Starting phenix.real_space_refine on Thu Jul 2 11:18:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fjf_31620/07_2026/7fjf_31620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjf_31620/07_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_31620/07_2026/7fjf_31620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjf_31620/07_2026/7fjf_31620.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fjf_31620/07_2026/7fjf_31620.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fjf_31620/07_2026/7fjf_31620.cif" model { file = "/net/cci-nas-00/data/ceres_data/7fjf_31620/07_2026/7fjf_31620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjf_31620/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 1.58, per 1000 atoms: 0.19 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: 0.61 Conformation dependent library (CDL) restraints added in 499.2 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: 0.15 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: 1.08 Time building geometry restraints manager: 0.85 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: 4748 16.50 - 33.00: 264 33.00 - 49.50: 78 49.50 - 66.00: 19 66.00 - 82.50: 10 Dihedral angle restraints: 5119 sinusoidal: 2043 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 5116 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 12.136 75.568 3106 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/Z covalent geometry : bond 0.01045 / 0.47 ( 8561) covalent geometry : angle 1.34460 / 0.70 (11624) SS BOND : bond 0.03071 / 1.63 ( 13) SS BOND : angle 2.31005 / 1.19 ( 26) hydrogen bonds : bond 0.24154 / 15.48 ( 325) hydrogen bonds : angle 8.04943 / 5.36 ( 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 : 0.202 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: 0.0936 time to fit residues: 24.6130 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 : 0.362 ------------------------------------------------------------------------------- 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... d 36 ASN f 60 GLN f 65 ASN g 29 HIS m 102 GLN n 25 GLN n 47 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 272 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.184693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.151057 restraints weight = 9759.841| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.83 r_work: 0.3260 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3129 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= 0.173 Angle : 0.698 9.810 11650 Z= 0.365 Chirality : 0.045 0.218 1308 Planarity : 0.005 0.047 1468 Dihedral : 6.512 56.629 1173 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 2.27 % Allowed : 9.06 % Favored : 88.67 % 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: -1.82 (0.25), residues: 1040 helix: 1.59 (0.33), residues: 245 sheet: -0.41 (0.32), residues: 289 loop : -3.32 (0.21), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 91 TYR 0.020 0.002 TYR n 50 PHE 0.024 0.002 PHE m 157 TRP 0.016 0.001 TRP d 43 HIS 0.004 0.001 HIS d 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 8561) covalent geometry : angle 0.69699 / 0.36 (11624) SS BOND : bond 0.00389 / 0.24 ( 13) SS BOND : angle 1.04022 / 0.57 ( 26) hydrogen bonds : bond 0.07043 / 4.29 ( 325) hydrogen bonds : angle 4.90364 / 3.27 ( 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 167 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.375 Fit side-chains REVERT: e 125 MET cc_start: 0.8475 (mmt) cc_final: 0.8118 (mmt) REVERT: e 128 MET cc_start: 0.7560 (mmm) cc_final: 0.7297 (mmt) REVERT: f 111 TYR cc_start: 0.8621 (m-10) cc_final: 0.8367 (m-80) REVERT: g 30 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7515 (pp) REVERT: g 77 ASN cc_start: 0.8539 (p0) cc_final: 0.8260 (p0) REVERT: m 145 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7403 (ttm110) REVERT: m 148 LYS cc_start: 0.7790 (ptmm) cc_final: 0.7505 (ptpt) REVERT: m 185 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8046 (mtm-85) REVERT: n 80 PRO cc_start: 0.7166 (Cg_endo) cc_final: 0.6781 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7541 (mp0) cc_final: 0.7075 (mp0) REVERT: n 252 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: n 261 ARG cc_start: 0.8300 (ppt-90) cc_final: 0.7877 (ptt180) outliers start: 21 outliers final: 4 residues processed: 162 average time/residue: 0.0896 time to fit residues: 19.3228 Evaluate side-chains 125 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 m residue 126 THR Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.0040 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.0070 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN ** 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 = 0.4051 r_free = 0.4051 target = 0.185573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.149597 restraints weight = 9644.669| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.00 r_work: 0.3256 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8574 Z= 0.114 Angle : 0.578 9.590 11650 Z= 0.303 Chirality : 0.041 0.205 1308 Planarity : 0.004 0.044 1468 Dihedral : 5.432 56.420 1165 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 2.05 % Allowed : 10.90 % Favored : 87.06 % 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: -0.82 (0.26), residues: 1040 helix: 2.93 (0.33), residues: 238 sheet: 0.30 (0.34), residues: 268 loop : -2.85 (0.22), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 91 TYR 0.015 0.001 TYR n 50 PHE 0.021 0.001 PHE n 29 TRP 0.011 0.001 TRP m 197 HIS 0.006 0.001 HIS n 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8561) covalent geometry : angle 0.57647 / 0.30 (11624) SS BOND : bond 0.00563 / 0.32 ( 13) SS BOND : angle 1.07250 / 0.51 ( 26) hydrogen bonds : bond 0.05049 / 3.09 ( 325) hydrogen bonds : angle 4.29220 / 2.87 ( 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 154 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.230 Fit side-chains REVERT: e 128 MET cc_start: 0.7314 (mmm) cc_final: 0.7003 (mmt) REVERT: g 30 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7687 (pp) REVERT: g 77 ASN cc_start: 0.8536 (p0) cc_final: 0.8186 (p0) REVERT: g 79 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7642 (mttm) REVERT: m 145 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7319 (ttm110) REVERT: m 185 ARG cc_start: 0.8468 (mtp-110) cc_final: 0.7937 (mtm-85) REVERT: m 207 ASN cc_start: 0.7608 (m-40) cc_final: 0.7146 (p0) REVERT: n 80 PRO cc_start: 0.7111 (Cg_endo) cc_final: 0.6782 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7547 (mp0) cc_final: 0.7229 (mp0) REVERT: n 252 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: n 261 ARG cc_start: 0.8246 (ppt-90) cc_final: 0.7794 (ptt180) REVERT: n 263 ASP cc_start: 0.6907 (m-30) cc_final: 0.6687 (m-30) outliers start: 19 outliers final: 7 residues processed: 148 average time/residue: 0.0894 time to fit residues: 17.7689 Evaluate side-chains 131 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 41 ILE 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 n residue 252 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... f 60 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.177368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138627 restraints weight = 9562.167| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.28 r_work: 0.3059 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8574 Z= 0.140 Angle : 0.637 10.998 11650 Z= 0.330 Chirality : 0.043 0.185 1308 Planarity : 0.004 0.033 1468 Dihedral : 5.490 56.901 1165 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 2.91 % Allowed : 11.33 % Favored : 85.76 % 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: 3.11 (0.33), residues: 242 sheet: 0.45 (0.33), residues: 289 loop : -2.74 (0.22), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG n 228 TYR 0.017 0.002 TYR g 34 PHE 0.012 0.002 PHE f 87 TRP 0.015 0.002 TRP d 43 HIS 0.004 0.001 HIS n 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8561) covalent geometry : angle 0.63580 / 0.33 (11624) SS BOND : bond 0.00517 / 0.34 ( 13) SS BOND : angle 1.16231 / 0.64 ( 26) hydrogen bonds : bond 0.06213 / 3.79 ( 325) hydrogen bonds : angle 4.25019 / 2.85 ( 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: 27 poor density : 132 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7261 (pp) REVERT: e 37 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8434 (mttp) REVERT: e 128 MET cc_start: 0.7528 (mmm) cc_final: 0.7170 (mmt) REVERT: f 101 ARG cc_start: 0.7103 (tpt-90) cc_final: 0.6631 (tpt170) REVERT: f 125 MET cc_start: 0.8368 (mmm) cc_final: 0.7306 (mmt) REVERT: g 30 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7757 (pp) REVERT: m 145 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7406 (ttm110) REVERT: m 173 ASP cc_start: 0.8274 (m-30) cc_final: 0.8002 (m-30) REVERT: m 207 ASN cc_start: 0.7998 (m-40) cc_final: 0.7339 (p0) REVERT: m 229 VAL cc_start: 0.8077 (t) cc_final: 0.7756 (m) REVERT: n 50 TYR cc_start: 0.5213 (OUTLIER) cc_final: 0.4839 (p90) REVERT: n 80 PRO cc_start: 0.7182 (Cg_endo) cc_final: 0.6854 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: n 261 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8390 (ptt180) outliers start: 27 outliers final: 13 residues processed: 152 average time/residue: 0.0829 time to fit residues: 17.2712 Evaluate side-chains 131 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 LEU 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 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 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 208 CYS 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 n residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN g 105 GLN m 199 ASN n 25 GLN n 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.176420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129781 restraints weight = 9360.330| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.39 r_work: 0.3149 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8574 Z= 0.119 Angle : 0.591 9.361 11650 Z= 0.308 Chirality : 0.042 0.193 1308 Planarity : 0.004 0.032 1468 Dihedral : 5.198 55.746 1165 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 1.94 % Allowed : 13.05 % Favored : 85.01 % 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: 3.60 (0.32), residues: 236 sheet: 0.51 (0.32), residues: 291 loop : -2.54 (0.23), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 91 TYR 0.014 0.001 TYR n 50 PHE 0.011 0.001 PHE n 29 TRP 0.014 0.001 TRP n 259 HIS 0.002 0.001 HIS n 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 8561) covalent geometry : angle 0.59102 / 0.31 (11624) SS BOND : bond 0.00420 / 0.29 ( 13) SS BOND : angle 0.74641 / 0.44 ( 26) hydrogen bonds : bond 0.05339 / 3.24 ( 325) hydrogen bonds : angle 4.05458 / 2.71 ( 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 139 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7158 (pp) REVERT: e 37 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8263 (mttp) REVERT: f 101 ARG cc_start: 0.7183 (tpt-90) cc_final: 0.6734 (tpt170) REVERT: f 104 LYS cc_start: 0.8677 (tttt) cc_final: 0.7891 (mttt) REVERT: g 79 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7621 (mttm) REVERT: g 92 ASN cc_start: 0.7001 (m110) cc_final: 0.5850 (t0) REVERT: m 145 ARG cc_start: 0.7704 (mtm180) cc_final: 0.7173 (ttm110) REVERT: m 207 ASN cc_start: 0.7887 (m-40) cc_final: 0.7321 (p0) REVERT: m 229 VAL cc_start: 0.8048 (t) cc_final: 0.7790 (m) REVERT: m 230 LYS cc_start: 0.8742 (mttt) cc_final: 0.8330 (mmtt) REVERT: n 50 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.4861 (p90) REVERT: n 80 PRO cc_start: 0.7348 (Cg_endo) cc_final: 0.7047 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8126 (pt0) REVERT: n 261 ARG cc_start: 0.8517 (ppt-90) cc_final: 0.8144 (ptt180) outliers start: 18 outliers final: 12 residues processed: 135 average time/residue: 0.0952 time to fit residues: 17.3908 Evaluate side-chains 133 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 LEU 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 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 182 LEU 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 252 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 76 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN g 105 GLN ** n 48 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 = 0.3895 r_free = 0.3895 target = 0.172581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121362 restraints weight = 9374.382| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.49 r_work: 0.3030 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5626 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= 0.136 Angle : 0.614 10.532 11650 Z= 0.317 Chirality : 0.042 0.182 1308 Planarity : 0.004 0.030 1468 Dihedral : 5.178 55.721 1163 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 3.02 % Allowed : 12.41 % Favored : 84.57 % 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: -0.11 (0.26), residues: 1040 helix: 3.70 (0.31), residues: 236 sheet: 0.60 (0.33), residues: 287 loop : -2.50 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG n 228 TYR 0.014 0.001 TYR n 50 PHE 0.011 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/Z covalent geometry : bond 0.00303 / 0.14 ( 8561) covalent geometry : angle 0.61277 / 0.32 (11624) SS BOND : bond 0.00450 / 0.30 ( 13) SS BOND : angle 1.03506 / 0.61 ( 26) hydrogen bonds : bond 0.05839 / 3.55 ( 325) hydrogen bonds : angle 4.06838 / 2.70 ( 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 151 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7191 (pp) REVERT: e 37 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8263 (mttp) REVERT: f 101 ARG cc_start: 0.7335 (tpt-90) cc_final: 0.6749 (tpt170) REVERT: f 104 LYS cc_start: 0.8860 (tttt) cc_final: 0.8083 (mttt) REVERT: g 79 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7495 (mttm) REVERT: g 92 ASN cc_start: 0.7082 (m110) cc_final: 0.5915 (t0) REVERT: m 145 ARG cc_start: 0.7851 (mtm180) cc_final: 0.7222 (ttm110) REVERT: m 207 ASN cc_start: 0.7755 (m-40) cc_final: 0.7337 (p0) REVERT: m 229 VAL cc_start: 0.8077 (t) cc_final: 0.7858 (m) REVERT: m 230 LYS cc_start: 0.8767 (mttt) cc_final: 0.8301 (mmtt) REVERT: n 28 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7427 (mtmm) REVERT: n 50 TYR cc_start: 0.5342 (OUTLIER) cc_final: 0.4708 (p90) REVERT: n 67 TYR cc_start: 0.7162 (p90) cc_final: 0.6860 (p90) REVERT: n 80 PRO cc_start: 0.7347 (Cg_endo) cc_final: 0.7033 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8244 (tt) REVERT: n 252 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: n 261 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (ptt180) outliers start: 28 outliers final: 17 residues processed: 145 average time/residue: 0.0849 time to fit residues: 17.2754 Evaluate side-chains 140 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 LEU 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 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 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 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 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 296 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN g 105 GLN m 211 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.173206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124372 restraints weight = 9548.594| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.61 r_work: 0.3035 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8574 Z= 0.119 Angle : 0.587 9.537 11650 Z= 0.303 Chirality : 0.042 0.191 1308 Planarity : 0.004 0.029 1468 Dihedral : 5.029 55.722 1163 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 2.91 % Allowed : 13.38 % 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: 0.08 (0.27), residues: 1040 helix: 3.90 (0.30), residues: 236 sheet: 0.67 (0.32), residues: 297 loop : -2.42 (0.23), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG m 63 TYR 0.013 0.001 TYR n 50 PHE 0.010 0.001 PHE f 87 TRP 0.015 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8561) covalent geometry : angle 0.58618 / 0.30 (11624) SS BOND : bond 0.00420 / 0.28 ( 13) SS BOND : angle 0.85028 / 0.52 ( 26) hydrogen bonds : bond 0.05347 / 3.23 ( 325) hydrogen bonds : angle 3.95646 / 2.62 ( 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 145 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7184 (pp) REVERT: e 37 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8271 (mttp) REVERT: f 101 ARG cc_start: 0.7482 (tpt-90) cc_final: 0.6871 (tpt170) REVERT: f 104 LYS cc_start: 0.8906 (tttt) cc_final: 0.8114 (mttt) REVERT: g 79 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7525 (mttm) REVERT: g 92 ASN cc_start: 0.7008 (m110) cc_final: 0.5846 (t0) REVERT: m 145 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7398 (mtt90) REVERT: m 148 LYS cc_start: 0.7889 (ptmm) cc_final: 0.7466 (mttt) REVERT: m 207 ASN cc_start: 0.7653 (m-40) cc_final: 0.7293 (p0) REVERT: m 229 VAL cc_start: 0.8259 (t) cc_final: 0.8005 (m) REVERT: n 28 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7474 (mtmm) REVERT: n 50 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.4762 (p90) REVERT: n 80 PRO cc_start: 0.7399 (Cg_endo) cc_final: 0.7110 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8265 (tt) REVERT: n 252 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: n 261 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8323 (ptt180) outliers start: 27 outliers final: 21 residues processed: 137 average time/residue: 0.0810 time to fit residues: 15.3851 Evaluate side-chains 145 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain m residue 211 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 211 ASN ** 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 = 0.172122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121802 restraints weight = 9341.311| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.58 r_work: 0.3076 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8574 Z= 0.132 Angle : 0.607 10.205 11650 Z= 0.313 Chirality : 0.042 0.179 1308 Planarity : 0.004 0.030 1468 Dihedral : 5.072 55.543 1163 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 2.70 % Allowed : 13.92 % 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: 0.09 (0.27), residues: 1040 helix: 3.90 (0.30), residues: 236 sheet: 0.74 (0.33), residues: 286 loop : -2.39 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG n 228 TYR 0.014 0.001 TYR n 50 PHE 0.011 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/Z covalent geometry : bond 0.00297 / 0.13 ( 8561) covalent geometry : angle 0.60635 / 0.31 (11624) SS BOND : bond 0.00399 / 0.27 ( 13) SS BOND : angle 0.94532 / 0.58 ( 26) hydrogen bonds : bond 0.05638 / 3.41 ( 325) hydrogen bonds : angle 3.97138 / 2.63 ( 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 147 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.282 Fit side-chains REVERT: d 99 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7256 (pp) REVERT: e 37 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8383 (mttp) REVERT: f 101 ARG cc_start: 0.7568 (tpt-90) cc_final: 0.6886 (tpt170) REVERT: g 79 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7658 (mttm) REVERT: g 92 ASN cc_start: 0.7231 (m110) cc_final: 0.5782 (t0) REVERT: m 145 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7536 (mtt90) REVERT: m 148 LYS cc_start: 0.7960 (ptmm) cc_final: 0.7485 (mttt) REVERT: m 207 ASN cc_start: 0.7700 (m-40) cc_final: 0.7326 (p0) REVERT: m 229 VAL cc_start: 0.8198 (t) cc_final: 0.7940 (m) REVERT: n 28 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7657 (mtmm) REVERT: n 50 TYR cc_start: 0.5419 (OUTLIER) cc_final: 0.4805 (p90) REVERT: n 67 TYR cc_start: 0.7400 (p90) cc_final: 0.7089 (p90) REVERT: n 80 PRO cc_start: 0.7495 (Cg_endo) cc_final: 0.7188 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8286 (tt) REVERT: n 252 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: n 261 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8556 (ptt180) outliers start: 25 outliers final: 18 residues processed: 141 average time/residue: 0.0763 time to fit residues: 14.8818 Evaluate side-chains 142 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 0.0570 chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN m 211 ASN ** n 48 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 = 0.3905 r_free = 0.3905 target = 0.172905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120947 restraints weight = 9376.876| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.48 r_work: 0.3062 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8574 Z= 0.115 Angle : 0.578 9.380 11650 Z= 0.299 Chirality : 0.041 0.190 1308 Planarity : 0.004 0.028 1468 Dihedral : 4.911 55.507 1163 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 2.80 % Allowed : 13.81 % 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: 0.20 (0.27), residues: 1040 helix: 3.83 (0.31), residues: 242 sheet: 0.84 (0.32), residues: 296 loop : -2.39 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG n 228 TYR 0.013 0.001 TYR n 50 PHE 0.010 0.001 PHE f 87 TRP 0.017 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8561) covalent geometry : angle 0.57779 / 0.30 (11624) SS BOND : bond 0.00360 / 0.24 ( 13) SS BOND : angle 0.80956 / 0.50 ( 26) hydrogen bonds : bond 0.05020 / 3.03 ( 325) hydrogen bonds : angle 3.85031 / 2.55 ( 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: 26 poor density : 123 time to evaluate : 0.340 Fit side-chains REVERT: d 99 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7314 (pp) REVERT: e 37 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8278 (mttp) REVERT: f 86 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8184 (mm-30) REVERT: f 101 ARG cc_start: 0.7566 (tpt-90) cc_final: 0.6870 (tpt170) REVERT: g 79 LYS cc_start: 0.7786 (mmtm) cc_final: 0.7567 (mttm) REVERT: g 92 ASN cc_start: 0.7267 (m110) cc_final: 0.5861 (t0) REVERT: m 82 ARG cc_start: 0.5950 (mtm180) cc_final: 0.5448 (mtm-85) REVERT: m 121 THR cc_start: 0.6997 (m) cc_final: 0.6516 (p) REVERT: m 145 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7371 (mtt90) REVERT: m 148 LYS cc_start: 0.7836 (ptmm) cc_final: 0.7418 (mttt) REVERT: m 207 ASN cc_start: 0.7534 (m-40) cc_final: 0.7310 (p0) REVERT: m 211 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.7809 (m-40) REVERT: m 229 VAL cc_start: 0.8172 (t) cc_final: 0.7911 (m) REVERT: n 28 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7544 (mtmm) REVERT: n 50 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4744 (p90) REVERT: n 67 TYR cc_start: 0.7373 (p90) cc_final: 0.7019 (p90) REVERT: n 80 PRO cc_start: 0.7563 (Cg_endo) cc_final: 0.7287 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8236 (tt) REVERT: n 252 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: n 261 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8298 (ptt180) REVERT: n 263 ASP cc_start: 0.7647 (m-30) cc_final: 0.7386 (m-30) outliers start: 26 outliers final: 19 residues processed: 142 average time/residue: 0.0941 time to fit residues: 18.2421 Evaluate side-chains 139 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 g residue 30 LEU Chi-restraints excluded: chain g residue 52 ASN 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 182 LEU Chi-restraints excluded: chain m residue 211 ASN 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 Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 211 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.171567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119542 restraints weight = 9316.394| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.45 r_work: 0.3027 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.6167 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= 0.142 Angle : 0.623 9.950 11650 Z= 0.321 Chirality : 0.043 0.178 1308 Planarity : 0.004 0.031 1468 Dihedral : 5.053 55.314 1163 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 2.48 % Allowed : 14.02 % Favored : 83.50 % 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: 0.23 (0.27), residues: 1040 helix: 3.92 (0.30), residues: 236 sheet: 0.84 (0.33), residues: 286 loop : -2.27 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 91 TYR 0.014 0.001 TYR n 50 PHE 0.012 0.001 PHE f 87 TRP 0.016 0.001 TRP n 259 HIS 0.003 0.001 HIS n 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8561) covalent geometry : angle 0.62180 / 0.32 (11624) SS BOND : bond 0.00417 / 0.28 ( 13) SS BOND : angle 1.00782 / 0.62 ( 26) hydrogen bonds : bond 0.05742 / 3.47 ( 325) hydrogen bonds : angle 3.95272 / 2.60 ( 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 146 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8354 (pt0) cc_final: 0.8136 (pt0) REVERT: d 99 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7381 (pp) REVERT: e 37 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8314 (mttp) REVERT: f 101 ARG cc_start: 0.7577 (tpt-90) cc_final: 0.6800 (tpt170) REVERT: f 125 MET cc_start: 0.7729 (mmm) cc_final: 0.7486 (mmt) REVERT: g 79 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7609 (mttm) REVERT: g 92 ASN cc_start: 0.7252 (m110) cc_final: 0.6786 (m-40) REVERT: m 82 ARG cc_start: 0.5860 (mtm180) cc_final: 0.5359 (mtm-85) REVERT: m 121 THR cc_start: 0.7056 (m) cc_final: 0.6579 (p) REVERT: m 145 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7348 (mtt90) REVERT: m 148 LYS cc_start: 0.7850 (ptmm) cc_final: 0.7434 (mttt) REVERT: m 211 ASN cc_start: 0.8429 (t0) cc_final: 0.7830 (m-40) REVERT: m 229 VAL cc_start: 0.8212 (t) cc_final: 0.7964 (m) REVERT: n 28 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7620 (mtmm) REVERT: n 50 TYR cc_start: 0.5237 (OUTLIER) cc_final: 0.4592 (p90) REVERT: n 67 TYR cc_start: 0.7470 (p90) cc_final: 0.7138 (p90) REVERT: n 80 PRO cc_start: 0.7587 (Cg_endo) cc_final: 0.7311 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8251 (tt) REVERT: n 252 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: n 261 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8382 (ptt180) REVERT: n 263 ASP cc_start: 0.7776 (m-30) cc_final: 0.7502 (m-30) outliers start: 23 outliers final: 18 residues processed: 141 average time/residue: 0.0899 time to fit residues: 17.3327 Evaluate side-chains 148 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 182 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 Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN m 211 ASN ** n 48 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 = 0.3922 r_free = 0.3922 target = 0.174741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134658 restraints weight = 9353.615| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.70 r_work: 0.2994 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8574 Z= 0.117 Angle : 0.586 9.373 11650 Z= 0.303 Chirality : 0.041 0.195 1308 Planarity : 0.004 0.031 1468 Dihedral : 4.864 55.571 1163 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 2.59 % Allowed : 14.02 % 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: 0.29 (0.27), residues: 1040 helix: 3.86 (0.31), residues: 242 sheet: 0.86 (0.33), residues: 286 loop : -2.23 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG n 228 TYR 0.013 0.001 TYR n 50 PHE 0.009 0.001 PHE f 87 TRP 0.017 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 8561) covalent geometry : angle 0.58520 / 0.30 (11624) SS BOND : bond 0.00322 / 0.21 ( 13) SS BOND : angle 0.79360 / 0.48 ( 26) hydrogen bonds : bond 0.05011 / 3.02 ( 325) hydrogen bonds : angle 3.82885 / 2.53 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2085.49 seconds wall clock time: 36 minutes 16.29 seconds (2176.29 seconds total)