Starting phenix.real_space_refine on Thu Mar 5 11:30:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbb_11149/03_2026/6zbb_11149_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbb_11149/03_2026/6zbb_11149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zbb_11149/03_2026/6zbb_11149_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbb_11149/03_2026/6zbb_11149_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zbb_11149/03_2026/6zbb_11149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbb_11149/03_2026/6zbb_11149.map" } resolution = 3.61 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= 0.001 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 55 5.16 5 C 6974 2.51 5 N 1617 2.21 5 O 1836 1.98 5 H 10592 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21082 Number of models: 1 Model: "" Number of chains: 20 Chain: "8" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 696 Classifications: {'peptide': 41} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "K" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1078 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3557 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "b" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1791 Classifications: {'peptide': 112} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "d" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 893 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 45} Chain: "e" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 975 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 84 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "b" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 161 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "f" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 3.78, per 1000 atoms: 0.18 Number of scatterers: 21082 At special positions: 0 Unit cell: (111.088, 125.76, 121.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 8 15.00 O 1836 8.00 N 1617 7.00 C 6974 6.00 H 10592 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 528.2 milliseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 1 sheets defined 85.6% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain '8' and resid 1 through 7 removed outlier: 5.455A pdb=" N THR 8 6 " --> pdb=" O GLN 8 3 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N SER 8 7 " --> pdb=" O LEU 8 4 " (cutoff:3.500A) Processing helix chain '8' and resid 8 through 21 removed outlier: 3.554A pdb=" N THR 8 19 " --> pdb=" O SER 8 15 " (cutoff:3.500A) Processing helix chain '8' and resid 23 through 29 removed outlier: 3.568A pdb=" N SER 8 29 " --> pdb=" O GLN 8 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 15 Processing helix chain 'K' and resid 17 through 39 removed outlier: 3.811A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 73 removed outlier: 3.934A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 15 removed outlier: 4.355A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 39 removed outlier: 4.139A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 73 removed outlier: 3.892A pdb=" N LEU L 52 " --> pdb=" O SER L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 15 removed outlier: 5.097A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 39 removed outlier: 4.241A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN M 39 " --> pdb=" O GLY M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 4.271A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 Processing helix chain 'N' and resid 18 through 39 removed outlier: 3.638A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 74 removed outlier: 3.833A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 17 through 39 removed outlier: 4.194A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 74 removed outlier: 4.268A pdb=" N VAL O 67 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 17 through 39 removed outlier: 4.115A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 73 removed outlier: 3.737A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 15 Processing helix chain 'Q' and resid 17 through 39 removed outlier: 4.015A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 74 removed outlier: 4.619A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 16 removed outlier: 3.673A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 39 removed outlier: 4.091A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 73 removed outlier: 3.762A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 10 Processing helix chain 'a' and resid 19 through 24 removed outlier: 3.852A pdb=" N ILE a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 40 through 58 removed outlier: 4.072A pdb=" N GLN a 46 " --> pdb=" O PHE a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 67 Processing helix chain 'a' and resid 68 through 87 removed outlier: 3.634A pdb=" N LEU a 84 " --> pdb=" O GLY a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 127 Proline residue: a 107 - end of helix removed outlier: 7.486A pdb=" N LYS a 122 " --> pdb=" O ARG a 118 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA a 123 " --> pdb=" O ASN a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 136 No H-bonds generated for 'chain 'a' and resid 134 through 136' Processing helix chain 'a' and resid 137 through 182 removed outlier: 4.665A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE a 147 " --> pdb=" O ILE a 143 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN a 152 " --> pdb=" O SER a 148 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 3.656A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY a 167 " --> pdb=" O ASN a 163 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS a 172 " --> pdb=" O HIS a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 225 removed outlier: 3.753A pdb=" N ALA a 189 " --> pdb=" O SER a 185 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 16 No H-bonds generated for 'chain 'b' and resid 14 through 16' Processing helix chain 'b' and resid 19 through 30 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 31 through 48 removed outlier: 4.626A pdb=" N TYR b 35 " --> pdb=" O VAL b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 112 removed outlier: 3.621A pdb=" N PHE b 58 " --> pdb=" O THR b 54 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 122 removed outlier: 3.677A pdb=" N LYS d 120 " --> pdb=" O LYS d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 130 Processing helix chain 'd' and resid 131 through 139 removed outlier: 3.877A pdb=" N GLU d 137 " --> pdb=" O GLU d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 143 removed outlier: 3.718A pdb=" N LYS d 143 " --> pdb=" O PRO d 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 140 through 143' Processing helix chain 'd' and resid 145 through 149 Processing helix chain 'e' and resid 7 through 57 Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 18 through 26 Processing helix chain 'f' and resid 30 through 49 removed outlier: 3.856A pdb=" N ALA f 36 " --> pdb=" O GLY f 32 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 74 removed outlier: 4.727A pdb=" N VAL f 62 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN f 70 " --> pdb=" O TYR f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 75 through 80 removed outlier: 4.222A pdb=" N HIS f 80 " --> pdb=" O LYS f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 37 removed outlier: 4.113A pdb=" N ARG g 25 " --> pdb=" O TYR g 21 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA g 27 " --> pdb=" O LYS g 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR g 32 " --> pdb=" O THR g 28 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 62 removed outlier: 4.551A pdb=" N THR g 47 " --> pdb=" O ALA g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 67 Processing helix chain 'g' and resid 68 through 94 removed outlier: 3.568A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 10 Processing helix chain 'j' and resid 13 through 19 Processing helix chain 'j' and resid 20 through 22 No H-bonds generated for 'chain 'j' and resid 20 through 22' Processing helix chain 'j' and resid 23 through 48 Processing helix chain 'k' and resid 13 through 18 Processing helix chain 'k' and resid 22 through 46 removed outlier: 3.879A pdb=" N ARG k 26 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET k 27 " --> pdb=" O LEU k 23 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU k 46 " --> pdb=" O LEU k 42 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 12 through 13 825 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10438 1.03 - 1.23: 265 1.23 - 1.43: 4165 1.43 - 1.62: 6307 1.62 - 1.82: 114 Bond restraints: 21289 Sorted by residual: bond pdb=" CA M3L N 43 " pdb=" HA M3L N 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" CA M3L O 43 " pdb=" HA M3L O 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" CA M3L M 43 " pdb=" HA M3L M 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" CA M3L P 43 " pdb=" HA M3L P 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" CA M3L Q 43 " pdb=" HA M3L Q 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 21284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 37871 2.48 - 4.97: 431 4.97 - 7.45: 69 7.45 - 9.93: 33 9.93 - 12.41: 8 Bond angle restraints: 38412 Sorted by residual: angle pdb=" C51 CDL b 302 " pdb=" CB5 CDL b 302 " pdb=" OB6 CDL b 302 " ideal model delta sigma weight residual 111.33 121.07 -9.74 1.32e+00 5.72e-01 5.43e+01 angle pdb=" C11 CDL b 302 " pdb=" CA5 CDL b 302 " pdb=" OA6 CDL b 302 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C11 CDL a 301 " pdb=" CA5 CDL a 301 " pdb=" OA6 CDL a 301 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.59e+01 angle pdb=" C11 CDL b 301 " pdb=" CA5 CDL b 301 " pdb=" OA6 CDL b 301 " ideal model delta sigma weight residual 111.33 119.92 -8.59 1.32e+00 5.72e-01 4.22e+01 angle pdb=" C51 CDL a 301 " pdb=" CB5 CDL a 301 " pdb=" OB6 CDL a 301 " ideal model delta sigma weight residual 111.33 119.88 -8.55 1.32e+00 5.72e-01 4.18e+01 ... (remaining 38407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 8916 20.26 - 40.52: 766 40.52 - 60.79: 408 60.79 - 81.05: 19 81.05 - 101.31: 8 Dihedral angle restraints: 10117 sinusoidal: 5579 harmonic: 4538 Sorted by residual: dihedral pdb=" CA LEU M 62 " pdb=" C LEU M 62 " pdb=" N PHE M 63 " pdb=" CA PHE M 63 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS b 48 " pdb=" C LYS b 48 " pdb=" N GLU b 49 " pdb=" CA GLU b 49 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE M 29 " pdb=" C PHE M 29 " pdb=" N GLY M 30 " pdb=" CA GLY M 30 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 10114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1068 0.034 - 0.069: 424 0.069 - 0.103: 111 0.103 - 0.137: 39 0.137 - 0.172: 9 Chirality restraints: 1651 Sorted by residual: chirality pdb=" CB ILE R 9 " pdb=" CA ILE R 9 " pdb=" CG1 ILE R 9 " pdb=" CG2 ILE R 9 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PRO a 89 " pdb=" N PRO a 89 " pdb=" C PRO a 89 " pdb=" CB PRO a 89 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA LEU M 62 " pdb=" N LEU M 62 " pdb=" C LEU M 62 " pdb=" CB LEU M 62 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1648 not shown) Planarity restraints: 2982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 101 " -0.067 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C8 LHG f 101 " 0.020 2.00e-02 2.50e+03 pdb=" O7 LHG f 101 " 0.021 2.00e-02 2.50e+03 pdb=" O9 LHG f 101 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG f 101 " -0.057 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C24 LHG f 101 " 0.017 2.00e-02 2.50e+03 pdb=" O10 LHG f 101 " 0.021 2.00e-02 2.50e+03 pdb=" O8 LHG f 101 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 102 " 0.054 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" C8 LHG f 102 " -0.016 2.00e-02 2.50e+03 pdb=" O7 LHG f 102 " -0.017 2.00e-02 2.50e+03 pdb=" O9 LHG f 102 " -0.022 2.00e-02 2.50e+03 ... (remaining 2979 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 436 2.08 - 2.71: 36417 2.71 - 3.34: 64600 3.34 - 3.97: 76496 3.97 - 4.60: 122694 Nonbonded interactions: 300643 Sorted by model distance: nonbonded pdb="HH22 ARG a 36 " pdb=" O PRO b 3 " model vdw 1.453 2.450 nonbonded pdb=" O ILE R 2 " pdb=" H ALA R 6 " model vdw 1.491 2.450 nonbonded pdb=" OD1 ASN 8 32 " pdb=" H PHE 8 33 " model vdw 1.527 2.450 nonbonded pdb=" H THR d 131 " pdb=" OD2 ASP d 134 " model vdw 1.528 2.450 nonbonded pdb=" OE1 GLU d 113 " pdb=" H GLU d 113 " model vdw 1.532 2.450 ... (remaining 300638 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 'K' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = (chain 'P' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 through 74) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.890 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: 0.070 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.050 Find NCS groups from input model: 0.120 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.012 0.893 10698 Z= 0.954 Angle : 1.035 12.413 14408 Z= 0.515 Chirality : 0.042 0.172 1651 Planarity : 0.004 0.041 1726 Dihedral : 17.259 101.309 3971 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1270 helix: 0.37 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -1.79 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG b 13 TYR 0.013 0.001 TYR N 49 PHE 0.036 0.002 PHE M 47 TRP 0.010 0.001 TRP g 85 HIS 0.013 0.002 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00763 (10697) covalent geometry : angle 1.03462 (14408) hydrogen bonds : bond 0.11334 ( 825) hydrogen bonds : angle 5.89794 ( 2427) Misc. bond : bond 0.89327 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.8113 (m-30) cc_final: 0.7760 (m-30) REVERT: P 58 GLU cc_start: 0.7446 (tt0) cc_final: 0.7143 (tt0) REVERT: b 102 LYS cc_start: 0.9141 (tttt) cc_final: 0.8912 (tttt) REVERT: d 158 GLU cc_start: 0.8501 (pm20) cc_final: 0.8173 (pm20) REVERT: g 82 VAL cc_start: 0.9055 (m) cc_final: 0.8842 (p) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1803 time to fit residues: 67.0134 Evaluate side-chains 200 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088091 restraints weight = 73380.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.091263 restraints weight = 29872.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093126 restraints weight = 17992.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094112 restraints weight = 13526.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094745 restraints weight = 11620.999| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10698 Z= 0.171 Angle : 0.647 6.882 14408 Z= 0.339 Chirality : 0.039 0.140 1651 Planarity : 0.004 0.057 1726 Dihedral : 14.308 107.520 1740 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.53 % Allowed : 8.92 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1270 helix: 0.57 (0.16), residues: 1031 sheet: None (None), residues: 0 loop : -1.15 (0.43), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 38 TYR 0.014 0.001 TYR f 71 PHE 0.027 0.002 PHE M 47 TRP 0.006 0.001 TRP 8 9 HIS 0.010 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00369 (10697) covalent geometry : angle 0.64738 (14408) hydrogen bonds : bond 0.05063 ( 825) hydrogen bonds : angle 4.78704 ( 2427) Misc. bond : bond 0.00386 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.7961 (m-30) cc_final: 0.7586 (m-30) REVERT: K 54 PHE cc_start: 0.8124 (t80) cc_final: 0.7919 (t80) REVERT: b 51 TYR cc_start: 0.8438 (t80) cc_final: 0.8157 (t80) REVERT: d 158 GLU cc_start: 0.8473 (pm20) cc_final: 0.8109 (pm20) outliers start: 16 outliers final: 12 residues processed: 244 average time/residue: 0.1897 time to fit residues: 68.4459 Evaluate side-chains 220 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain k residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.106736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.087460 restraints weight = 73090.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090536 restraints weight = 31502.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092347 restraints weight = 19422.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093416 restraints weight = 14735.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093781 restraints weight = 12572.457| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10698 Z= 0.190 Angle : 0.611 6.202 14408 Z= 0.322 Chirality : 0.038 0.150 1651 Planarity : 0.004 0.059 1726 Dihedral : 13.408 108.189 1740 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.21 % Allowed : 11.12 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1270 helix: 0.72 (0.16), residues: 1039 sheet: None (None), residues: 0 loop : -1.07 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 38 TYR 0.012 0.001 TYR f 71 PHE 0.024 0.001 PHE L 63 TRP 0.004 0.001 TRP g 85 HIS 0.006 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00414 (10697) covalent geometry : angle 0.61119 (14408) hydrogen bonds : bond 0.04801 ( 825) hydrogen bonds : angle 4.59469 ( 2427) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.8004 (m-30) cc_final: 0.7602 (m-30) REVERT: d 158 GLU cc_start: 0.8475 (pm20) cc_final: 0.8106 (pm20) outliers start: 23 outliers final: 18 residues processed: 232 average time/residue: 0.1897 time to fit residues: 65.8540 Evaluate side-chains 219 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087732 restraints weight = 73095.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.090992 restraints weight = 29480.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.092931 restraints weight = 17545.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094052 restraints weight = 13076.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094669 restraints weight = 11076.734| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10698 Z= 0.157 Angle : 0.590 6.886 14408 Z= 0.308 Chirality : 0.038 0.149 1651 Planarity : 0.004 0.056 1726 Dihedral : 12.564 107.333 1740 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.11 % Allowed : 12.37 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1270 helix: 0.90 (0.16), residues: 1039 sheet: None (None), residues: 0 loop : -0.88 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 38 TYR 0.013 0.001 TYR L 49 PHE 0.023 0.001 PHE K 63 TRP 0.005 0.001 TRP g 85 HIS 0.005 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00339 (10697) covalent geometry : angle 0.59025 (14408) hydrogen bonds : bond 0.04588 ( 825) hydrogen bonds : angle 4.39769 ( 2427) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.7979 (m-30) cc_final: 0.7591 (m-30) REVERT: d 158 GLU cc_start: 0.8527 (pm20) cc_final: 0.8171 (pm20) outliers start: 22 outliers final: 17 residues processed: 237 average time/residue: 0.2005 time to fit residues: 70.0709 Evaluate side-chains 225 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.107051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087564 restraints weight = 72893.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090824 restraints weight = 29208.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.092711 restraints weight = 17498.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.093814 restraints weight = 13135.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094303 restraints weight = 11154.241| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10698 Z= 0.161 Angle : 0.580 7.452 14408 Z= 0.303 Chirality : 0.037 0.184 1651 Planarity : 0.004 0.054 1726 Dihedral : 11.943 106.991 1740 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.49 % Allowed : 12.75 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1270 helix: 1.00 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.85 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 38 TYR 0.011 0.001 TYR e 15 PHE 0.025 0.001 PHE K 63 TRP 0.005 0.001 TRP g 85 HIS 0.004 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00351 (10697) covalent geometry : angle 0.57978 (14408) hydrogen bonds : bond 0.04493 ( 825) hydrogen bonds : angle 4.31410 ( 2427) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.7955 (m-30) cc_final: 0.7558 (m-30) REVERT: d 158 GLU cc_start: 0.8486 (pm20) cc_final: 0.8158 (pm20) REVERT: j 7 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7690 (mmmt) REVERT: j 23 GLU cc_start: 0.8335 (mp0) cc_final: 0.7924 (mp0) outliers start: 26 outliers final: 22 residues processed: 232 average time/residue: 0.1876 time to fit residues: 64.7842 Evaluate side-chains 232 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087792 restraints weight = 72822.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091058 restraints weight = 29132.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.092944 restraints weight = 17428.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094054 restraints weight = 13103.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094487 restraints weight = 11124.019| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10698 Z= 0.161 Angle : 0.579 7.548 14408 Z= 0.302 Chirality : 0.037 0.164 1651 Planarity : 0.004 0.032 1726 Dihedral : 11.447 106.769 1740 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.40 % Allowed : 13.23 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1270 helix: 1.10 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 38 TYR 0.010 0.001 TYR f 71 PHE 0.026 0.001 PHE K 63 TRP 0.006 0.001 TRP g 85 HIS 0.004 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00355 (10697) covalent geometry : angle 0.57946 (14408) hydrogen bonds : bond 0.04406 ( 825) hydrogen bonds : angle 4.25675 ( 2427) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.7980 (m-30) cc_final: 0.7576 (m-30) REVERT: M 62 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7221 (mp) REVERT: d 158 GLU cc_start: 0.8464 (pm20) cc_final: 0.8167 (pm20) REVERT: j 7 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7717 (mmmt) outliers start: 25 outliers final: 22 residues processed: 234 average time/residue: 0.1843 time to fit residues: 64.6432 Evaluate side-chains 233 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087984 restraints weight = 72969.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.091242 restraints weight = 29129.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093139 restraints weight = 17448.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094140 restraints weight = 13100.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094477 restraints weight = 11262.048| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10698 Z= 0.160 Angle : 0.576 7.820 14408 Z= 0.299 Chirality : 0.037 0.153 1651 Planarity : 0.004 0.032 1726 Dihedral : 11.145 106.545 1740 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.30 % Allowed : 14.09 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.24), residues: 1270 helix: 1.16 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -1.05 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 38 TYR 0.010 0.001 TYR f 71 PHE 0.027 0.001 PHE K 63 TRP 0.010 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00351 (10697) covalent geometry : angle 0.57612 (14408) hydrogen bonds : bond 0.04363 ( 825) hydrogen bonds : angle 4.20997 ( 2427) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.8010 (m-30) cc_final: 0.7618 (m-30) REVERT: d 158 GLU cc_start: 0.8460 (pm20) cc_final: 0.8173 (pm20) outliers start: 24 outliers final: 23 residues processed: 233 average time/residue: 0.1829 time to fit residues: 63.1303 Evaluate side-chains 234 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.087711 restraints weight = 72951.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090882 restraints weight = 30413.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.092715 restraints weight = 18566.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.093606 restraints weight = 14057.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094302 restraints weight = 12230.243| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10698 Z= 0.169 Angle : 0.578 7.882 14408 Z= 0.301 Chirality : 0.037 0.147 1651 Planarity : 0.004 0.032 1726 Dihedral : 10.985 106.615 1740 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.59 % Allowed : 14.29 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1270 helix: 1.21 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -1.08 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 38 TYR 0.010 0.001 TYR f 71 PHE 0.027 0.001 PHE K 63 TRP 0.014 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00371 (10697) covalent geometry : angle 0.57816 (14408) hydrogen bonds : bond 0.04317 ( 825) hydrogen bonds : angle 4.19145 ( 2427) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.7952 (m-30) cc_final: 0.7552 (m-30) REVERT: O 56 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6507 (tt) REVERT: d 158 GLU cc_start: 0.8430 (pm20) cc_final: 0.8152 (pm20) outliers start: 27 outliers final: 25 residues processed: 234 average time/residue: 0.1898 time to fit residues: 66.2098 Evaluate side-chains 234 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.107597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.088245 restraints weight = 72934.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091456 restraints weight = 30330.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093333 restraints weight = 18416.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094177 restraints weight = 13889.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.094909 restraints weight = 12135.870| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10698 Z= 0.148 Angle : 0.574 7.855 14408 Z= 0.298 Chirality : 0.037 0.171 1651 Planarity : 0.004 0.032 1726 Dihedral : 10.736 105.837 1740 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.78 % Allowed : 14.57 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1270 helix: 1.30 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -1.01 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 38 TYR 0.013 0.001 TYR Q 49 PHE 0.028 0.001 PHE K 63 TRP 0.014 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00322 (10697) covalent geometry : angle 0.57428 (14408) hydrogen bonds : bond 0.04247 ( 825) hydrogen bonds : angle 4.14343 ( 2427) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.7931 (m-30) cc_final: 0.7533 (m-30) REVERT: O 56 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6502 (tt) REVERT: Q 47 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.6372 (t80) REVERT: d 158 GLU cc_start: 0.8438 (pm20) cc_final: 0.8152 (pm20) outliers start: 29 outliers final: 24 residues processed: 236 average time/residue: 0.1860 time to fit residues: 65.4674 Evaluate side-chains 238 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 121 optimal weight: 0.0970 chunk 89 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 96 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.088534 restraints weight = 72871.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.091841 restraints weight = 29282.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093787 restraints weight = 17486.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094788 restraints weight = 13070.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095469 restraints weight = 11230.815| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10698 Z= 0.140 Angle : 0.570 7.597 14408 Z= 0.295 Chirality : 0.037 0.160 1651 Planarity : 0.004 0.032 1726 Dihedral : 10.481 105.360 1740 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.78 % Allowed : 14.86 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1270 helix: 1.42 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.92 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 38 TYR 0.011 0.001 TYR L 49 PHE 0.028 0.001 PHE K 63 TRP 0.028 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00305 (10697) covalent geometry : angle 0.57022 (14408) hydrogen bonds : bond 0.04172 ( 825) hydrogen bonds : angle 4.08598 ( 2427) Misc. bond : bond 0.00037 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.7944 (m-30) cc_final: 0.7545 (m-30) REVERT: O 56 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6474 (tt) REVERT: Q 47 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6376 (t80) REVERT: Q 58 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7755 (mm-30) REVERT: R 60 MET cc_start: 0.7438 (tpp) cc_final: 0.7128 (tpt) outliers start: 29 outliers final: 25 residues processed: 235 average time/residue: 0.1976 time to fit residues: 69.5457 Evaluate side-chains 239 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 9 ILE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain a residue 127 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.107778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.088419 restraints weight = 73227.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.091613 restraints weight = 30209.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.093489 restraints weight = 18344.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094339 restraints weight = 13849.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094959 restraints weight = 12077.760| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10698 Z= 0.151 Angle : 0.576 7.616 14408 Z= 0.298 Chirality : 0.037 0.159 1651 Planarity : 0.004 0.035 1726 Dihedral : 10.445 105.526 1740 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.78 % Allowed : 14.86 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.24), residues: 1270 helix: 1.45 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 38 TYR 0.011 0.001 TYR Q 49 PHE 0.027 0.001 PHE K 63 TRP 0.023 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd covalent geometry : bond 0.00333 (10697) covalent geometry : angle 0.57585 (14408) hydrogen bonds : bond 0.04158 ( 825) hydrogen bonds : angle 4.08610 ( 2427) Misc. bond : bond 0.00036 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3546.43 seconds wall clock time: 61 minutes 12.99 seconds (3672.99 seconds total)