Starting phenix.real_space_refine on Mon Oct 26 18:02:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbb_11149/10_2026/6zbb_11149_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbb_11149/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zbb_11149/10_2026/6zbb_11149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbb_11149/10_2026/6zbb_11149.map" model { file = "/net/cci-nas-00/data/ceres_data/6zbb_11149/10_2026/6zbb_11149_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbb_11149/10_2026/6zbb_11149_trim.cif" } 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-2.3rc1-6221/lib/python3.11/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: 3.75, 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: 2.21 Conformation dependent library (CDL) restraints added in 590.4 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: 0.24 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: 4.36 Time building geometry restraints manager: 2.95 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 - 2.74: 37953 2.74 - 5.47: 348 5.47 - 8.21: 68 8.21 - 10.94: 26 10.94 - 13.68: 17 Bond angle restraints: 38412 Sorted by residual: angle pdb=" OB2 CDL a 301 " pdb=" PB2 CDL a 301 " pdb=" OB5 CDL a 301 " ideal model delta sigma weight residual 96.70 110.38 -13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" OB2 CDL b 302 " pdb=" PB2 CDL b 302 " pdb=" OB5 CDL b 302 " ideal model delta sigma weight residual 96.70 110.06 -13.36 3.00e+00 1.11e-01 1.98e+01 angle pdb=" OA2 CDL b 302 " pdb=" PA1 CDL b 302 " pdb=" OA5 CDL b 302 " ideal model delta sigma weight residual 97.81 111.03 -13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" OB3 CDL b 301 " pdb=" PB2 CDL b 301 " pdb=" OB4 CDL b 301 " ideal model delta sigma weight residual 121.80 108.63 13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" OB3 CDL b 302 " pdb=" PB2 CDL b 302 " pdb=" OB4 CDL b 302 " ideal model delta sigma weight residual 121.80 109.30 12.50 3.00e+00 1.11e-01 1.74e+01 ... (remaining 38407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8773 17.68 - 35.37: 881 35.37 - 53.05: 361 53.05 - 70.73: 130 70.73 - 88.42: 20 Dihedral angle restraints: 10165 sinusoidal: 5627 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 10162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1070 0.034 - 0.069: 422 0.069 - 0.103: 110 0.103 - 0.137: 40 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: 12.830 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: 0.050 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 19.900 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.893 10698 Z= 0.918 Angle : 1.102 13.680 14408 Z= 0.476 Chirality : 0.042 0.172 1651 Planarity : 0.004 0.041 1726 Dihedral : 16.448 88.133 4019 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/Z covalent geometry : bond 0.00678 / 0.31 (10697) covalent geometry : angle 1.10150 / 0.48 (14408) hydrogen bonds : bond 0.11334 / 6.94 ( 825) hydrogen bonds : angle 5.89794 / 4.34 ( 2427) Misc. bond : bond 0.89327 / 42.54 ( 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 : 0.568 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: 0.1907 time to fit residues: 72.2175 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 : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 0.2980 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: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.107159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088107 restraints weight = 73407.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091273 restraints weight = 29886.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093113 restraints weight = 18016.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094191 restraints weight = 13574.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094715 restraints weight = 11543.523| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1373 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= 0.171 Angle : 0.651 6.720 14408 Z= 0.339 Chirality : 0.039 0.141 1651 Planarity : 0.004 0.058 1726 Dihedral : 12.909 84.884 1788 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.44 % Allowed : 9.01 % 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: 0.28 (0.24), residues: 1270 helix: 0.58 (0.16), residues: 1031 sheet: None (None), residues: 0 loop : -1.14 (0.43), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 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 a 109 HIS 0.009 0.001 HIS b 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (10697) covalent geometry : angle 0.65133 / 0.34 (14408) hydrogen bonds : bond 0.05076 / 3.35 ( 825) hydrogen bonds : angle 4.79137 / 3.48 ( 2427) Misc. bond : bond 0.00017 / 0.01 ( 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 252 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 0.578 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: K 3 ASP cc_start: 0.7967 (m-30) cc_final: 0.7625 (m-30) REVERT: K 54 PHE cc_start: 0.8130 (t80) cc_final: 0.7923 (t80) REVERT: b 51 TYR cc_start: 0.8443 (t80) cc_final: 0.8161 (t80) REVERT: d 158 GLU cc_start: 0.8474 (pm20) cc_final: 0.8112 (pm20) REVERT: g 82 VAL cc_start: 0.9051 (m) cc_final: 0.8848 (p) outliers start: 15 outliers final: 11 residues processed: 242 average time/residue: 0.1930 time to fit residues: 70.2538 Evaluate side-chains 219 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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: [80, 28, 1, 60, 101, 43, 0, 115, 113, 47, 116] chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3684 r_free = 0.3684 target = 0.106380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087242 restraints weight = 73169.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090375 restraints weight = 30055.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.092202 restraints weight = 18319.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093036 restraints weight = 13865.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093777 restraints weight = 12098.934| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1683 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= 0.180 Angle : 0.614 6.272 14408 Z= 0.321 Chirality : 0.038 0.147 1651 Planarity : 0.004 0.058 1726 Dihedral : 12.441 84.106 1788 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.30 % Allowed : 10.83 % Favored : 86.86 % 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: 0.54 (0.24), residues: 1270 helix: 0.74 (0.16), residues: 1039 sheet: None (None), residues: 0 loop : -1.02 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 38 TYR 0.011 0.001 TYR f 71 PHE 0.019 0.001 PHE P 63 TRP 0.004 0.001 TRP g 85 HIS 0.007 0.001 HIS b 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (10697) covalent geometry : angle 0.61414 / 0.32 (14408) hydrogen bonds : bond 0.04775 / 3.16 ( 825) hydrogen bonds : angle 4.57018 / 3.32 ( 2427) Misc. bond : bond 0.00046 / 0.02 ( 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 251 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.464 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: K 3 ASP cc_start: 0.7973 (m-30) cc_final: 0.7566 (m-30) REVERT: d 158 GLU cc_start: 0.8460 (pm20) cc_final: 0.8092 (pm20) outliers start: 24 outliers final: 19 residues processed: 237 average time/residue: 0.1917 time to fit residues: 68.6571 Evaluate side-chains 219 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [64, 75, 2, 122, 36, 27, 47, 88, 85, 65, 105] chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 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: 0.9980 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3706 r_free = 0.3706 target = 0.107729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.088304 restraints weight = 73055.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091574 restraints weight = 29033.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.093478 restraints weight = 17358.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094569 restraints weight = 13000.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095194 restraints weight = 11077.611| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1964 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= 0.151 Angle : 0.591 6.794 14408 Z= 0.307 Chirality : 0.037 0.154 1651 Planarity : 0.004 0.055 1726 Dihedral : 12.103 81.389 1788 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.92 % Allowed : 12.08 % Favored : 86.00 % 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: 0.86 (0.24), residues: 1270 helix: 0.94 (0.16), residues: 1039 sheet: None (None), residues: 0 loop : -0.82 (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 0.021 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/Z covalent geometry : bond 0.00324 / 0.15 (10697) covalent geometry : angle 0.59061 / 0.31 (14408) hydrogen bonds : bond 0.04560 / 3.02 ( 825) hydrogen bonds : angle 4.36931 / 3.17 ( 2427) Misc. bond : bond 0.00012 / 0.01 ( 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: 20 poor density : 229 time to evaluate : 0.509 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: 0.7953 (m-30) cc_final: 0.7569 (m-30) REVERT: b 51 TYR cc_start: 0.8436 (t80) cc_final: 0.8153 (t80) REVERT: j 31 MET cc_start: 0.8839 (tmm) cc_final: 0.8427 (tmm) outliers start: 20 outliers final: 16 residues processed: 238 average time/residue: 0.1804 time to fit residues: 65.0431 Evaluate side-chains 226 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU 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: [106, 111, 45, 71, 27, 53, 34, 117, 1, 11, 110] chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.107124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087639 restraints weight = 72913.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090913 restraints weight = 29191.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092810 restraints weight = 17456.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093887 restraints weight = 13103.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094566 restraints weight = 11170.553| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2122 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= 0.168 Angle : 0.590 7.618 14408 Z= 0.307 Chirality : 0.037 0.184 1651 Planarity : 0.004 0.053 1726 Dihedral : 11.865 81.127 1788 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 12.56 % Favored : 85.14 % 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: 0.94 (0.24), residues: 1270 helix: 1.01 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.84 (0.43), residues: 230 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 0.024 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/Z covalent geometry : bond 0.00364 / 0.17 (10697) covalent geometry : angle 0.58998 / 0.31 (14408) hydrogen bonds : bond 0.04501 / 2.98 ( 825) hydrogen bonds : angle 4.31634 / 3.13 ( 2427) Misc. bond : bond 0.00011 / 0.01 ( 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 242 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.587 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: 0.7959 (m-30) cc_final: 0.7561 (m-30) REVERT: j 7 LYS cc_start: 0.8058 (mmmt) cc_final: 0.7714 (mmmt) REVERT: j 23 GLU cc_start: 0.8352 (mp0) cc_final: 0.8028 (mp0) outliers start: 24 outliers final: 20 residues processed: 230 average time/residue: 0.1889 time to fit residues: 65.9557 Evaluate side-chains 230 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 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: [42, 50, 52, 43, 84, 97, 12, 48, 7, 99, 15] chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3695 r_free = 0.3695 target = 0.107074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.087514 restraints weight = 73002.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090795 restraints weight = 29268.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.092700 restraints weight = 17548.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093773 restraints weight = 13178.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094287 restraints weight = 11245.084| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10698 Z= 0.173 Angle : 0.587 7.882 14408 Z= 0.306 Chirality : 0.038 0.168 1651 Planarity : 0.004 0.032 1726 Dihedral : 11.664 80.618 1788 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 0.99 (0.24), residues: 1270 helix: 1.09 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -1.06 (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 0.026 0.001 PHE K 63 TRP 0.008 0.001 TRP g 85 HIS 0.004 0.001 HIS b 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (10697) covalent geometry : angle 0.58710 / 0.31 (14408) hydrogen bonds : bond 0.04431 / 2.95 ( 825) hydrogen bonds : angle 4.30191 / 3.12 ( 2427) Misc. bond : bond 0.00014 / 0.01 ( 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 247 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.571 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: 0.7963 (m-30) cc_final: 0.7554 (m-30) REVERT: j 7 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7749 (mmmt) outliers start: 25 outliers final: 20 residues processed: 237 average time/residue: 0.1872 time to fit residues: 66.7687 Evaluate side-chains 230 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [68, 63, 43, 71, 62, 65, 36, 72, 75, 93, 5] chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3702 r_free = 0.3702 target = 0.107438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087806 restraints weight = 73177.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091106 restraints weight = 29438.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093021 restraints weight = 17607.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093980 restraints weight = 13182.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094668 restraints weight = 11382.431| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10698 Z= 0.159 Angle : 0.575 7.945 14408 Z= 0.299 Chirality : 0.037 0.161 1651 Planarity : 0.004 0.032 1726 Dihedral : 11.406 80.305 1788 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.30 % Allowed : 13.90 % Favored : 83.80 % 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: 1.12 (0.24), residues: 1270 helix: 1.19 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -1.03 (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 0.026 0.001 PHE K 63 TRP 0.009 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (10697) covalent geometry : angle 0.57491 / 0.30 (14408) hydrogen bonds : bond 0.04356 / 2.89 ( 825) hydrogen bonds : angle 4.21703 / 3.06 ( 2427) Misc. bond : bond 0.00017 / 0.01 ( 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 241 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 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: symmetry clash revert: symmetry clash REVERT: K 3 ASP cc_start: 0.7979 (m-30) cc_final: 0.7579 (m-30) REVERT: j 7 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7697 (mmmt) outliers start: 24 outliers final: 21 residues processed: 232 average time/residue: 0.1895 time to fit residues: 66.4274 Evaluate side-chains 232 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [18, 71, 31, 47, 78, 24, 124, 114, 34, 19, 107] chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 0.0020 chunk 24 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.107850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088313 restraints weight = 72529.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091607 restraints weight = 28992.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093518 restraints weight = 17333.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094633 restraints weight = 12996.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095123 restraints weight = 11039.731| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10698 Z= 0.150 Angle : 0.570 7.838 14408 Z= 0.295 Chirality : 0.037 0.156 1651 Planarity : 0.004 0.036 1726 Dihedral : 11.377 80.250 1788 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.30 % Allowed : 14.19 % Favored : 83.51 % 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: 1.25 (0.24), residues: 1270 helix: 1.28 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.99 (0.42), residues: 236 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 0.028 0.001 PHE K 63 TRP 0.013 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10697) covalent geometry : angle 0.56971 / 0.30 (14408) hydrogen bonds : bond 0.04278 / 2.84 ( 825) hydrogen bonds : angle 4.16537 / 3.02 ( 2427) Misc. bond : bond 0.00012 / 0.01 ( 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 249 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.562 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: 0.7982 (m-30) cc_final: 0.7584 (m-30) outliers start: 24 outliers final: 22 residues processed: 238 average time/residue: 0.1833 time to fit residues: 65.6268 Evaluate side-chains 235 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 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 K residue 69 PHE Chi-restraints excluded: chain L residue 41 SER 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 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 a residue 151 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [21, 38, 93, 83, 33, 115, 1, 118, 16, 4, 54] chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.0020 chunk 83 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3710 r_free = 0.3710 target = 0.108156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.088621 restraints weight = 72671.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.091921 restraints weight = 28833.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093842 restraints weight = 17337.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094978 restraints weight = 12983.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095465 restraints weight = 10997.051| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10698 Z= 0.143 Angle : 0.570 7.710 14408 Z= 0.295 Chirality : 0.037 0.166 1651 Planarity : 0.004 0.037 1726 Dihedral : 11.141 79.946 1788 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.68 % Allowed : 13.90 % Favored : 83.41 % 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: 1.38 (0.24), residues: 1270 helix: 1.37 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 38 TYR 0.011 0.001 TYR Q 49 PHE 0.026 0.001 PHE K 63 TRP 0.017 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10697) covalent geometry : angle 0.56989 / 0.30 (14408) hydrogen bonds : bond 0.04225 / 2.81 ( 825) hydrogen bonds : angle 4.13933 / 3.00 ( 2427) Misc. bond : bond 0.00009 / 0.00 ( 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 252 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.464 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: K 3 ASP cc_start: 0.7970 (m-30) cc_final: 0.7569 (m-30) REVERT: Q 47 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6399 (t80) outliers start: 28 outliers final: 22 residues processed: 238 average time/residue: 0.1889 time to fit residues: 67.4993 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 : 0.585 ------------------------------------------------------------------------------- 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 M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU 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 Q residue 47 PHE Chi-restraints excluded: chain Q residue 72 LEU 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 151 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [121, 89, 97, 15, 86, 56, 96, 109, 59, 58, 21] chunk 121 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.107891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.088264 restraints weight = 73036.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091576 restraints weight = 29159.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093477 restraints weight = 17467.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094553 restraints weight = 13151.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094994 restraints weight = 11231.053| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10698 Z= 0.157 Angle : 0.586 7.666 14408 Z= 0.304 Chirality : 0.038 0.158 1651 Planarity : 0.004 0.040 1726 Dihedral : 11.060 80.816 1788 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.40 % Allowed : 15.05 % Favored : 82.55 % 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: 1.42 (0.24), residues: 1270 helix: 1.40 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.93 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 38 TYR 0.015 0.001 TYR L 49 PHE 0.026 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/Z covalent geometry : bond 0.00345 / 0.16 (10697) covalent geometry : angle 0.58606 / 0.30 (14408) hydrogen bonds : bond 0.04227 / 2.82 ( 825) hydrogen bonds : angle 4.13971 / 3.00 ( 2427) Misc. bond : bond 0.00011 / 0.01 ( 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 242 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.576 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: 0.7984 (m-30) cc_final: 0.7582 (m-30) REVERT: Q 47 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6390 (t80) outliers start: 25 outliers final: 24 residues processed: 232 average time/residue: 0.1836 time to fit residues: 64.2196 Evaluate side-chains 238 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 47 PHE 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 Q residue 72 LEU 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 a residue 151 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [3, 71, 118, 32, 7, 108, 21, 60, 96, 11, 73] chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 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: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3702 r_free = 0.3702 target = 0.107679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088087 restraints weight = 73481.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.091419 restraints weight = 29125.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093329 restraints weight = 17349.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094450 restraints weight = 13020.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094982 restraints weight = 11028.927| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2588 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= 0.164 Angle : 0.584 7.461 14408 Z= 0.303 Chirality : 0.038 0.163 1651 Planarity : 0.004 0.040 1726 Dihedral : 11.029 81.369 1788 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.68 % Allowed : 14.86 % Favored : 82.45 % 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: 1.43 (0.24), residues: 1270 helix: 1.42 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.99 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 38 TYR 0.013 0.001 TYR L 49 PHE 0.025 0.001 PHE K 63 TRP 0.024 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10697) covalent geometry : angle 0.58448 / 0.30 (14408) hydrogen bonds : bond 0.04207 / 2.81 ( 825) hydrogen bonds : angle 4.13812 / 3.00 ( 2427) Misc. bond : bond 0.00009 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3568.26 seconds wall clock time: 61 minutes 33.49 seconds (3693.49 seconds total)