planarity : 0.005 0.053 1466 Dihedral : 7.269 56.140 1275 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.47 % Allowed : 7.49 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.83 (0.25), residues: 1040 helix: 1.62 (0.33), residues: 241 sheet: -0.31 (0.31), residues: 287 loop : -3.38 (0.21), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 115 TYR 0.032 0.002 TYR n 50 PHE 0.019 0.002 PHE m 157 TRP 0.016 0.001 TRP m 197 HIS 0.004 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8535) covalent geometry : angle 0.66525 (11586) SS BOND : bond 0.00726 ( 13) SS BOND : angle 1.34873 ( 26) hydrogen bonds : bond 0.07871 ( 353) hydrogen bonds : angle 4.97305 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7909 (mt) REVERT: d 99 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7128 (pp) REVERT: e 41 SER cc_start: 0.9130 (t) cc_final: 0.8891 (p) REVERT: e 57 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8489 (tt) REVERT: e 141 THR cc_start: 0.8486 (m) cc_final: 0.8232 (m) REVERT: f 80 ASP cc_start: 0.8123 (t70) cc_final: 0.7710 (t0) REVERT: f 101 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7525 (tpp-160) REVERT: f 141 THR cc_start: 0.8641 (t) cc_final: 0.8418 (m) REVERT: g 30 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.7519 (mp) REVERT: m 100 ASP cc_start: 0.7074 (m-30) cc_final: 0.6767 (t0) REVERT: m 173 ASP cc_start: 0.7906 (m-30) cc_final: 0.7210 (p0) REVERT: m 211 ASN cc_start: 0.8762 (t160) cc_final: 0.8391 (t0) REVERT: n 33 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7465 (ptmt) REVERT: n 92 ASP cc_start: 0.7667 (m-30) cc_final: 0.6764 (t70) REVERT: n 96 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7373 (mtt90) REVERT: n 121 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6764 (mp0) REVERT: n 302 MET cc_start: 0.7504 (ttp) cc_final: 0.5844 (mmt) outliers start: 32 outliers final: 18 residues processed: 171 average time/residue: 0.0970 time to fit residues: 22.3573 Evaluate side-chains 148 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 71 LYS Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 95 SER Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS g 52 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 28 GLN m 168 GLN n 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113279 restraints weight = 9913.160| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.00 r_work: 0.2948 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8548 Z= 0.119 Angle : 0.567 8.970 11612 Z= 0.301 Chirality : 0.042 0.193 1305 Planarity : 0.004 0.046 1466 Dihedral : 6.092 47.767 1275 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.37 % Allowed : 11.18 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.95 (0.26), residues: 1040 helix: 2.77 (0.33), residues: 241 sheet: 0.22 (0.31), residues: 303 loop : -3.16 (0.22), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 117 TYR 0.025 0.001 TYR n 50 PHE 0.014 0.001 PHE m 157 TRP 0.012 0.001 TRP m 197 HIS 0.005 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8535) covalent geometry : angle 0.56548 (11586) SS BOND : bond 0.00294 ( 13) SS BOND : angle 1.04000 ( 26) hydrogen bonds : bond 0.05719 ( 353) hydrogen bonds : angle 4.31076 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.354 Fit side-chains REVERT: d 27 GLU cc_start: 0.8208 (pt0) cc_final: 0.7942 (pt0) REVERT: d 29 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7670 (mm) REVERT: d 99 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7102 (pp) REVERT: d 117 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7554 (tp) REVERT: e 57 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8472 (tt) REVERT: e 79 GLU cc_start: 0.8002 (pm20) cc_final: 0.7759 (pm20) REVERT: e 80 ASP cc_start: 0.8372 (p0) cc_final: 0.8062 (p0) REVERT: e 104 LYS cc_start: 0.8011 (mmtp) cc_final: 0.7348 (ttpt) REVERT: e 144 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7499 (tp) REVERT: f 39 SER cc_start: 0.8435 (t) cc_final: 0.8195 (m) REVERT: f 80 ASP cc_start: 0.8156 (t70) cc_final: 0.7685 (t0) REVERT: f 106 GLU cc_start: 0.8296 (pt0) cc_final: 0.7770 (pt0) REVERT: f 117 ARG cc_start: 0.8531 (ttm170) cc_final: 0.8257 (ttm-80) REVERT: m 100 ASP cc_start: 0.7003 (m-30) cc_final: 0.6750 (t0) REVERT: m 200 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7919 (ptpt) REVERT: m 211 ASN cc_start: 0.8746 (t160) cc_final: 0.8419 (t0) REVERT: n 33 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7574 (ptmt) REVERT: n 38 MET cc_start: 0.7971 (tpt) cc_final: 0.7500 (tmm) REVERT: n 46 MET cc_start: 0.4335 (tmm) cc_final: 0.3878 (tmm) REVERT: n 50 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.5502 (p90) REVERT: n 92 ASP cc_start: 0.7676 (m-30) cc_final: 0.6799 (t70) REVERT: n 96 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7341 (mtt90) REVERT: n 121 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6681 (mp0) outliers start: 31 outliers final: 18 residues processed: 167 average time/residue: 0.1055 time to fit residues: 23.3867 Evaluate side-chains 153 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.149541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112882 restraints weight = 10262.987| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.18 r_work: 0.2896 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8548 Z= 0.140 Angle : 0.587 8.958 11612 Z= 0.308 Chirality : 0.043 0.200 1305 Planarity : 0.004 0.044 1466 Dihedral : 5.682 45.439 1273 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.56 % Allowed : 11.83 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.67 (0.26), residues: 1040 helix: 2.96 (0.32), residues: 242 sheet: 0.37 (0.32), residues: 309 loop : -2.99 (0.22), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG f 115 TYR 0.025 0.001 TYR n 50 PHE 0.013 0.001 PHE m 157 TRP 0.011 0.001 TRP d 43 HIS 0.005 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8535) covalent geometry : angle 0.58385 (11586) SS BOND : bond 0.00354 ( 13) SS BOND : angle 1.32696 ( 26) hydrogen bonds : bond 0.06333 ( 353) hydrogen bonds : angle 4.30508 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.311 Fit side-chains REVERT: d 27 GLU cc_start: 0.8245 (pt0) cc_final: 0.8004 (pt0) REVERT: d 29 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7790 (mm) REVERT: d 99 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6991 (pp) REVERT: d 117 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7640 (tp) REVERT: e 57 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8479 (tt) REVERT: e 79 GLU cc_start: 0.8045 (pm20) cc_final: 0.7827 (pm20) REVERT: e 80 ASP cc_start: 0.8396 (p0) cc_final: 0.8048 (p0) REVERT: e 104 LYS cc_start: 0.7963 (mmtp) cc_final: 0.7314 (ttpt) REVERT: e 144 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7511 (tp) REVERT: f 39 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8264 (m) REVERT: f 80 ASP cc_start: 0.8172 (t70) cc_final: 0.7653 (t0) REVERT: f 106 GLU cc_start: 0.8190 (pt0) cc_final: 0.7646 (pt0) REVERT: f 117 ARG cc_start: 0.8500 (ttm170) cc_final: 0.8267 (ttm-80) REVERT: m 100 ASP cc_start: 0.7056 (m-30) cc_final: 0.6758 (t0) REVERT: m 145 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7573 (mtp85) REVERT: m 173 ASP cc_start: 0.8055 (m-30) cc_final: 0.7254 (p0) REVERT: m 200 LYS cc_start: 0.8296 (ptmt) cc_final: 0.8082 (pttp) REVERT: m 211 ASN cc_start: 0.8806 (t160) cc_final: 0.8454 (t0) REVERT: n 33 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7595 (ptmt) REVERT: n 44 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6391 (pt0) REVERT: n 46 MET cc_start: 0.4505 (tmm) cc_final: 0.3556 (tmm) REVERT: n 50 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5489 (p90) REVERT: n 92 ASP cc_start: 0.7668 (m-30) cc_final: 0.6793 (t70) REVERT: n 96 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7448 (mtt90) REVERT: n 121 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6658 (mp0) REVERT: n 252 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7416 (pt0) outliers start: 42 outliers final: 24 residues processed: 172 average time/residue: 0.1083 time to fit residues: 24.4976 Evaluate side-chains 164 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 71 LYS Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 85 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 HIS ** 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 = 0.3635 r_free = 0.3635 target = 0.147638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110764 restraints weight = 9929.262| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.91 r_work: 0.2885 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8548 Z= 0.151 Angle : 0.602 9.084 11612 Z= 0.315 Chirality : 0.043 0.192 1305 Planarity : 0.004 0.043 1466 Dihedral : 5.605 45.000 1273 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.23 % Allowed : 12.81 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.51 (0.27), residues: 1040 helix: 3.13 (0.31), residues: 242 sheet: 0.54 (0.32), residues: 301 loop : -2.92 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 52 TYR 0.025 0.002 TYR n 50 PHE 0.013 0.002 PHE m 157 TRP 0.011 0.001 TRP d 43 HIS 0.005 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8535) covalent geometry : angle 0.59920 (11586) SS BOND : bond 0.00345 ( 13) SS BOND : angle 1.45610 ( 26) hydrogen bonds : bond 0.06668 ( 353) hydrogen bonds : angle 4.31464 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.303 Fit side-chains REVERT: d 27 GLU cc_start: 0.8391 (pt0) cc_final: 0.8175 (pt0) REVERT: d 29 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7698 (mm) REVERT: d 99 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6794 (pp) REVERT: d 117 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7588 (tp) REVERT: d 123 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6079 (t80) REVERT: e 57 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8526 (tt) REVERT: e 79 GLU cc_start: 0.8296 (pm20) cc_final: 0.8062 (pm20) REVERT: e 80 ASP cc_start: 0.8346 (p0) cc_final: 0.7959 (p0) REVERT: e 144 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7360 (tp) REVERT: f 80 ASP cc_start: 0.8214 (t70) cc_final: 0.7641 (t0) REVERT: f 106 GLU cc_start: 0.8280 (pt0) cc_final: 0.7703 (pt0) REVERT: f 117 ARG cc_start: 0.8610 (ttm170) cc_final: 0.8393 (ttm-80) REVERT: m 100 ASP cc_start: 0.7231 (m-30) cc_final: 0.6778 (t0) REVERT: m 145 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7607 (mtp85) REVERT: m 173 ASP cc_start: 0.8074 (m-30) cc_final: 0.7225 (p0) REVERT: m 211 ASN cc_start: 0.8793 (t160) cc_final: 0.8466 (t0) REVERT: n 33 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7553 (ptmt) REVERT: n 44 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6900 (pt0) REVERT: n 50 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5271 (p90) REVERT: n 92 ASP cc_start: 0.7674 (m-30) cc_final: 0.6691 (t70) REVERT: n 96 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7400 (mtt90) REVERT: n 121 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6497 (mp0) REVERT: n 252 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7335 (pt0) outliers start: 39 outliers final: 28 residues processed: 165 average time/residue: 0.1049 time to fit residues: 22.9244 Evaluate side-chains 166 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 196 LEU Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 44 GLN ** n 173 HIS ** 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 = 0.3670 r_free = 0.3670 target = 0.150850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114786 restraints weight = 9821.262| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.60 r_work: 0.2888 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8548 Z= 0.155 Angle : 0.608 8.923 11612 Z= 0.317 Chirality : 0.043 0.204 1305 Planarity : 0.004 0.042 1466 Dihedral : 5.618 45.026 1273 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.89 % Allowed : 12.92 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.44 (0.26), residues: 1040 helix: 3.19 (0.31), residues: 241 sheet: 0.67 (0.33), residues: 289 loop : -2.84 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 52 TYR 0.025 0.002 TYR n 50 PHE 0.013 0.002 PHE f 110 TRP 0.013 0.001 TRP d 43 HIS 0.006 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8535) covalent geometry : angle 0.60606 (11586) SS BOND : bond 0.00341 ( 13) SS BOND : angle 1.22888 ( 26) hydrogen bonds : bond 0.06843 ( 353) hydrogen bonds : angle 4.32051 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 0.353 Fit side-chains REVERT: d 27 GLU cc_start: 0.8376 (pt0) cc_final: 0.8141 (pt0) REVERT: d 29 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7703 (mm) REVERT: d 99 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6643 (pp) REVERT: d 117 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7523 (tp) REVERT: d 123 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.5893 (t80) REVERT: e 57 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8525 (tt) REVERT: e 79 GLU cc_start: 0.8267 (pm20) cc_final: 0.8046 (pm20) REVERT: e 144 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7293 (tp) REVERT: f 80 ASP cc_start: 0.8274 (t70) cc_final: 0.7638 (t0) REVERT: f 106 GLU cc_start: 0.8111 (pt0) cc_final: 0.7512 (pt0) REVERT: f 117 ARG cc_start: 0.8624 (ttm170) cc_final: 0.8421 (ttm-80) REVERT: m 100 ASP cc_start: 0.7245 (m-30) cc_final: 0.6915 (t0) REVERT: m 113 MET cc_start: 0.6843 (mtm) cc_final: 0.6594 (mtm) REVERT: m 145 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7570 (mtp85) REVERT: m 173 ASP cc_start: 0.8057 (m-30) cc_final: 0.7205 (p0) REVERT: m 211 ASN cc_start: 0.8796 (t160) cc_final: 0.8461 (t0) REVERT: n 33 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7468 (ptmt) REVERT: n 38 MET cc_start: 0.8049 (tpt) cc_final: 0.7683 (tmm) REVERT: n 50 TYR cc_start: 0.6325 (OUTLIER) cc_final: 0.5263 (p90) REVERT: n 92 ASP cc_start: 0.7611 (m-30) cc_final: 0.6676 (t70) REVERT: n 96 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7327 (mtt90) REVERT: n 121 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6445 (mp0) REVERT: n 252 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7285 (pt0) outliers start: 45 outliers final: 34 residues processed: 166 average time/residue: 0.1044 time to fit residues: 22.9741 Evaluate side-chains 169 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Chi-restraints excluded: chain n residue 299 LEU Chi-restraints excluded: chain n residue 302 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 47 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN n 44 GLN ** n 173 HIS ** 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 = 0.3641 r_free = 0.3641 target = 0.148363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111723 restraints weight = 9928.903| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.01 r_work: 0.2887 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8548 Z= 0.137 Angle : 0.578 8.848 11612 Z= 0.302 Chirality : 0.043 0.191 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.497 44.594 1273 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.10 % Allowed : 13.14 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.29 (0.27), residues: 1040 helix: 3.37 (0.31), residues: 241 sheet: 0.72 (0.32), residues: 297 loop : -2.80 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 115 TYR 0.024 0.001 TYR n 50 PHE 0.012 0.001 PHE m 157 TRP 0.012 0.001 TRP d 43 HIS 0.005 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8535) covalent geometry : angle 0.57487 (11586) SS BOND : bond 0.00297 ( 13) SS BOND : angle 1.35511 ( 26) hydrogen bonds : bond 0.06346 ( 353) hydrogen bonds : angle 4.24442 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.237 Fit side-chains REVERT: b 34 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7535 (mt) REVERT: d 27 GLU cc_start: 0.8381 (pt0) cc_final: 0.8162 (pt0) REVERT: d 29 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7722 (mm) REVERT: d 99 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6773 (pp) REVERT: d 117 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7565 (tp) REVERT: d 123 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.5868 (t80) REVERT: e 57 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8530 (tt) REVERT: e 79 GLU cc_start: 0.8294 (pm20) cc_final: 0.8091 (pm20) REVERT: e 144 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7359 (tp) REVERT: f 80 ASP cc_start: 0.8281 (t70) cc_final: 0.7633 (t0) REVERT: f 106 GLU cc_start: 0.8100 (pt0) cc_final: 0.7458 (pt0) REVERT: m 100 ASP cc_start: 0.7261 (m-30) cc_final: 0.6939 (t0) REVERT: m 145 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7610 (mtp85) REVERT: m 173 ASP cc_start: 0.8090 (m-30) cc_final: 0.7273 (p0) REVERT: m 211 ASN cc_start: 0.8761 (t0) cc_final: 0.8440 (t0) REVERT: n 33 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7528 (ptmt) REVERT: n 50 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5370 (p90) REVERT: n 92 ASP cc_start: 0.7648 (m-30) cc_final: 0.6737 (t70) REVERT: n 96 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7387 (mtt90) REVERT: n 121 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6554 (mp0) REVERT: n 252 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7320 (pt0) outliers start: 47 outliers final: 33 residues processed: 164 average time/residue: 0.0980 time to fit residues: 21.4599 Evaluate side-chains 168 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Chi-restraints excluded: chain n residue 299 LEU Chi-restraints excluded: chain n residue 302 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 44 GLN ** n 173 HIS ** 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 = 0.3645 r_free = 0.3645 target = 0.148760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112168 restraints weight = 9798.035| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.73 r_work: 0.2883 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8548 Z= 0.159 Angle : 0.615 9.061 11612 Z= 0.320 Chirality : 0.044 0.198 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.600 44.785 1273 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.67 % Allowed : 14.55 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.30 (0.27), residues: 1040 helix: 3.33 (0.30), residues: 241 sheet: 0.75 (0.33), residues: 294 loop : -2.80 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 115 TYR 0.025 0.002 TYR n 50 PHE 0.013 0.002 PHE f 110 TRP 0.012 0.001 TRP d 43 HIS 0.005 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8535) covalent geometry : angle 0.61073 (11586) SS BOND : bond 0.00330 ( 13) SS BOND : angle 1.66190 ( 26) hydrogen bonds : bond 0.06830 ( 353) hydrogen bonds : angle 4.30623 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.274 Fit side-chains REVERT: b 34 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7468 (mt) REVERT: d 27 GLU cc_start: 0.8375 (pt0) cc_final: 0.8171 (pt0) REVERT: d 29 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7729 (mm) REVERT: d 99 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6659 (pp) REVERT: d 117 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7534 (tp) REVERT: d 123 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.5798 (t80) REVERT: e 57 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8529 (tt) REVERT: e 79 GLU cc_start: 0.8291 (pm20) cc_final: 0.8079 (pm20) REVERT: e 144 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7308 (tp) REVERT: f 80 ASP cc_start: 0.8266 (t70) cc_final: 0.7623 (t0) REVERT: m 100 ASP cc_start: 0.7236 (m-30) cc_final: 0.6917 (t0) REVERT: m 145 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7543 (mtp85) REVERT: m 173 ASP cc_start: 0.8071 (m-30) cc_final: 0.7219 (p0) REVERT: m 211 ASN cc_start: 0.8745 (t0) cc_final: 0.8413 (t0) REVERT: n 33 LYS cc_start: 0.7835 (ttpt) cc_final: 0.7522 (ptmt) REVERT: n 38 MET cc_start: 0.8010 (tpt) cc_final: 0.7588 (tmm) REVERT: n 46 MET cc_start: 0.4326 (tmm) cc_final: 0.3614 (tmm) REVERT: n 50 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5336 (p90) REVERT: n 92 ASP cc_start: 0.7610 (m-30) cc_final: 0.6676 (t70) REVERT: n 96 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7371 (mtt90) REVERT: n 121 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6503 (mp0) REVERT: n 134 GLU cc_start: 0.8128 (pp20) cc_final: 0.7835 (tp30) REVERT: n 252 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7297 (pt0) outliers start: 43 outliers final: 34 residues processed: 156 average time/residue: 0.0959 time to fit residues: 20.1807 Evaluate side-chains 165 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Chi-restraints excluded: chain n residue 299 LEU Chi-restraints excluded: chain n residue 302 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 128 HIS n 44 GLN ** n 173 HIS ** 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 = 0.3584 r_free = 0.3584 target = 0.143495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106690 restraints weight = 9932.113| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.97 r_work: 0.2825 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8548 Z= 0.231 Angle : 0.711 10.695 11612 Z= 0.369 Chirality : 0.047 0.217 1305 Planarity : 0.005 0.042 1466 Dihedral : 6.094 46.792 1273 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.78 % Allowed : 14.33 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.54 (0.26), residues: 1040 helix: 2.96 (0.30), residues: 241 sheet: 0.52 (0.32), residues: 298 loop : -2.81 (0.23), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 91 TYR 0.029 0.002 TYR n 50 PHE 0.018 0.002 PHE f 110 TRP 0.013 0.002 TRP d 43 HIS 0.006 0.002 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 8535) covalent geometry : angle 0.70599 (11586) SS BOND : bond 0.00429 ( 13) SS BOND : angle 1.93634 ( 26) hydrogen bonds : bond 0.08423 ( 353) hydrogen bonds : angle 4.54872 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.355 Fit side-chains REVERT: b 34 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7531 (mt) REVERT: d 29 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7915 (mm) REVERT: d 99 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6710 (pp) REVERT: d 117 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7566 (tp) REVERT: d 123 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.5738 (t80) REVERT: e 49 CYS cc_start: 0.7987 (t) cc_final: 0.7497 (t) REVERT: e 57 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8512 (tt) REVERT: e 79 GLU cc_start: 0.8318 (pm20) cc_final: 0.8059 (pm20) REVERT: e 90 LEU cc_start: 0.8651 (tp) cc_final: 0.8427 (tp) REVERT: e 144 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7353 (tp) REVERT: f 80 ASP cc_start: 0.8335 (t70) cc_final: 0.7699 (t0) REVERT: m 100 ASP cc_start: 0.7249 (m-30) cc_final: 0.6930 (t0) REVERT: m 145 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7563 (mtp85) REVERT: m 173 ASP cc_start: 0.8042 (m-30) cc_final: 0.7286 (p0) REVERT: m 211 ASN cc_start: 0.8774 (t0) cc_final: 0.8502 (t0) REVERT: n 33 LYS cc_start: 0.7881 (ttpt) cc_final: 0.7527 (ptmt) REVERT: n 38 MET cc_start: 0.8023 (tpt) cc_final: 0.7666 (tmm) REVERT: n 50 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.5310 (p90) REVERT: n 92 ASP cc_start: 0.7634 (m-30) cc_final: 0.6685 (t70) REVERT: n 96 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7428 (mtt90) REVERT: n 121 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6558 (mp0) REVERT: n 134 GLU cc_start: 0.8079 (pp20) cc_final: 0.7823 (tp30) REVERT: n 183 LYS cc_start: 0.8200 (mttt) cc_final: 0.7687 (mtpp) REVERT: n 252 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7323 (pt0) outliers start: 44 outliers final: 32 residues processed: 159 average time/residue: 0.0913 time to fit residues: 19.5708 Evaluate side-chains 164 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Chi-restraints excluded: chain n residue 299 LEU Chi-restraints excluded: chain n residue 302 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.148640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110603 restraints weight = 9865.593| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.96 r_work: 0.2889 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8548 Z= 0.122 Angle : 0.567 8.941 11612 Z= 0.296 Chirality : 0.042 0.181 1305 Planarity : 0.004 0.041 1466 Dihedral : 5.471 44.901 1273 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.47 % Allowed : 15.85 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.13 (0.27), residues: 1040 helix: 3.50 (0.30), residues: 242 sheet: 0.80 (0.33), residues: 295 loop : -2.69 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG f 115 TYR 0.022 0.001 TYR n 50 PHE 0.011 0.001 PHE m 157 TRP 0.014 0.001 TRP d 43 HIS 0.004 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8535) covalent geometry : angle 0.56432 (11586) SS BOND : bond 0.00291 ( 13) SS BOND : angle 1.22224 ( 26) hydrogen bonds : bond 0.05895 ( 353) hydrogen bonds : angle 4.20088 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.313 Fit side-chains REVERT: d 99 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6833 (pp) REVERT: d 117 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7526 (tp) REVERT: d 123 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.5740 (t80) REVERT: e 49 CYS cc_start: 0.7675 (t) cc_final: 0.7133 (t) REVERT: e 57 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8419 (tt) REVERT: e 144 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7231 (tp) REVERT: f 80 ASP cc_start: 0.8183 (t70) cc_final: 0.7557 (t0) REVERT: m 100 ASP cc_start: 0.7146 (m-30) cc_final: 0.6910 (t0) REVERT: m 145 ARG cc_start: 0.7777 (mtm180) cc_final: 0.7448 (mtp85) REVERT: m 173 ASP cc_start: 0.7883 (m-30) cc_final: 0.7190 (p0) REVERT: n 33 LYS cc_start: 0.7773 (ttpt) cc_final: 0.7473 (ptmt) REVERT: n 50 TYR cc_start: 0.6379 (OUTLIER) cc_final: 0.5304 (p90) REVERT: n 92 ASP cc_start: 0.7573 (m-30) cc_final: 0.6649 (t70) REVERT: n 96 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7353 (mtt90) REVERT: n 121 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6565 (mp0) REVERT: n 252 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7265 (pt0) outliers start: 32 outliers final: 23 residues processed: 153 average time/residue: 0.1026 time to fit residues: 21.1663 Evaluate side-chains 157 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 44 GLN Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 44 GLN ** n 173 HIS ** 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 = 0.3615 r_free = 0.3615 target = 0.146397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108374 restraints weight = 9835.237| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.00 r_work: 0.2860 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8548 Z= 0.156 Angle : 0.613 9.052 11612 Z= 0.319 Chirality : 0.044 0.193 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.579 44.366 1273 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.91 % Allowed : 15.53 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.14 (0.27), residues: 1040 helix: 3.48 (0.30), residues: 241 sheet: 0.82 (0.33), residues: 289 loop : -2.64 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 117 TYR 0.025 0.002 TYR n 50 PHE 0.013 0.002 PHE f 110 TRP 0.013 0.001 TRP d 43 HIS 0.005 0.001 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8535) covalent geometry : angle 0.60973 (11586) SS BOND : bond 0.00340 ( 13) SS BOND : angle 1.45847 ( 26) hydrogen bonds : bond 0.06686 ( 353) hydrogen bonds : angle 4.27245 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.34 seconds wall clock time: 40 minutes 35.15 seconds (2435.15 seconds total)