Starting phenix.real_space_refine on Sat May 17 03:44:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evg_28628/05_2025/8evg_28628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evg_28628/05_2025/8evg_28628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evg_28628/05_2025/8evg_28628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evg_28628/05_2025/8evg_28628.map" model { file = "/net/cci-nas-00/data/ceres_data/8evg_28628/05_2025/8evg_28628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evg_28628/05_2025/8evg_28628.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.078 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 32 5.16 5 C 8886 2.51 5 N 2827 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15577 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 9.57, per 1000 atoms: 0.61 Number of scatterers: 15577 At special positions: 0 Unit cell: (138.336, 125.664, 124.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 294 15.00 O 3538 8.00 N 2827 7.00 C 8886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 23 sheets defined 46.1% alpha, 18.2% beta 116 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.525A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.776A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.590A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.587A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.848A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.845A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.597A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.577A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.177A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.317A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.695A pdb=" N THR M 139 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR M 54 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR M 74 " --> pdb=" O TYR M 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.695A pdb=" N THR M 139 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 40 through 43 Processing sheet with id=AB5, first strand: chain 'M' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.683A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 211 through 212 removed outlier: 6.531A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 3.676A pdb=" N GLY N 71 " --> pdb=" O TRP N 58 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.191A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 163 through 164 removed outlier: 3.624A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.531A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.439A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 277 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 5.78 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1968 1.31 - 1.43: 6054 1.43 - 1.56: 7989 1.56 - 1.69: 408 1.69 - 1.82: 55 Bond restraints: 16474 Sorted by residual: bond pdb=" O3' DG I 117 " pdb=" P DG I 118 " ideal model delta sigma weight residual 1.607 1.339 0.268 1.50e-02 4.44e+03 3.19e+02 bond pdb=" O3' DG J 80 " pdb=" P DG J 81 " ideal model delta sigma weight residual 1.607 1.359 0.248 1.50e-02 4.44e+03 2.73e+02 bond pdb=" O3' DG I 85 " pdb=" P DA I 86 " ideal model delta sigma weight residual 1.607 1.364 0.243 1.50e-02 4.44e+03 2.62e+02 bond pdb=" O3' DC I 107 " pdb=" P DA I 108 " ideal model delta sigma weight residual 1.607 1.370 0.237 1.50e-02 4.44e+03 2.49e+02 bond pdb=" O3' DT I 35 " pdb=" P DG I 36 " ideal model delta sigma weight residual 1.607 1.376 0.231 1.50e-02 4.44e+03 2.38e+02 ... (remaining 16469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.87: 22934 5.87 - 11.74: 464 11.74 - 17.62: 101 17.62 - 23.49: 17 23.49 - 29.36: 5 Bond angle restraints: 23521 Sorted by residual: angle pdb=" O3' DC I 96 " pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 111.50 90.34 21.16 1.50e+00 4.44e-01 1.99e+02 angle pdb=" O3' DA J 82 " pdb=" C3' DA J 82 " pdb=" C2' DA J 82 " ideal model delta sigma weight residual 111.50 90.71 20.79 1.50e+00 4.44e-01 1.92e+02 angle pdb=" O3' DA J 97 " pdb=" C3' DA J 97 " pdb=" C2' DA J 97 " ideal model delta sigma weight residual 111.50 130.96 -19.46 1.50e+00 4.44e-01 1.68e+02 angle pdb=" C4' DT I 131 " pdb=" C3' DT I 131 " pdb=" O3' DT I 131 " ideal model delta sigma weight residual 110.00 129.08 -19.08 1.50e+00 4.44e-01 1.62e+02 angle pdb=" O3' DC J 19 " pdb=" C3' DC J 19 " pdb=" C2' DC J 19 " ideal model delta sigma weight residual 111.50 130.56 -19.06 1.50e+00 4.44e-01 1.62e+02 ... (remaining 23516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 7209 32.94 - 65.88: 1834 65.88 - 98.82: 116 98.82 - 131.76: 2 131.76 - 164.70: 4 Dihedral angle restraints: 9165 sinusoidal: 5645 harmonic: 3520 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 24.70 -164.70 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT I 131 " pdb=" C3' DT I 131 " pdb=" O3' DT I 131 " pdb=" P DT I 132 " ideal model delta sinusoidal sigma weight residual -140.00 24.49 -164.49 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 92 " pdb=" C3' DC I 92 " pdb=" O3' DC I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual 220.00 62.35 157.65 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 2394 0.209 - 0.418: 211 0.418 - 0.627: 34 0.627 - 0.836: 11 0.836 - 1.045: 2 Chirality restraints: 2652 Sorted by residual: chirality pdb=" C3' DG I 53 " pdb=" C4' DG I 53 " pdb=" O3' DG I 53 " pdb=" C2' DG I 53 " both_signs ideal model delta sigma weight residual False -2.66 -1.61 -1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" C3' DC I 92 " pdb=" C4' DC I 92 " pdb=" O3' DC I 92 " pdb=" C2' DC I 92 " both_signs ideal model delta sigma weight residual False -2.66 -1.68 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" P DT I 87 " pdb=" OP1 DT I 87 " pdb=" OP2 DT I 87 " pdb=" O5' DT I 87 " both_signs ideal model delta sigma weight residual True 2.35 -1.55 0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 2649 not shown) Planarity restraints: 1948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 68 " -0.119 2.00e-02 2.50e+03 6.09e-02 9.28e+01 pdb=" N1 DT J 68 " 0.098 2.00e-02 2.50e+03 pdb=" C2 DT J 68 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DT J 68 " 0.064 2.00e-02 2.50e+03 pdb=" N3 DT J 68 " -0.079 2.00e-02 2.50e+03 pdb=" C4 DT J 68 " -0.015 2.00e-02 2.50e+03 pdb=" O4 DT J 68 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DT J 68 " 0.045 2.00e-02 2.50e+03 pdb=" C7 DT J 68 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT J 68 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 98 " 0.117 2.00e-02 2.50e+03 5.78e-02 9.19e+01 pdb=" N9 DA I 98 " -0.123 2.00e-02 2.50e+03 pdb=" C8 DA I 98 " 0.029 2.00e-02 2.50e+03 pdb=" N7 DA I 98 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 98 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DA I 98 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 98 " 0.024 2.00e-02 2.50e+03 pdb=" N1 DA I 98 " 0.061 2.00e-02 2.50e+03 pdb=" C2 DA I 98 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA I 98 " -0.040 2.00e-02 2.50e+03 pdb=" C4 DA I 98 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 122 " 0.098 2.00e-02 2.50e+03 5.04e-02 7.61e+01 pdb=" N9 DG J 122 " -0.063 2.00e-02 2.50e+03 pdb=" C8 DG J 122 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 122 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DG J 122 " 0.034 2.00e-02 2.50e+03 pdb=" C6 DG J 122 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG J 122 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG J 122 " 0.050 2.00e-02 2.50e+03 pdb=" C2 DG J 122 " 0.012 2.00e-02 2.50e+03 pdb=" N2 DG J 122 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG J 122 " -0.104 2.00e-02 2.50e+03 pdb=" C4 DG J 122 " -0.026 2.00e-02 2.50e+03 ... (remaining 1945 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 27 2.42 - 3.04: 8939 3.04 - 3.66: 23614 3.66 - 4.28: 41684 4.28 - 4.90: 62662 Nonbonded interactions: 136926 Sorted by model distance: nonbonded pdb=" N2 DG I 109 " pdb=" O2 DC J 54 " model vdw 1.794 3.120 nonbonded pdb=" N2 DG I 25 " pdb=" O2 DC J 138 " model vdw 1.815 2.496 nonbonded pdb=" O2 DC I 134 " pdb=" N2 DG J 29 " model vdw 2.066 2.496 nonbonded pdb=" OD2 ASP M 95 " pdb=" OG SER M 98 " model vdw 2.219 3.040 nonbonded pdb=" N2 DG I 53 " pdb=" O2 DT J 111 " model vdw 2.227 3.120 ... (remaining 136921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 41.370 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.020 0.268 16478 Z= 1.096 Angle : 2.029 29.362 23529 Z= 1.164 Chirality : 0.131 1.045 2652 Planarity : 0.010 0.086 1948 Dihedral : 28.950 164.699 6897 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.29 % Allowed : 20.41 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1188 helix: 2.19 (0.22), residues: 543 sheet: -0.04 (0.35), residues: 226 loop : -0.74 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 69 HIS 0.004 0.001 HIS M 249 PHE 0.013 0.001 PHE D 67 TYR 0.024 0.001 TYR H 37 ARG 0.008 0.000 ARG N 219 Details of bonding type rmsd hydrogen bonds : bond 0.21737 ( 796) hydrogen bonds : angle 9.61473 ( 2028) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.37826 ( 8) covalent geometry : bond 0.02007 (16474) covalent geometry : angle 2.02965 (23521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.7907 (mtt) cc_final: 0.7703 (mtt) outliers start: 3 outliers final: 1 residues processed: 289 average time/residue: 1.7126 time to fit residues: 531.0136 Evaluate side-chains 191 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN D 46 HIS E 39 HIS E 108 ASN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 81 ASN N 25 GLN N 196 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.108074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.071538 restraints weight = 30845.900| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.10 r_work: 0.2953 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16478 Z= 0.191 Angle : 0.678 8.721 23529 Z= 0.391 Chirality : 0.041 0.212 2652 Planarity : 0.005 0.048 1948 Dihedral : 30.372 177.755 4574 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.01 % Allowed : 22.93 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1188 helix: 2.55 (0.22), residues: 544 sheet: 0.26 (0.35), residues: 226 loop : -0.74 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 132 HIS 0.008 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR N 117 ARG 0.006 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 796) hydrogen bonds : angle 3.38899 ( 2028) SS BOND : bond 0.00357 ( 4) SS BOND : angle 1.65883 ( 8) covalent geometry : bond 0.00433 (16474) covalent geometry : angle 0.67761 (23521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8315 (pt0) cc_final: 0.7883 (pm20) REVERT: B 44 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8366 (mttp) REVERT: C 90 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8627 (t70) REVERT: C 91 GLU cc_start: 0.8742 (tp30) cc_final: 0.8456 (tp30) REVERT: D 39 TYR cc_start: 0.8230 (t80) cc_final: 0.7432 (t80) REVERT: D 113 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8792 (ttpt) REVERT: E 42 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7536 (mmm-85) REVERT: E 90 MET cc_start: 0.8711 (mmm) cc_final: 0.8493 (tpp) REVERT: G 90 ASP cc_start: 0.8958 (t0) cc_final: 0.8573 (t0) REVERT: M 45 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7797 (tmtm) REVERT: M 84 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7977 (pt0) REVERT: M 251 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8329 (mm-30) REVERT: N 95 ASP cc_start: 0.8200 (t0) cc_final: 0.7869 (t0) REVERT: N 161 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8792 (tptp) REVERT: N 173 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8483 (tm) outliers start: 31 outliers final: 6 residues processed: 232 average time/residue: 1.5843 time to fit residues: 397.0960 Evaluate side-chains 194 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 123 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN D 46 HIS E 39 HIS E 55 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN M 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072287 restraints weight = 30565.847| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.09 r_work: 0.2973 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16478 Z= 0.147 Angle : 0.588 9.175 23529 Z= 0.344 Chirality : 0.036 0.167 2652 Planarity : 0.004 0.037 1948 Dihedral : 30.014 179.261 4573 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.62 % Allowed : 23.42 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1188 helix: 2.75 (0.22), residues: 545 sheet: 0.49 (0.35), residues: 226 loop : -0.73 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 199 HIS 0.005 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR G 57 ARG 0.007 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 796) hydrogen bonds : angle 3.17126 ( 2028) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.28336 ( 8) covalent geometry : bond 0.00321 (16474) covalent geometry : angle 0.58799 (23521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8397 (pt0) cc_final: 0.7961 (pm20) REVERT: A 90 MET cc_start: 0.8829 (mmm) cc_final: 0.8622 (mmp) REVERT: B 22 LEU cc_start: 0.8688 (mp) cc_final: 0.8444 (mt) REVERT: B 44 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8271 (mttp) REVERT: C 91 GLU cc_start: 0.8703 (tp30) cc_final: 0.8404 (tp30) REVERT: D 30 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.6544 (mmm-85) REVERT: D 39 TYR cc_start: 0.8194 (t80) cc_final: 0.7342 (t80) REVERT: D 68 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7987 (mt-10) REVERT: D 76 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7941 (mtm-85) REVERT: D 113 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8700 (ttpt) REVERT: E 39 HIS cc_start: 0.6639 (t70) cc_final: 0.6354 (t70) REVERT: E 54 TYR cc_start: 0.8944 (m-80) cc_final: 0.8722 (m-80) REVERT: E 90 MET cc_start: 0.8695 (mmm) cc_final: 0.8425 (tpp) REVERT: G 90 ASP cc_start: 0.8853 (t0) cc_final: 0.8383 (t0) REVERT: H 39 TYR cc_start: 0.8504 (t80) cc_final: 0.8264 (t80) REVERT: H 60 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8630 (m110) REVERT: M 34 VAL cc_start: 0.7810 (t) cc_final: 0.7600 (p) REVERT: N 84 GLU cc_start: 0.7901 (tp30) cc_final: 0.7580 (mp0) REVERT: N 95 ASP cc_start: 0.8376 (t70) cc_final: 0.7981 (t70) REVERT: N 104 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8075 (mm-30) REVERT: N 111 GLU cc_start: 0.9183 (pt0) cc_final: 0.8863 (pp20) REVERT: N 235 ASN cc_start: 0.8199 (p0) cc_final: 0.7894 (p0) REVERT: N 237 GLU cc_start: 0.7600 (pm20) cc_final: 0.7177 (pm20) outliers start: 27 outliers final: 5 residues processed: 214 average time/residue: 1.5545 time to fit residues: 360.7086 Evaluate side-chains 191 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 185 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 113 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 0.0770 chunk 18 optimal weight: 0.0980 chunk 109 optimal weight: 8.9990 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN D 64 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 81 ASN M 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069841 restraints weight = 30559.948| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.05 r_work: 0.2917 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16478 Z= 0.163 Angle : 0.578 9.773 23529 Z= 0.335 Chirality : 0.036 0.171 2652 Planarity : 0.004 0.038 1948 Dihedral : 29.856 178.067 4573 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.72 % Allowed : 23.81 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1188 helix: 2.77 (0.22), residues: 544 sheet: 0.58 (0.36), residues: 226 loop : -0.80 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 199 HIS 0.005 0.001 HIS A 39 PHE 0.008 0.001 PHE A 67 TYR 0.011 0.001 TYR G 57 ARG 0.007 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 796) hydrogen bonds : angle 3.19734 ( 2028) SS BOND : bond 0.00504 ( 4) SS BOND : angle 1.35597 ( 8) covalent geometry : bond 0.00367 (16474) covalent geometry : angle 0.57784 (23521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8558 (pt0) cc_final: 0.8116 (pm20) REVERT: B 22 LEU cc_start: 0.8651 (mp) cc_final: 0.8415 (mt) REVERT: B 44 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8293 (mttp) REVERT: C 13 LYS cc_start: 0.8277 (tptt) cc_final: 0.8010 (tptp) REVERT: C 91 GLU cc_start: 0.8852 (tp30) cc_final: 0.8377 (tp30) REVERT: D 39 TYR cc_start: 0.8168 (t80) cc_final: 0.7269 (t80) REVERT: D 68 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7994 (mt-10) REVERT: E 39 HIS cc_start: 0.6879 (t70) cc_final: 0.6392 (t70) REVERT: E 54 TYR cc_start: 0.8956 (m-80) cc_final: 0.8670 (m-80) REVERT: E 90 MET cc_start: 0.8782 (mmm) cc_final: 0.8436 (tpp) REVERT: F 44 LYS cc_start: 0.8696 (mtpp) cc_final: 0.8307 (mttp) REVERT: F 79 LYS cc_start: 0.8788 (ptpt) cc_final: 0.8211 (ptpp) REVERT: G 90 ASP cc_start: 0.8837 (t0) cc_final: 0.8401 (t0) REVERT: H 60 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8648 (m-40) REVERT: M 34 VAL cc_start: 0.8162 (t) cc_final: 0.7829 (p) REVERT: N 84 GLU cc_start: 0.8124 (tp30) cc_final: 0.7859 (mp0) REVERT: N 95 ASP cc_start: 0.8498 (t70) cc_final: 0.8109 (t70) REVERT: N 103 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.9112 (ttm) REVERT: N 104 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7968 (mm-30) REVERT: N 111 GLU cc_start: 0.9207 (pt0) cc_final: 0.8972 (pp20) outliers start: 28 outliers final: 10 residues processed: 210 average time/residue: 1.4314 time to fit residues: 326.7940 Evaluate side-chains 195 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 0.0170 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.108125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.071364 restraints weight = 31234.755| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.07 r_work: 0.2961 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16478 Z= 0.141 Angle : 0.554 8.820 23529 Z= 0.322 Chirality : 0.035 0.136 2652 Planarity : 0.004 0.037 1948 Dihedral : 29.519 179.147 4573 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.33 % Allowed : 24.30 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1188 helix: 2.86 (0.22), residues: 543 sheet: 0.61 (0.36), residues: 226 loop : -0.73 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.004 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.012 0.001 TYR H 37 ARG 0.012 0.000 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 796) hydrogen bonds : angle 3.09931 ( 2028) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.73233 ( 8) covalent geometry : bond 0.00308 (16474) covalent geometry : angle 0.55400 (23521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8554 (pt0) cc_final: 0.8100 (pm20) REVERT: B 44 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8221 (mttp) REVERT: C 90 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8541 (t70) REVERT: D 39 TYR cc_start: 0.8122 (t80) cc_final: 0.7179 (t80) REVERT: D 68 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7962 (mt-10) REVERT: D 76 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7872 (mtm-85) REVERT: E 39 HIS cc_start: 0.6929 (t70) cc_final: 0.6474 (t70) REVERT: E 54 TYR cc_start: 0.8944 (m-80) cc_final: 0.8686 (m-80) REVERT: E 90 MET cc_start: 0.8736 (mmm) cc_final: 0.8439 (tpp) REVERT: E 97 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: F 44 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8405 (mtmm) REVERT: G 13 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8811 (mmtt) REVERT: G 90 ASP cc_start: 0.8656 (t0) cc_final: 0.8171 (t0) REVERT: H 73 GLU cc_start: 0.9125 (tp30) cc_final: 0.8876 (tp30) REVERT: M 34 VAL cc_start: 0.8230 (t) cc_final: 0.7894 (p) REVERT: M 234 ASN cc_start: 0.7743 (p0) cc_final: 0.6830 (m-40) REVERT: N 32 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7837 (mm-30) REVERT: N 84 GLU cc_start: 0.8173 (tp30) cc_final: 0.7885 (mp0) REVERT: N 95 ASP cc_start: 0.8493 (t70) cc_final: 0.8094 (t70) REVERT: N 104 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8101 (tp30) REVERT: N 111 GLU cc_start: 0.9190 (pt0) cc_final: 0.8903 (pp20) outliers start: 24 outliers final: 12 residues processed: 208 average time/residue: 1.5218 time to fit residues: 343.2289 Evaluate side-chains 200 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS F 75 HIS G 73 ASN H 44 GLN N 196 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.063735 restraints weight = 30756.878| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.11 r_work: 0.2794 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 16478 Z= 0.380 Angle : 0.689 9.319 23529 Z= 0.391 Chirality : 0.044 0.166 2652 Planarity : 0.005 0.047 1948 Dihedral : 30.398 178.068 4573 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.21 % Allowed : 25.17 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1188 helix: 2.35 (0.22), residues: 542 sheet: 0.32 (0.35), residues: 226 loop : -1.01 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 132 HIS 0.006 0.002 HIS N 249 PHE 0.013 0.002 PHE E 67 TYR 0.019 0.002 TYR M 131 ARG 0.011 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.05352 ( 796) hydrogen bonds : angle 3.59852 ( 2028) SS BOND : bond 0.00776 ( 4) SS BOND : angle 1.65154 ( 8) covalent geometry : bond 0.00881 (16474) covalent geometry : angle 0.68867 (23521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8393 (mt) cc_final: 0.8097 (mp) REVERT: B 44 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8374 (mttp) REVERT: C 56 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: D 39 TYR cc_start: 0.8480 (t80) cc_final: 0.7709 (t80) REVERT: E 90 MET cc_start: 0.8855 (mmm) cc_final: 0.8556 (tpp) REVERT: E 97 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: F 44 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8540 (mtmm) REVERT: F 79 LYS cc_start: 0.8818 (ptpt) cc_final: 0.8274 (ptpp) REVERT: G 90 ASP cc_start: 0.8774 (t0) cc_final: 0.8338 (t0) REVERT: M 34 VAL cc_start: 0.8409 (t) cc_final: 0.8002 (p) REVERT: M 45 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8455 (tptt) REVERT: M 234 ASN cc_start: 0.7997 (p0) cc_final: 0.7426 (m-40) REVERT: N 95 ASP cc_start: 0.8521 (t70) cc_final: 0.8048 (t0) REVERT: N 104 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8005 (mm-30) REVERT: N 111 GLU cc_start: 0.9169 (pt0) cc_final: 0.8834 (pp20) REVERT: N 237 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7452 (pm20) outliers start: 33 outliers final: 12 residues processed: 203 average time/residue: 1.6251 time to fit residues: 357.1867 Evaluate side-chains 195 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 162 MET Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 135 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 61 GLN N 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.067834 restraints weight = 30680.795| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.04 r_work: 0.2874 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16478 Z= 0.160 Angle : 0.582 8.704 23529 Z= 0.336 Chirality : 0.036 0.141 2652 Planarity : 0.004 0.045 1948 Dihedral : 29.631 177.818 4573 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.65 % Allowed : 27.31 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1188 helix: 2.62 (0.22), residues: 543 sheet: 0.42 (0.36), residues: 224 loop : -0.87 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS A 39 PHE 0.010 0.001 PHE A 67 TYR 0.013 0.001 TYR H 37 ARG 0.013 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 796) hydrogen bonds : angle 3.28069 ( 2028) SS BOND : bond 0.00377 ( 4) SS BOND : angle 1.11833 ( 8) covalent geometry : bond 0.00361 (16474) covalent geometry : angle 0.58187 (23521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8328 (mttp) REVERT: C 91 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8550 (tp30) REVERT: D 39 TYR cc_start: 0.8188 (t80) cc_final: 0.7247 (t80) REVERT: D 68 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7994 (mt-10) REVERT: E 39 HIS cc_start: 0.7083 (t70) cc_final: 0.6629 (t70) REVERT: E 90 MET cc_start: 0.8820 (mmm) cc_final: 0.8581 (tpp) REVERT: E 97 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: F 79 LYS cc_start: 0.8760 (ptpt) cc_final: 0.8164 (ptpp) REVERT: G 90 ASP cc_start: 0.8610 (t0) cc_final: 0.8132 (t0) REVERT: H 60 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8625 (m110) REVERT: M 34 VAL cc_start: 0.8410 (t) cc_final: 0.8004 (p) REVERT: M 112 ASP cc_start: 0.8313 (t0) cc_final: 0.7810 (m-30) REVERT: M 219 ARG cc_start: 0.8690 (mtp180) cc_final: 0.8143 (mtp180) REVERT: M 234 ASN cc_start: 0.8066 (p0) cc_final: 0.7414 (m-40) REVERT: N 32 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7708 (mm-30) REVERT: N 95 ASP cc_start: 0.8531 (t70) cc_final: 0.8107 (t0) REVERT: N 104 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8243 (tp30) REVERT: N 111 GLU cc_start: 0.9147 (pt0) cc_final: 0.8818 (pp20) outliers start: 17 outliers final: 10 residues processed: 201 average time/residue: 1.5995 time to fit residues: 347.0399 Evaluate side-chains 193 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 65 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065013 restraints weight = 30395.200| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.02 r_work: 0.2819 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 16478 Z= 0.281 Angle : 0.636 9.316 23529 Z= 0.361 Chirality : 0.039 0.148 2652 Planarity : 0.005 0.043 1948 Dihedral : 29.959 177.993 4573 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.72 % Allowed : 26.04 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1188 helix: 2.47 (0.22), residues: 543 sheet: 0.28 (0.36), residues: 220 loop : -0.97 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 132 HIS 0.005 0.001 HIS N 249 PHE 0.010 0.002 PHE E 67 TYR 0.016 0.002 TYR H 37 ARG 0.012 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 796) hydrogen bonds : angle 3.41026 ( 2028) SS BOND : bond 0.00659 ( 4) SS BOND : angle 1.33153 ( 8) covalent geometry : bond 0.00653 (16474) covalent geometry : angle 0.63570 (23521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8505 (mp) cc_final: 0.8170 (mt) REVERT: B 44 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8331 (mttp) REVERT: C 56 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: C 91 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: D 39 TYR cc_start: 0.8325 (t80) cc_final: 0.7405 (t80) REVERT: D 68 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8011 (mt-10) REVERT: E 90 MET cc_start: 0.8820 (mmm) cc_final: 0.8522 (tpp) REVERT: E 97 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: E 115 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8872 (mtmm) REVERT: F 44 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8514 (mtmm) REVERT: F 79 LYS cc_start: 0.8751 (ptpt) cc_final: 0.8197 (ptpp) REVERT: G 90 ASP cc_start: 0.8694 (t0) cc_final: 0.8257 (t0) REVERT: H 60 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8717 (m-40) REVERT: M 34 VAL cc_start: 0.8512 (t) cc_final: 0.8113 (p) REVERT: M 45 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8455 (tptt) REVERT: M 109 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8329 (m) REVERT: M 112 ASP cc_start: 0.8342 (t0) cc_final: 0.7906 (m-30) REVERT: M 234 ASN cc_start: 0.8222 (p0) cc_final: 0.7501 (m-40) REVERT: N 95 ASP cc_start: 0.8532 (t70) cc_final: 0.8082 (t0) REVERT: N 104 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8090 (mm-30) REVERT: N 111 GLU cc_start: 0.9143 (pt0) cc_final: 0.8801 (pp20) outliers start: 28 outliers final: 15 residues processed: 199 average time/residue: 1.7174 time to fit residues: 372.0405 Evaluate side-chains 198 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 162 MET Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 225 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.066179 restraints weight = 30531.818| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.02 r_work: 0.2843 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16478 Z= 0.180 Angle : 0.608 9.822 23529 Z= 0.348 Chirality : 0.037 0.144 2652 Planarity : 0.005 0.050 1948 Dihedral : 29.904 178.107 4573 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.43 % Allowed : 26.43 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1188 helix: 2.55 (0.22), residues: 543 sheet: 0.33 (0.36), residues: 218 loop : -0.90 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 58 HIS 0.004 0.001 HIS M 249 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR H 37 ARG 0.013 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 796) hydrogen bonds : angle 3.34695 ( 2028) SS BOND : bond 0.00509 ( 4) SS BOND : angle 1.15170 ( 8) covalent geometry : bond 0.00410 (16474) covalent geometry : angle 0.60778 (23521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8483 (mp) cc_final: 0.8164 (mt) REVERT: B 44 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8307 (mttp) REVERT: C 56 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: C 90 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8517 (t70) REVERT: C 91 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8569 (tp30) REVERT: D 39 TYR cc_start: 0.8226 (t80) cc_final: 0.7315 (t80) REVERT: D 54 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8653 (mptt) REVERT: D 68 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7954 (mt-10) REVERT: D 76 ARG cc_start: 0.8244 (mtm180) cc_final: 0.8017 (mtm-85) REVERT: E 39 HIS cc_start: 0.7065 (t70) cc_final: 0.6721 (t70) REVERT: E 90 MET cc_start: 0.8806 (mmm) cc_final: 0.8518 (tpp) REVERT: E 97 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: E 115 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8866 (mtmm) REVERT: F 44 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8428 (mtmm) REVERT: F 79 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8165 (ptpp) REVERT: G 90 ASP cc_start: 0.8654 (t0) cc_final: 0.8200 (t0) REVERT: H 60 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8723 (m-40) REVERT: M 34 VAL cc_start: 0.8487 (t) cc_final: 0.8093 (p) REVERT: M 45 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8443 (tptt) REVERT: M 64 ARG cc_start: 0.8891 (ttm110) cc_final: 0.8637 (ttp80) REVERT: M 109 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8287 (m) REVERT: M 112 ASP cc_start: 0.8337 (t0) cc_final: 0.7945 (m-30) REVERT: M 234 ASN cc_start: 0.8188 (p0) cc_final: 0.7443 (m-40) REVERT: N 32 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7723 (mm-30) REVERT: N 95 ASP cc_start: 0.8520 (t70) cc_final: 0.8064 (t0) REVERT: N 104 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8086 (mm-30) REVERT: N 111 GLU cc_start: 0.9138 (pt0) cc_final: 0.8802 (pp20) outliers start: 25 outliers final: 16 residues processed: 199 average time/residue: 1.6470 time to fit residues: 353.2914 Evaluate side-chains 205 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 162 MET Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain M residue 225 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067412 restraints weight = 30687.193| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.02 r_work: 0.2877 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16478 Z= 0.156 Angle : 0.593 11.071 23529 Z= 0.339 Chirality : 0.036 0.159 2652 Planarity : 0.004 0.044 1948 Dihedral : 29.687 178.381 4573 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.04 % Allowed : 27.02 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1188 helix: 2.64 (0.22), residues: 543 sheet: 0.36 (0.36), residues: 218 loop : -0.85 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS M 249 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.014 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 796) hydrogen bonds : angle 3.27212 ( 2028) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.95807 ( 8) covalent geometry : bond 0.00351 (16474) covalent geometry : angle 0.59260 (23521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8488 (mp) cc_final: 0.8130 (mt) REVERT: B 44 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8350 (mttm) REVERT: C 56 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: C 91 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8546 (tp30) REVERT: D 39 TYR cc_start: 0.8186 (t80) cc_final: 0.7250 (t80) REVERT: D 54 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8656 (mptt) REVERT: D 68 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8006 (mt-10) REVERT: D 76 ARG cc_start: 0.8243 (mtm180) cc_final: 0.7816 (mtm-85) REVERT: E 39 HIS cc_start: 0.7061 (t70) cc_final: 0.6748 (t70) REVERT: E 90 MET cc_start: 0.8784 (mmm) cc_final: 0.8488 (tpp) REVERT: E 97 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: E 115 LYS cc_start: 0.9142 (mtpp) cc_final: 0.8865 (mtmm) REVERT: F 44 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8412 (mtmm) REVERT: F 79 LYS cc_start: 0.8739 (ptpt) cc_final: 0.8149 (ptpp) REVERT: G 90 ASP cc_start: 0.8597 (t0) cc_final: 0.8140 (t0) REVERT: H 60 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8606 (m110) REVERT: M 34 VAL cc_start: 0.8470 (t) cc_final: 0.8075 (p) REVERT: M 45 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8445 (tptp) REVERT: M 109 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8285 (m) REVERT: M 112 ASP cc_start: 0.8335 (t0) cc_final: 0.7956 (m-30) REVERT: M 234 ASN cc_start: 0.8207 (p0) cc_final: 0.7482 (m-40) REVERT: N 32 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7770 (mm-30) REVERT: N 95 ASP cc_start: 0.8527 (t70) cc_final: 0.8093 (t0) REVERT: N 104 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8253 (tp30) REVERT: N 111 GLU cc_start: 0.9126 (pt0) cc_final: 0.8815 (pp20) outliers start: 21 outliers final: 11 residues processed: 203 average time/residue: 1.6324 time to fit residues: 357.1102 Evaluate side-chains 193 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 225 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 130 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.105765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.068705 restraints weight = 30559.394| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.01 r_work: 0.2896 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16478 Z= 0.146 Angle : 0.583 12.065 23529 Z= 0.334 Chirality : 0.035 0.166 2652 Planarity : 0.004 0.040 1948 Dihedral : 29.528 178.487 4573 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.85 % Allowed : 27.02 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1188 helix: 2.71 (0.22), residues: 543 sheet: 0.41 (0.36), residues: 224 loop : -0.70 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.003 0.001 HIS A 39 PHE 0.010 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.014 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 796) hydrogen bonds : angle 3.21250 ( 2028) SS BOND : bond 0.00274 ( 4) SS BOND : angle 0.89501 ( 8) covalent geometry : bond 0.00325 (16474) covalent geometry : angle 0.58295 (23521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10791.07 seconds wall clock time: 186 minutes 4.95 seconds (11164.95 seconds total)