Starting phenix.real_space_refine on Tue Mar 3 20:08:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjf_31620/03_2026/7fjf_31620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjf_31620/03_2026/7fjf_31620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjf_31620/03_2026/7fjf_31620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjf_31620/03_2026/7fjf_31620.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjf_31620/03_2026/7fjf_31620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjf_31620/03_2026/7fjf_31620.cif" } resolution = 3.1 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 56 5.16 5 C 5352 2.51 5 N 1370 2.21 5 O 1599 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: 8377 Number of models: 1 Model: "" Number of chains: 10 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: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} 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: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1924 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2246 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "m" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'C3S': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'C3S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.91, per 1000 atoms: 0.23 Number of scatterers: 8377 At special positions: 0 Unit cell: (91.3, 97.9, 140.8, 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 56 16.00 O 1599 8.00 N 1370 7.00 C 5352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS b 32 " - pdb=" SG CYS a 32 " distance=2.14 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=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.04 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.03 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: 0.60 Conformation dependent library (CDL) restraints added in 197.4 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: 17 helices and 21 sheets defined 25.9% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'b' and resid 29 through 53 removed outlier: 3.529A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL b 44 " --> pdb=" O PHE b 40 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU b 46 " --> pdb=" O TYR b 42 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL b 53 " --> pdb=" O LEU b 49 " (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 102 through 124 removed outlier: 4.496A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.709A pdb=" N ASP e 107 " --> pdb=" O LYS e 104 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 104 through 108' Processing helix chain 'e' and resid 127 through 154 removed outlier: 3.608A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.599A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) removed outlier: 3.896A 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 154 removed outlier: 4.551A pdb=" N GLY f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU f 145 " --> pdb=" O THR f 141 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU f 146 " --> pdb=" O GLY f 142 " (cutoff:3.500A) 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: 4.055A pdb=" N ILE g 115 " --> pdb=" O ASN g 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY g 138 " --> pdb=" O TYR g 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 106 removed outlier: 3.818A pdb=" N ASP m 105 " --> pdb=" O GLN m 102 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER m 106 " --> pdb=" O PRO m 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 102 through 106' Processing helix chain 'm' and resid 231 through 235 removed outlier: 3.573A pdb=" N LYS m 234 " --> pdb=" O LEU m 231 " (cutoff:3.500A) Processing helix chain 'm' and resid 240 through 272 removed outlier: 3.846A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 3.949A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 158 removed outlier: 3.755A 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 270 through 308 removed outlier: 4.452A pdb=" N LYS n 308 " --> pdb=" O MET n 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 54 removed outlier: 4.434A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS a 54 " --> pdb=" O PHE a 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 28 removed outlier: 5.977A 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: 6.851A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS d 73 " --> pdb=" O SER d 84 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN e 60 " --> pdb=" O VAL e 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 39 through 40 removed outlier: 3.551A pdb=" N LEU e 82 " --> pdb=" O LEU e 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 40 removed outlier: 3.513A pdb=" N VAL f 45 " --> pdb=" O LEU f 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 65 through 66 removed outlier: 3.514A pdb=" N ILE f 66 " --> pdb=" O TRP f 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 111 through 117 removed outlier: 6.875A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU g 97 " --> pdb=" O TYR g 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.641A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 60 through 65 removed outlier: 3.583A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE g 64 " --> pdb=" O ILE g 53 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE g 53 " --> pdb=" O PHE g 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.839A pdb=" N TYR m 109 " --> pdb=" O THR m 126 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET m 70 " --> pdb=" O TRP m 57 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG m 59 " --> pdb=" O LEU m 68 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU m 68 " --> pdb=" O ARG m 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.839A pdb=" N TYR m 109 " --> pdb=" O THR m 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 40 through 46 removed outlier: 3.626A pdb=" N ILE m 98 " --> pdb=" O VAL m 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU m 96 " --> pdb=" O LEU m 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR m 93 " --> pdb=" O ASP m 88 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN m 86 " --> pdb=" O SER m 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'm' and resid 141 through 143 removed outlier: 3.519A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 180 through 184 removed outlier: 3.549A pdb=" N THR m 180 " --> pdb=" O SER m 193 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU m 182 " --> pdb=" O SER m 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE m 189 " --> pdb=" O MET m 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 29 through 33 removed outlier: 3.588A pdb=" N THR n 131 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU n 32 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR n 133 " --> pdb=" O LEU n 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 38 through 40 removed outlier: 3.800A pdb=" N MET n 38 " --> pdb=" O LEU n 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 73 through 76 removed outlier: 7.348A pdb=" N ILE n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL n 69 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR n 67 " --> pdb=" O ASP n 75 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY n 61 " --> pdb=" O ASP n 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP n 57 " --> pdb=" O GLY n 61 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER n 52 " --> pdb=" O ALA n 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE n 109 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.583A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.583A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'n' and resid 183 through 184 removed outlier: 3.619A pdb=" N LYS n 183 " --> pdb=" O VAL n 180 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 972 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: 1.05 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2281 1.33 - 1.46: 2075 1.46 - 1.58: 4126 1.58 - 1.71: 3 1.71 - 1.83: 76 Bond restraints: 8561 Sorted by residual: bond pdb=" O3 C3S m1001 " pdb=" S1 C3S m1001 " ideal model delta sigma weight residual 1.467 1.644 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" O3 C3S n 401 " pdb=" S1 C3S n 401 " ideal model delta sigma weight residual 1.467 1.632 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" C SER f 103 " pdb=" N LYS f 104 " ideal model delta sigma weight residual 1.331 1.220 0.111 2.07e-02 2.33e+03 2.88e+01 bond pdb=" O6 C3S n 401 " pdb=" S1 C3S n 401 " ideal model delta sigma weight residual 1.637 1.536 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O6 C3S m1001 " pdb=" S1 C3S m1001 " ideal model delta sigma weight residual 1.637 1.545 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 8556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 11576 6.18 - 12.35: 38 12.35 - 18.53: 7 18.53 - 24.71: 1 24.71 - 30.88: 2 Bond angle restraints: 11624 Sorted by residual: angle pdb=" O2 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O4 C3S m1001 " ideal model delta sigma weight residual 114.52 83.64 30.88 3.00e+00 1.11e-01 1.06e+02 angle pdb=" O3 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O4 C3S m1001 " ideal model delta sigma weight residual 113.45 84.47 28.98 3.00e+00 1.11e-01 9.33e+01 angle pdb=" N ILE d 78 " pdb=" CA ILE d 78 " pdb=" C ILE d 78 " ideal model delta sigma weight residual 109.34 125.01 -15.67 2.08e+00 2.31e-01 5.67e+01 angle pdb=" O4 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O6 C3S m1001 " ideal model delta sigma weight residual 105.67 84.46 21.21 3.00e+00 1.11e-01 5.00e+01 angle pdb=" CG LYS b 30 " pdb=" CD LYS b 30 " pdb=" CE LYS b 30 " ideal model delta sigma weight residual 111.30 126.51 -15.21 2.30e+00 1.89e-01 4.37e+01 ... (remaining 11619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 4844 16.50 - 33.00: 278 33.00 - 49.50: 82 49.50 - 66.00: 21 66.00 - 82.50: 10 Dihedral angle restraints: 5235 sinusoidal: 2159 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 180.00 127.09 52.91 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ASP d 77 " pdb=" C ASP d 77 " pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta harmonic sigma weight residual -180.00 -133.97 -46.03 0 5.00e+00 4.00e-02 8.48e+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 -134.18 -45.82 0 5.00e+00 4.00e-02 8.40e+01 ... (remaining 5232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1100 0.094 - 0.189: 194 0.189 - 0.283: 11 0.283 - 0.377: 2 0.377 - 0.472: 1 Chirality restraints: 1308 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 0.47 2.00e-01 2.50e+01 5.56e+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 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU d 29 " pdb=" CB LEU d 29 " pdb=" CD1 LEU d 29 " pdb=" CD2 LEU d 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1305 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN n 222 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO n 223 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO n 223 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO n 223 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.026 2.00e-02 2.50e+03 2.13e-02 9.08e+00 pdb=" CG TYR d 90 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN m 102 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO m 103 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO m 103 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO m 103 " -0.040 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1730 2.78 - 3.31: 6761 3.31 - 3.84: 12261 3.84 - 4.37: 13401 4.37 - 4.90: 24676 Nonbonded interactions: 58829 Sorted by model distance: nonbonded pdb=" O VAL f 148 " pdb=" OG SER f 152 " model vdw 2.256 3.040 nonbonded pdb=" NH2 ARG m 253 " pdb=" OD1 ASP a 36 " model vdw 2.258 3.120 nonbonded pdb=" NE1 TRP m 271 " pdb=" O4 C3S m1001 " model vdw 2.289 3.120 nonbonded pdb=" OE1 GLN d 94 " pdb=" OG SER a 23 " model vdw 2.292 3.040 nonbonded pdb=" O TYR e 149 " pdb=" OG SER e 152 " model vdw 2.318 3.040 ... (remaining 58824 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' } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 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: 1.050 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.290 Find NCS groups from input model: 0.070 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 0.177 8574 Z= 0.473 Angle : 1.348 30.884 11650 Z= 0.704 Chirality : 0.070 0.472 1308 Planarity : 0.008 0.075 1468 Dihedral : 12.223 75.568 3222 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.94 % Favored : 90.77 % Rotamer: Outliers : 1.73 % Allowed : 5.29 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.70 % 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: -3.59 (0.21), residues: 1040 helix: -1.06 (0.29), residues: 229 sheet: -1.40 (0.30), residues: 277 loop : -3.68 (0.19), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG m 253 TYR 0.051 0.005 TYR d 90 PHE 0.040 0.004 PHE m 157 TRP 0.025 0.004 TRP n 179 HIS 0.017 0.004 HIS n 173 Details of bonding type rmsd covalent geometry : bond 0.01045 ( 8561) covalent geometry : angle 1.34460 (11624) SS BOND : bond 0.03071 ( 13) SS BOND : angle 2.31005 ( 26) hydrogen bonds : bond 0.24154 ( 325) hydrogen bonds : angle 8.04943 ( 972) *********************** 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 198 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.194 Fit side-chains REVERT: b 39 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7845 (mp) REVERT: b 54 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.5059 (tttm) REVERT: d 27 GLU cc_start: 0.7935 (pt0) cc_final: 0.7688 (pt0) REVERT: d 56 THR cc_start: 0.8023 (p) cc_final: 0.7797 (p) REVERT: e 74 ASN cc_start: 0.8041 (m-40) cc_final: 0.7729 (m-40) REVERT: e 85 LYS cc_start: 0.8654 (mttt) cc_final: 0.8441 (mmtt) REVERT: e 124 GLU cc_start: 0.7486 (tt0) cc_final: 0.6966 (tt0) REVERT: e 128 MET cc_start: 0.7294 (mmm) cc_final: 0.7081 (mmm) REVERT: f 51 GLN cc_start: 0.6480 (mt0) cc_final: 0.5824 (mp10) REVERT: f 83 SER cc_start: 0.8253 (m) cc_final: 0.7960 (p) REVERT: g 30 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7167 (pp) REVERT: m 104 SER cc_start: 0.7053 (m) cc_final: 0.6530 (p) REVERT: m 145 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7052 (ttm110) REVERT: m 184 MET cc_start: 0.8548 (ptm) cc_final: 0.8308 (ptm) REVERT: n 80 PRO cc_start: 0.7073 (Cg_endo) cc_final: 0.6721 (Cg_exo) REVERT: n 261 ARG cc_start: 0.7142 (ppt-90) cc_final: 0.6680 (ptt180) outliers start: 16 outliers final: 1 residues processed: 196 average time/residue: 0.1027 time to fit residues: 26.7402 Evaluate side-chains 121 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain g residue 30 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 ASN g 29 HIS m 102 GLN n 47 ASN n 272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.185877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153536 restraints weight = 9768.581| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.69 r_work: 0.3171 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8574 Z= 0.167 Angle : 0.699 9.830 11650 Z= 0.367 Chirality : 0.045 0.228 1308 Planarity : 0.005 0.047 1468 Dihedral : 6.986 56.104 1289 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 2.16 % Allowed : 8.74 % Favored : 89.10 % 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: -1.87 (0.25), residues: 1040 helix: 1.51 (0.33), residues: 245 sheet: -0.40 (0.32), residues: 289 loop : -3.35 (0.21), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG n 113 TYR 0.020 0.002 TYR n 50 PHE 0.022 0.002 PHE m 157 TRP 0.015 0.001 TRP d 43 HIS 0.004 0.001 HIS d 89 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8561) covalent geometry : angle 0.69800 (11624) SS BOND : bond 0.00444 ( 13) SS BOND : angle 1.18665 ( 26) hydrogen bonds : bond 0.07439 ( 325) hydrogen bonds : angle 5.04107 ( 972) *********************** 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 164 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.303 Fit side-chains REVERT: e 125 MET cc_start: 0.8387 (mmt) cc_final: 0.8002 (mmt) REVERT: e 128 MET cc_start: 0.7536 (mmm) cc_final: 0.7222 (mmt) REVERT: f 111 TYR cc_start: 0.8608 (m-10) cc_final: 0.8341 (m-80) REVERT: g 30 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7302 (pp) REVERT: g 77 ASN cc_start: 0.8470 (p0) cc_final: 0.8161 (p0) REVERT: m 56 MET cc_start: 0.8031 (mpp) cc_final: 0.7792 (mpp) REVERT: m 102 GLN cc_start: 0.7656 (mt0) cc_final: 0.7449 (mm-40) REVERT: m 104 SER cc_start: 0.7496 (m) cc_final: 0.6905 (p) REVERT: m 145 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7353 (ttm110) REVERT: m 185 ARG cc_start: 0.8480 (mtp-110) cc_final: 0.8019 (mtm-85) REVERT: n 80 PRO cc_start: 0.7108 (Cg_endo) cc_final: 0.6696 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7372 (mp0) cc_final: 0.6843 (mp0) REVERT: n 261 ARG cc_start: 0.8259 (ppt-90) cc_final: 0.7826 (ptt180) outliers start: 20 outliers final: 4 residues processed: 159 average time/residue: 0.1156 time to fit residues: 24.0085 Evaluate side-chains 125 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 25 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.177349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127660 restraints weight = 9499.516| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.49 r_work: 0.3096 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8574 Z= 0.169 Angle : 0.689 9.634 11650 Z= 0.359 Chirality : 0.045 0.232 1308 Planarity : 0.005 0.042 1468 Dihedral : 6.332 56.060 1281 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.92 % Favored : 92.98 % Rotamer: Outliers : 3.02 % Allowed : 10.25 % Favored : 86.73 % 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: -1.07 (0.26), residues: 1040 helix: 2.52 (0.33), residues: 243 sheet: 0.04 (0.34), residues: 274 loop : -2.92 (0.22), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 91 TYR 0.020 0.002 TYR g 34 PHE 0.017 0.002 PHE n 29 TRP 0.015 0.002 TRP n 259 HIS 0.006 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8561) covalent geometry : angle 0.68681 (11624) SS BOND : bond 0.01134 ( 13) SS BOND : angle 1.31955 ( 26) hydrogen bonds : bond 0.07239 ( 325) hydrogen bonds : angle 4.54643 ( 972) *********************** 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 163 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7304 (pp) REVERT: e 37 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8441 (mttp) REVERT: e 128 MET cc_start: 0.7722 (mmm) cc_final: 0.7521 (mmm) REVERT: g 30 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7904 (pp) REVERT: g 32 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8522 (mmtm) REVERT: m 145 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7513 (ttm110) REVERT: m 207 ASN cc_start: 0.7633 (m-40) cc_final: 0.7300 (p0) REVERT: m 229 VAL cc_start: 0.8261 (t) cc_final: 0.7969 (m) REVERT: n 80 PRO cc_start: 0.7292 (Cg_endo) cc_final: 0.6951 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7909 (mp0) cc_final: 0.7629 (mp0) REVERT: n 252 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: n 261 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8430 (ptt180) outliers start: 28 outliers final: 9 residues processed: 156 average time/residue: 0.1044 time to fit residues: 21.7250 Evaluate side-chains 132 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 105 GLN n 25 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 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 = 0.3855 r_free = 0.3855 target = 0.169053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118919 restraints weight = 9537.666| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.61 r_work: 0.2982 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8574 Z= 0.175 Angle : 0.694 10.100 11650 Z= 0.358 Chirality : 0.045 0.192 1308 Planarity : 0.005 0.036 1468 Dihedral : 6.338 56.016 1281 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 3.02 % Allowed : 11.33 % Favored : 85.65 % 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: -0.77 (0.26), residues: 1040 helix: 2.70 (0.32), residues: 243 sheet: 0.45 (0.33), residues: 275 loop : -2.85 (0.22), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG n 228 TYR 0.018 0.002 TYR e 52 PHE 0.015 0.002 PHE m 157 TRP 0.018 0.002 TRP n 259 HIS 0.005 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8561) covalent geometry : angle 0.69146 (11624) SS BOND : bond 0.00596 ( 13) SS BOND : angle 1.32653 ( 26) hydrogen bonds : bond 0.07330 ( 325) hydrogen bonds : angle 4.47008 ( 972) *********************** 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 159 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7184 (pp) REVERT: e 37 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8325 (mttp) REVERT: e 128 MET cc_start: 0.7546 (mmm) cc_final: 0.7316 (mmm) REVERT: f 101 ARG cc_start: 0.7426 (tpt-90) cc_final: 0.6910 (tpt170) REVERT: f 104 LYS cc_start: 0.8929 (tttt) cc_final: 0.8123 (mttt) REVERT: g 58 ASP cc_start: 0.8186 (m-30) cc_final: 0.7938 (m-30) REVERT: g 92 ASN cc_start: 0.6948 (m110) cc_final: 0.5791 (t0) REVERT: g 103 MET cc_start: 0.7596 (mtp) cc_final: 0.7214 (mmm) REVERT: m 145 ARG cc_start: 0.7919 (mtm180) cc_final: 0.7267 (ttm110) REVERT: m 207 ASN cc_start: 0.7875 (m-40) cc_final: 0.7427 (p0) REVERT: m 229 VAL cc_start: 0.8079 (t) cc_final: 0.7867 (m) REVERT: m 230 LYS cc_start: 0.8842 (mttt) cc_final: 0.8360 (mmtt) REVERT: n 28 LYS cc_start: 0.7814 (mtmt) cc_final: 0.7399 (mtmm) REVERT: n 32 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7558 (pp) REVERT: n 50 TYR cc_start: 0.5390 (OUTLIER) cc_final: 0.4665 (p90) REVERT: n 80 PRO cc_start: 0.7395 (Cg_endo) cc_final: 0.7076 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8346 (tt) REVERT: n 252 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: n 261 ARG cc_start: 0.8710 (ppt-90) cc_final: 0.8429 (ptt180) outliers start: 28 outliers final: 14 residues processed: 154 average time/residue: 0.0931 time to fit residues: 19.7774 Evaluate side-chains 142 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 52 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.171141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122303 restraints weight = 9409.095| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.52 r_work: 0.2998 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8574 Z= 0.148 Angle : 0.652 9.834 11650 Z= 0.335 Chirality : 0.044 0.213 1308 Planarity : 0.004 0.032 1468 Dihedral : 5.994 56.037 1279 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.35 % Favored : 93.46 % Rotamer: Outliers : 2.91 % Allowed : 12.19 % Favored : 84.90 % 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: -0.50 (0.26), residues: 1040 helix: 3.24 (0.32), residues: 238 sheet: 0.39 (0.33), residues: 282 loop : -2.69 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG m 63 TYR 0.015 0.002 TYR e 52 PHE 0.013 0.001 PHE f 87 TRP 0.018 0.002 TRP n 259 HIS 0.003 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8561) covalent geometry : angle 0.65077 (11624) SS BOND : bond 0.00438 ( 13) SS BOND : angle 1.01469 ( 26) hydrogen bonds : bond 0.06540 ( 325) hydrogen bonds : angle 4.27450 ( 972) *********************** 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 147 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7301 (pp) REVERT: e 37 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8380 (mttp) REVERT: e 128 MET cc_start: 0.7618 (mmm) cc_final: 0.7413 (mmm) REVERT: f 101 ARG cc_start: 0.7558 (tpt-90) cc_final: 0.6892 (tpt170) REVERT: g 92 ASN cc_start: 0.7244 (m110) cc_final: 0.5857 (t0) REVERT: m 145 ARG cc_start: 0.8095 (mtm180) cc_final: 0.7374 (ttm110) REVERT: m 207 ASN cc_start: 0.7920 (m-40) cc_final: 0.7461 (p0) REVERT: m 229 VAL cc_start: 0.8131 (t) cc_final: 0.7838 (m) REVERT: m 230 LYS cc_start: 0.8881 (mttt) cc_final: 0.8380 (mmtt) REVERT: n 28 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7651 (mtmm) REVERT: n 50 TYR cc_start: 0.5444 (OUTLIER) cc_final: 0.4658 (p90) REVERT: n 80 PRO cc_start: 0.7489 (Cg_endo) cc_final: 0.7150 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: n 261 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8644 (ptt180) REVERT: a 26 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8722 (mt) outliers start: 27 outliers final: 16 residues processed: 141 average time/residue: 0.0884 time to fit residues: 16.9791 Evaluate side-chains 137 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain a residue 26 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 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 = 0.3872 r_free = 0.3872 target = 0.170339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117948 restraints weight = 9325.342| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.55 r_work: 0.3031 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8574 Z= 0.124 Angle : 0.607 9.505 11650 Z= 0.312 Chirality : 0.042 0.199 1308 Planarity : 0.004 0.030 1468 Dihedral : 5.748 55.904 1279 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 2.80 % Allowed : 12.51 % Favored : 84.68 % 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: -0.18 (0.27), residues: 1040 helix: 3.67 (0.31), residues: 236 sheet: 0.53 (0.33), residues: 283 loop : -2.52 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 91 TYR 0.013 0.001 TYR e 52 PHE 0.011 0.001 PHE m 157 TRP 0.016 0.001 TRP n 259 HIS 0.003 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8561) covalent geometry : angle 0.60579 (11624) SS BOND : bond 0.00399 ( 13) SS BOND : angle 0.90287 ( 26) hydrogen bonds : bond 0.05632 ( 325) hydrogen bonds : angle 4.02649 ( 972) *********************** 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 155 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8470 (pt0) cc_final: 0.8220 (tt0) REVERT: d 99 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7310 (pp) REVERT: e 37 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8324 (mttp) REVERT: e 128 MET cc_start: 0.7446 (mmm) cc_final: 0.7213 (mmm) REVERT: f 101 ARG cc_start: 0.7568 (tpt-90) cc_final: 0.6884 (tpt170) REVERT: g 92 ASN cc_start: 0.7260 (m110) cc_final: 0.5833 (t0) REVERT: g 103 MET cc_start: 0.7540 (mtp) cc_final: 0.7182 (mmm) REVERT: m 145 ARG cc_start: 0.8065 (mtm180) cc_final: 0.7511 (mtt90) REVERT: m 207 ASN cc_start: 0.7760 (m-40) cc_final: 0.7330 (p0) REVERT: m 229 VAL cc_start: 0.7999 (t) cc_final: 0.7678 (m) REVERT: m 230 LYS cc_start: 0.8853 (mttt) cc_final: 0.8335 (mmtt) REVERT: n 28 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7683 (mtmm) REVERT: n 32 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8327 (pp) REVERT: n 50 TYR cc_start: 0.5281 (OUTLIER) cc_final: 0.4554 (p90) REVERT: n 80 PRO cc_start: 0.7485 (Cg_endo) cc_final: 0.7147 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8342 (tt) REVERT: n 252 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: n 261 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8551 (ptt180) outliers start: 26 outliers final: 19 residues processed: 149 average time/residue: 0.0943 time to fit residues: 19.3728 Evaluate side-chains 150 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 190 SER Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 52 ASN ** n 48 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 = 0.3908 r_free = 0.3908 target = 0.172968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122380 restraints weight = 9404.371| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.48 r_work: 0.3067 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 8574 Z= 0.114 Angle : 0.582 9.528 11650 Z= 0.300 Chirality : 0.042 0.198 1308 Planarity : 0.004 0.031 1468 Dihedral : 5.558 55.801 1279 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 2.70 % Allowed : 13.59 % Favored : 83.71 % 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: 0.04 (0.27), residues: 1040 helix: 3.91 (0.31), residues: 236 sheet: 0.60 (0.33), residues: 287 loop : -2.38 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG m 269 TYR 0.012 0.001 TYR e 52 PHE 0.010 0.001 PHE n 29 TRP 0.016 0.001 TRP n 259 HIS 0.003 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8561) covalent geometry : angle 0.58178 (11624) SS BOND : bond 0.00349 ( 13) SS BOND : angle 0.77925 ( 26) hydrogen bonds : bond 0.05125 ( 325) hydrogen bonds : angle 3.87876 ( 972) *********************** 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 150 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.355 Fit side-chains REVERT: d 27 GLU cc_start: 0.8367 (pt0) cc_final: 0.8150 (tt0) REVERT: d 99 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7408 (pp) REVERT: e 37 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8364 (mttp) REVERT: e 128 MET cc_start: 0.7420 (mmm) cc_final: 0.7133 (mmm) REVERT: f 101 ARG cc_start: 0.7600 (tpt-90) cc_final: 0.6806 (tpt170) REVERT: g 51 LYS cc_start: 0.6700 (pttp) cc_final: 0.6450 (mttp) REVERT: g 92 ASN cc_start: 0.7366 (m110) cc_final: 0.5812 (t0) REVERT: m 121 THR cc_start: 0.6981 (m) cc_final: 0.6528 (p) REVERT: m 145 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7540 (mtt90) REVERT: m 161 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.6445 (p0) REVERT: m 207 ASN cc_start: 0.7620 (m-40) cc_final: 0.7274 (p0) REVERT: m 229 VAL cc_start: 0.8044 (t) cc_final: 0.7716 (m) REVERT: n 28 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7756 (mtmm) REVERT: n 32 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8365 (pp) REVERT: n 50 TYR cc_start: 0.5226 (OUTLIER) cc_final: 0.4549 (p90) REVERT: n 80 PRO cc_start: 0.7562 (Cg_endo) cc_final: 0.7249 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: n 261 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8531 (ptt180) REVERT: n 263 ASP cc_start: 0.7771 (m-30) cc_final: 0.7520 (m-30) outliers start: 25 outliers final: 16 residues processed: 144 average time/residue: 0.0930 time to fit residues: 18.4009 Evaluate side-chains 146 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.0050 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 52 ASN ** n 48 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 = 0.3901 r_free = 0.3901 target = 0.172414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122462 restraints weight = 9325.558| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.50 r_work: 0.3121 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 8574 Z= 0.113 Angle : 0.582 9.546 11650 Z= 0.300 Chirality : 0.042 0.204 1308 Planarity : 0.004 0.030 1468 Dihedral : 5.497 56.778 1279 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 3.13 % Allowed : 13.59 % Favored : 83.28 % 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: 0.16 (0.27), residues: 1040 helix: 4.00 (0.30), residues: 236 sheet: 0.67 (0.33), residues: 286 loop : -2.30 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG n 96 TYR 0.013 0.001 TYR e 52 PHE 0.009 0.001 PHE f 87 TRP 0.016 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8561) covalent geometry : angle 0.58199 (11624) SS BOND : bond 0.00319 ( 13) SS BOND : angle 0.76216 ( 26) hydrogen bonds : bond 0.04980 ( 325) hydrogen bonds : angle 3.83359 ( 972) *********************** 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 154 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8123 (pt0) cc_final: 0.7915 (tt0) REVERT: d 82 LYS cc_start: 0.7842 (mttt) cc_final: 0.7545 (mttt) REVERT: d 99 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7432 (pp) REVERT: e 37 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8298 (mttp) REVERT: e 128 MET cc_start: 0.7251 (mmm) cc_final: 0.6998 (mmm) REVERT: f 101 ARG cc_start: 0.7496 (tpt-90) cc_final: 0.6762 (tpt170) REVERT: f 125 MET cc_start: 0.7941 (mmm) cc_final: 0.7694 (mmt) REVERT: g 92 ASN cc_start: 0.7261 (m110) cc_final: 0.6823 (m-40) REVERT: m 121 THR cc_start: 0.7094 (m) cc_final: 0.6640 (p) REVERT: m 145 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7312 (mtt90) REVERT: m 161 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6345 (p0) REVERT: m 229 VAL cc_start: 0.8062 (t) cc_final: 0.7771 (m) REVERT: n 28 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7650 (mtmm) REVERT: n 32 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8303 (pp) REVERT: n 50 TYR cc_start: 0.5220 (OUTLIER) cc_final: 0.4599 (p90) REVERT: n 80 PRO cc_start: 0.7571 (Cg_endo) cc_final: 0.7280 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8242 (tt) REVERT: n 252 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: n 261 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8281 (ptt180) REVERT: n 263 ASP cc_start: 0.7671 (m-30) cc_final: 0.7433 (m-30) outliers start: 29 outliers final: 20 residues processed: 148 average time/residue: 0.0960 time to fit residues: 19.6464 Evaluate side-chains 150 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 52 ASN ** n 48 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 = 0.3892 r_free = 0.3892 target = 0.171560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120749 restraints weight = 9324.699| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.50 r_work: 0.3092 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8574 Z= 0.130 Angle : 0.606 9.560 11650 Z= 0.310 Chirality : 0.042 0.224 1308 Planarity : 0.004 0.032 1468 Dihedral : 5.555 56.846 1279 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.75 % Rotamer: Outliers : 3.24 % Allowed : 13.38 % Favored : 83.39 % 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: 0.14 (0.27), residues: 1040 helix: 3.94 (0.31), residues: 236 sheet: 0.69 (0.33), residues: 282 loop : -2.28 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG n 96 TYR 0.013 0.001 TYR e 52 PHE 0.011 0.001 PHE m 189 TRP 0.015 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8561) covalent geometry : angle 0.60557 (11624) SS BOND : bond 0.00381 ( 13) SS BOND : angle 0.87634 ( 26) hydrogen bonds : bond 0.05494 ( 325) hydrogen bonds : angle 3.89849 ( 972) *********************** 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 149 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8197 (pt0) cc_final: 0.7977 (tt0) REVERT: d 82 LYS cc_start: 0.7832 (mttt) cc_final: 0.7537 (mttt) REVERT: d 99 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7495 (pp) REVERT: e 37 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8325 (mttp) REVERT: e 128 MET cc_start: 0.7362 (mmm) cc_final: 0.7085 (mmm) REVERT: f 125 MET cc_start: 0.7798 (mmm) cc_final: 0.7586 (mmt) REVERT: g 92 ASN cc_start: 0.7235 (m110) cc_final: 0.6830 (m-40) REVERT: m 145 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7318 (mtt90) REVERT: m 161 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.6428 (p0) REVERT: m 229 VAL cc_start: 0.8103 (t) cc_final: 0.7808 (m) REVERT: n 28 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7636 (mtmm) REVERT: n 32 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8318 (pp) REVERT: n 50 TYR cc_start: 0.5334 (OUTLIER) cc_final: 0.4631 (p90) REVERT: n 80 PRO cc_start: 0.7663 (Cg_endo) cc_final: 0.7360 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8269 (tt) REVERT: n 252 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8144 (pt0) REVERT: n 261 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8352 (ptt180) REVERT: n 263 ASP cc_start: 0.7754 (m-30) cc_final: 0.7499 (m-30) outliers start: 30 outliers final: 20 residues processed: 142 average time/residue: 0.0931 time to fit residues: 18.3779 Evaluate side-chains 145 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 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 = 0.3897 r_free = 0.3897 target = 0.172152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.120540 restraints weight = 9367.537| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.61 r_work: 0.3009 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8574 Z= 0.129 Angle : 0.611 9.527 11650 Z= 0.313 Chirality : 0.042 0.238 1308 Planarity : 0.004 0.032 1468 Dihedral : 5.585 58.616 1279 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 3.02 % Allowed : 13.70 % Favored : 83.28 % 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: 0.20 (0.27), residues: 1040 helix: 3.91 (0.31), residues: 237 sheet: 0.81 (0.33), residues: 283 loop : -2.27 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 101 TYR 0.014 0.001 TYR e 52 PHE 0.011 0.001 PHE m 189 TRP 0.016 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8561) covalent geometry : angle 0.60986 (11624) SS BOND : bond 0.00371 ( 13) SS BOND : angle 0.89444 ( 26) hydrogen bonds : bond 0.05664 ( 325) hydrogen bonds : angle 3.92157 ( 972) ********************** 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 150 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: d 82 LYS cc_start: 0.7733 (mttt) cc_final: 0.7437 (mttt) REVERT: d 99 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7513 (pp) REVERT: e 37 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8285 (mttp) REVERT: e 128 MET cc_start: 0.7367 (mmm) cc_final: 0.7128 (mmm) REVERT: f 101 ARG cc_start: 0.7449 (ttt-90) cc_final: 0.6586 (tpt170) REVERT: f 125 MET cc_start: 0.7718 (mmm) cc_final: 0.7491 (mmt) REVERT: g 92 ASN cc_start: 0.7236 (m110) cc_final: 0.6838 (m-40) REVERT: m 82 ARG cc_start: 0.5481 (mtm180) cc_final: 0.5194 (mtm-85) REVERT: m 145 ARG cc_start: 0.7869 (mtm180) cc_final: 0.7329 (mtt90) REVERT: m 161 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6428 (p0) REVERT: m 229 VAL cc_start: 0.8117 (t) cc_final: 0.7808 (m) REVERT: n 28 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7673 (mtmm) REVERT: n 32 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8283 (pp) REVERT: n 50 TYR cc_start: 0.5202 (OUTLIER) cc_final: 0.4539 (p90) REVERT: n 80 PRO cc_start: 0.7680 (Cg_endo) cc_final: 0.7321 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8324 (tt) REVERT: n 252 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: n 261 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8390 (ptt180) outliers start: 28 outliers final: 21 residues processed: 143 average time/residue: 0.0968 time to fit residues: 19.1364 Evaluate side-chains 152 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.0000 chunk 41 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 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 = 0.3917 r_free = 0.3917 target = 0.174178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122462 restraints weight = 9347.439| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.57 r_work: 0.3068 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 8574 Z= 0.104 Angle : 0.569 9.553 11650 Z= 0.290 Chirality : 0.041 0.191 1308 Planarity : 0.003 0.028 1468 Dihedral : 5.331 59.196 1279 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 2.70 % Allowed : 14.13 % Favored : 83.17 % 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: 0.35 (0.27), residues: 1040 helix: 4.17 (0.30), residues: 236 sheet: 0.75 (0.33), residues: 286 loop : -2.15 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 101 TYR 0.013 0.001 TYR e 52 PHE 0.009 0.001 PHE m 157 TRP 0.017 0.001 TRP n 259 HIS 0.007 0.001 HIS n 66 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8561) covalent geometry : angle 0.56853 (11624) SS BOND : bond 0.00262 ( 13) SS BOND : angle 0.66283 ( 26) hydrogen bonds : bond 0.04584 ( 325) hydrogen bonds : angle 3.73498 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.20 seconds wall clock time: 43 minutes 14.97 seconds (2594.97 seconds total)