Starting phenix.real_space_refine on Fri Jun 13 16:35:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evg_28628/06_2025/8evg_28628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evg_28628/06_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_28628/06_2025/8evg_28628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evg_28628/06_2025/8evg_28628.map" model { file = "/net/cci-nas-00/data/ceres_data/8evg_28628/06_2025/8evg_28628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evg_28628/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.08, per 1000 atoms: 0.58 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: 3.39 Conformation dependent library (CDL) restraints added in 1.3 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: 6.86 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: 6.12 Time building geometry restraints manager: 4.15 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.420 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.680 ------------------------------------------------------------------------------- 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 : 1.215 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: 1.6916 time to fit residues: 524.6236 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 : 1.234 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.071534 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: 0.8295 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 : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8314 (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: 0.8988 (OUTLIER) cc_final: 0.8629 (t70) REVERT: C 91 GLU cc_start: 0.8742 (tp30) cc_final: 0.8456 (tp30) REVERT: D 39 TYR cc_start: 0.8229 (t80) cc_final: 0.7432 (t80) REVERT: D 113 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8795 (ttpt) REVERT: E 42 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7533 (mmm-85) REVERT: E 90 MET cc_start: 0.8712 (mmm) cc_final: 0.8495 (tpp) REVERT: G 90 ASP cc_start: 0.8960 (t0) cc_final: 0.8575 (t0) REVERT: M 45 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7795 (tmtm) REVERT: M 84 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7976 (pt0) REVERT: M 251 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8328 (mm-30) REVERT: N 95 ASP cc_start: 0.8197 (t0) cc_final: 0.7865 (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: 1.6496 time to fit residues: 413.1663 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 : 1.299 ------------------------------------------------------------------------------- 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: 0.6980 chunk 137 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 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: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 D 64 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.106288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069325 restraints weight = 30322.433| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.07 r_work: 0.2916 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16478 Z= 0.179 Angle : 0.607 9.103 23529 Z= 0.353 Chirality : 0.038 0.166 2652 Planarity : 0.004 0.038 1948 Dihedral : 30.180 179.710 4573 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.11 % Allowed : 22.74 % Favored : 74.15 % 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: 1.60 (0.25), residues: 1188 helix: 2.65 (0.22), residues: 544 sheet: 0.48 (0.36), residues: 226 loop : -0.79 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 199 HIS 0.006 0.001 HIS A 39 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR G 57 ARG 0.006 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 796) hydrogen bonds : angle 3.28404 ( 2028) SS BOND : bond 0.00374 ( 4) SS BOND : angle 1.57802 ( 8) covalent geometry : bond 0.00404 (16474) covalent geometry : angle 0.60690 (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 233 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8472 (pt0) cc_final: 0.7988 (pm20) REVERT: A 90 MET cc_start: 0.8818 (mmm) cc_final: 0.8572 (mmp) REVERT: B 22 LEU cc_start: 0.8696 (mp) cc_final: 0.8441 (mt) REVERT: B 44 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8243 (mttp) REVERT: B 84 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8662 (mmm) REVERT: C 90 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8550 (t70) REVERT: C 91 GLU cc_start: 0.8815 (tp30) cc_final: 0.8301 (tp30) REVERT: D 30 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.6648 (mmm-85) REVERT: D 39 TYR cc_start: 0.8172 (t80) cc_final: 0.7292 (t80) REVERT: D 68 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7906 (mt-10) REVERT: E 39 HIS cc_start: 0.6714 (t70) cc_final: 0.6274 (t70) REVERT: E 54 TYR cc_start: 0.8889 (m-80) cc_final: 0.8625 (m-80) REVERT: E 90 MET cc_start: 0.8740 (mmm) cc_final: 0.8435 (tpp) REVERT: G 13 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8821 (mmtt) REVERT: G 90 ASP cc_start: 0.8866 (t0) cc_final: 0.8399 (t0) REVERT: H 39 TYR cc_start: 0.8542 (t80) cc_final: 0.8277 (t80) REVERT: H 60 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8630 (m110) REVERT: M 34 VAL cc_start: 0.7869 (t) cc_final: 0.7617 (p) REVERT: N 84 GLU cc_start: 0.8014 (tp30) cc_final: 0.7689 (mp0) REVERT: N 95 ASP cc_start: 0.8383 (t70) cc_final: 0.7961 (t70) REVERT: N 104 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7969 (mm-30) REVERT: N 111 GLU cc_start: 0.9228 (pt0) cc_final: 0.8897 (pp20) REVERT: N 237 GLU cc_start: 0.7695 (pm20) cc_final: 0.7449 (pm20) outliers start: 32 outliers final: 9 residues processed: 217 average time/residue: 1.5702 time to fit residues: 368.7632 Evaluate side-chains 193 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET 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 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 39 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 163 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN F 75 HIS G 73 ASN N 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.102538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.065081 restraints weight = 30298.048| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.05 r_work: 0.2832 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16478 Z= 0.286 Angle : 0.651 9.277 23529 Z= 0.374 Chirality : 0.041 0.165 2652 Planarity : 0.005 0.051 1948 Dihedral : 30.416 178.360 4573 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.11 % Allowed : 23.32 % Favored : 73.57 % 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: 1.32 (0.25), residues: 1188 helix: 2.47 (0.22), residues: 542 sheet: 0.45 (0.36), residues: 226 loop : -1.06 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 132 HIS 0.005 0.001 HIS N 249 PHE 0.009 0.002 PHE F 61 TYR 0.015 0.002 TYR M 131 ARG 0.006 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 796) hydrogen bonds : angle 3.51742 ( 2028) SS BOND : bond 0.01280 ( 4) SS BOND : angle 1.94551 ( 8) covalent geometry : bond 0.00664 (16474) covalent geometry : angle 0.64975 (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 218 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8674 (mp) cc_final: 0.8394 (mt) REVERT: B 44 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8286 (mttm) REVERT: B 84 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8724 (tpt) REVERT: C 13 LYS cc_start: 0.8458 (tptt) cc_final: 0.8074 (tptp) REVERT: C 91 GLU cc_start: 0.8917 (tp30) cc_final: 0.8172 (tp30) REVERT: D 39 TYR cc_start: 0.8285 (t80) cc_final: 0.7404 (t80) REVERT: D 68 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7933 (mt-10) REVERT: D 105 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8418 (tttp) REVERT: E 54 TYR cc_start: 0.8914 (m-80) cc_final: 0.8711 (m-80) REVERT: E 90 MET cc_start: 0.8851 (mmm) cc_final: 0.8564 (tpp) REVERT: F 44 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8447 (mtmm) REVERT: G 90 ASP cc_start: 0.8704 (t0) cc_final: 0.8255 (t0) REVERT: M 34 VAL cc_start: 0.8272 (t) cc_final: 0.7931 (p) REVERT: M 103 MET cc_start: 0.9224 (ttp) cc_final: 0.9021 (ttm) REVERT: M 112 ASP cc_start: 0.8273 (t0) cc_final: 0.7885 (m-30) REVERT: M 161 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8884 (tppp) REVERT: N 95 ASP cc_start: 0.8579 (t70) cc_final: 0.8154 (t0) REVERT: N 104 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8007 (mm-30) REVERT: N 111 GLU cc_start: 0.9208 (pt0) cc_final: 0.8817 (pp20) REVERT: N 162 MET cc_start: 0.8484 (mmm) cc_final: 0.7804 (mmm) REVERT: N 172 SER cc_start: 0.8273 (t) cc_final: 0.7987 (m) REVERT: N 240 ASP cc_start: 0.8993 (m-30) cc_final: 0.8600 (m-30) outliers start: 32 outliers final: 13 residues processed: 204 average time/residue: 1.6045 time to fit residues: 353.9766 Evaluate side-chains 192 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 105 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 M residue 33 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 161 LYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER 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: 5.9990 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068661 restraints weight = 31010.350| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.07 r_work: 0.2911 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4688 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= 0.150 Angle : 0.572 8.585 23529 Z= 0.332 Chirality : 0.035 0.140 2652 Planarity : 0.004 0.038 1948 Dihedral : 29.756 179.429 4573 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.53 % Allowed : 23.71 % Favored : 73.76 % 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: 1.58 (0.25), residues: 1188 helix: 2.71 (0.22), residues: 543 sheet: 0.49 (0.35), residues: 226 loop : -0.93 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 69 HIS 0.004 0.001 HIS A 39 PHE 0.010 0.001 PHE A 67 TYR 0.012 0.001 TYR H 37 ARG 0.010 0.000 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 796) hydrogen bonds : angle 3.23232 ( 2028) SS BOND : bond 0.00365 ( 4) SS BOND : angle 1.04690 ( 8) covalent geometry : bond 0.00333 (16474) covalent geometry : angle 0.57224 (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 222 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8630 (mp) cc_final: 0.8021 (mt) REVERT: B 23 ARG cc_start: 0.8270 (tpp80) cc_final: 0.8047 (tpp80) REVERT: B 44 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8232 (mttm) REVERT: C 13 LYS cc_start: 0.8411 (tptt) cc_final: 0.8094 (tptp) REVERT: C 90 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8596 (t70) REVERT: D 68 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7959 (mt-10) REVERT: E 39 HIS cc_start: 0.6903 (t70) cc_final: 0.6401 (t70) REVERT: E 54 TYR cc_start: 0.8933 (m-80) cc_final: 0.8646 (m-80) REVERT: E 90 MET cc_start: 0.8788 (mmm) cc_final: 0.8514 (tpp) REVERT: F 44 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8414 (mtmm) REVERT: G 90 ASP cc_start: 0.8650 (t0) cc_final: 0.8167 (t0) REVERT: H 60 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8541 (m110) REVERT: M 34 VAL cc_start: 0.8307 (t) cc_final: 0.7970 (p) REVERT: M 45 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8286 (tptt) REVERT: M 95 ASP cc_start: 0.7833 (t0) cc_final: 0.7626 (t70) REVERT: M 112 ASP cc_start: 0.8506 (t0) cc_final: 0.7959 (m-30) REVERT: N 32 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7878 (mm-30) REVERT: N 84 GLU cc_start: 0.8256 (tp30) cc_final: 0.8042 (mt-10) REVERT: N 95 ASP cc_start: 0.8485 (t70) cc_final: 0.8065 (t0) REVERT: N 104 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8173 (tp30) REVERT: N 111 GLU cc_start: 0.9209 (pt0) cc_final: 0.8908 (pp20) outliers start: 26 outliers final: 9 residues processed: 210 average time/residue: 1.5558 time to fit residues: 354.2028 Evaluate side-chains 190 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP 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 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 59 VAL 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 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: 9.9990 chunk 17 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN H 81 ASN N 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064464 restraints weight = 30727.422| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.07 r_work: 0.2801 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 16478 Z= 0.305 Angle : 0.645 8.771 23529 Z= 0.369 Chirality : 0.040 0.156 2652 Planarity : 0.004 0.038 1948 Dihedral : 30.245 178.549 4573 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.62 % Allowed : 24.49 % Favored : 72.89 % 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: 1.29 (0.25), residues: 1188 helix: 2.48 (0.22), residues: 543 sheet: 0.28 (0.35), residues: 220 loop : -1.03 (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 0.007 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 796) hydrogen bonds : angle 3.46212 ( 2028) SS BOND : bond 0.00681 ( 4) SS BOND : angle 1.40865 ( 8) covalent geometry : bond 0.00712 (16474) covalent geometry : angle 0.64453 (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 203 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8656 (mp) cc_final: 0.7983 (mt) REVERT: B 23 ARG cc_start: 0.8311 (tpp80) cc_final: 0.8103 (tpp80) REVERT: B 44 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8331 (mttp) REVERT: C 13 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8151 (tptp) REVERT: C 90 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8607 (t70) REVERT: C 91 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8629 (tp30) REVERT: D 39 TYR cc_start: 0.8371 (t80) cc_final: 0.7502 (t80) REVERT: D 68 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7983 (mt-10) REVERT: E 39 HIS cc_start: 0.6929 (t70) cc_final: 0.6688 (t70) REVERT: E 90 MET cc_start: 0.8850 (mmm) cc_final: 0.8565 (tpp) REVERT: E 97 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: E 115 LYS cc_start: 0.9171 (mtpp) cc_final: 0.8880 (mtmm) REVERT: F 44 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8530 (mtmm) REVERT: G 90 ASP cc_start: 0.8722 (t0) cc_final: 0.8269 (t0) REVERT: H 60 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8753 (m-40) REVERT: M 34 VAL cc_start: 0.8482 (t) cc_final: 0.8084 (p) REVERT: M 45 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8439 (tptt) REVERT: M 95 ASP cc_start: 0.7936 (t0) cc_final: 0.7636 (t70) REVERT: M 112 ASP cc_start: 0.8371 (t0) cc_final: 0.8076 (m-30) REVERT: N 95 ASP cc_start: 0.8546 (t70) cc_final: 0.8074 (t0) REVERT: N 104 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8020 (mm-30) REVERT: N 111 GLU cc_start: 0.9150 (pt0) cc_final: 0.8795 (pp20) outliers start: 27 outliers final: 12 residues processed: 192 average time/residue: 1.6866 time to fit residues: 348.8267 Evaluate side-chains 190 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 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 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 59 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 214 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 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 = 0.3684 r_free = 0.3684 target = 0.103616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066198 restraints weight = 30745.385| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.04 r_work: 0.2840 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4817 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= 0.188 Angle : 0.600 9.439 23529 Z= 0.345 Chirality : 0.037 0.144 2652 Planarity : 0.004 0.041 1948 Dihedral : 30.057 178.597 4573 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.14 % Allowed : 25.07 % Favored : 72.79 % 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: 1.37 (0.25), residues: 1188 helix: 2.56 (0.22), residues: 543 sheet: 0.27 (0.35), residues: 220 loop : -0.96 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 132 HIS 0.005 0.001 HIS M 249 PHE 0.009 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.013 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 796) hydrogen bonds : angle 3.34206 ( 2028) SS BOND : bond 0.00476 ( 4) SS BOND : angle 1.00122 ( 8) covalent geometry : bond 0.00429 (16474) covalent geometry : angle 0.60004 (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 204 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 2.151 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8670 (mp) cc_final: 0.8042 (mt) REVERT: B 44 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8367 (mttm) REVERT: C 90 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8584 (t70) REVERT: C 91 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8633 (tp30) REVERT: D 39 TYR cc_start: 0.8306 (t80) cc_final: 0.7424 (t80) REVERT: D 68 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7949 (mt-10) REVERT: E 39 HIS cc_start: 0.6969 (t70) cc_final: 0.6631 (t70) REVERT: E 90 MET cc_start: 0.8826 (mmm) cc_final: 0.8545 (tpp) REVERT: E 97 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: E 115 LYS cc_start: 0.9156 (mtpp) cc_final: 0.8871 (mtmm) REVERT: F 44 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8530 (mtmm) REVERT: G 90 ASP cc_start: 0.8688 (t0) cc_final: 0.8218 (t0) REVERT: H 60 ASN cc_start: 0.9023 (OUTLIER) cc_final: 0.8738 (m-40) REVERT: M 34 VAL cc_start: 0.8433 (t) cc_final: 0.8065 (p) REVERT: M 45 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8482 (tptt) REVERT: M 95 ASP cc_start: 0.7944 (t0) cc_final: 0.7645 (t70) REVERT: M 112 ASP cc_start: 0.8299 (t0) cc_final: 0.8067 (m-30) REVERT: N 32 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7671 (mm-30) REVERT: N 95 ASP cc_start: 0.8567 (t70) cc_final: 0.8131 (t0) REVERT: N 104 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8043 (mm-30) REVERT: N 111 GLU cc_start: 0.9132 (pt0) cc_final: 0.8808 (pp20) outliers start: 22 outliers final: 12 residues processed: 195 average time/residue: 1.9913 time to fit residues: 419.1738 Evaluate side-chains 187 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU 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 39 SER Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 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 = 0.3670 r_free = 0.3670 target = 0.102849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065461 restraints weight = 30283.115| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.02 r_work: 0.2827 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16478 Z= 0.234 Angle : 0.617 9.275 23529 Z= 0.353 Chirality : 0.038 0.146 2652 Planarity : 0.004 0.037 1948 Dihedral : 29.990 178.223 4573 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 25.17 % Favored : 71.91 % 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: 1.32 (0.25), residues: 1188 helix: 2.51 (0.22), residues: 543 sheet: 0.26 (0.35), residues: 220 loop : -0.99 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 132 HIS 0.006 0.001 HIS M 249 PHE 0.009 0.001 PHE A 67 TYR 0.016 0.001 TYR H 37 ARG 0.008 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 796) hydrogen bonds : angle 3.37576 ( 2028) SS BOND : bond 0.00561 ( 4) SS BOND : angle 1.32126 ( 8) covalent geometry : bond 0.00542 (16474) covalent geometry : angle 0.61634 (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 212 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8460 (mp) cc_final: 0.8248 (mt) REVERT: B 44 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8391 (mttp) REVERT: C 90 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8604 (t70) REVERT: C 91 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8484 (tp30) REVERT: D 39 TYR cc_start: 0.8368 (t80) cc_final: 0.7460 (t80) REVERT: D 46 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.6298 (m90) REVERT: D 68 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7961 (mt-10) REVERT: E 39 HIS cc_start: 0.6903 (t70) cc_final: 0.6663 (t70) REVERT: E 90 MET cc_start: 0.8840 (mmm) cc_final: 0.8552 (tpp) REVERT: E 97 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: E 115 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8898 (mtmm) REVERT: F 44 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8544 (mtmm) REVERT: G 90 ASP cc_start: 0.8679 (t0) cc_final: 0.8224 (t0) REVERT: H 60 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8745 (m-40) REVERT: M 34 VAL cc_start: 0.8507 (t) cc_final: 0.8091 (p) REVERT: M 45 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8500 (tptp) REVERT: M 95 ASP cc_start: 0.8020 (t0) cc_final: 0.7711 (t70) REVERT: M 176 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8238 (ttm110) REVERT: M 219 ARG cc_start: 0.8706 (mtp180) cc_final: 0.8022 (mtm110) REVERT: M 234 ASN cc_start: 0.8066 (p0) cc_final: 0.7516 (m-40) REVERT: N 95 ASP cc_start: 0.8579 (t70) cc_final: 0.8132 (t0) REVERT: N 104 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8121 (mm-30) REVERT: N 111 GLU cc_start: 0.9108 (pt0) cc_final: 0.8795 (pp20) outliers start: 30 outliers final: 14 residues processed: 203 average time/residue: 1.7073 time to fit residues: 377.1340 Evaluate side-chains 197 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 ASP 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 45 LYS Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 173 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 134 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 = 0.3695 r_free = 0.3695 target = 0.104482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067098 restraints weight = 30528.378| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.08 r_work: 0.2869 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5026 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= 0.153 Angle : 0.589 9.802 23529 Z= 0.338 Chirality : 0.036 0.148 2652 Planarity : 0.004 0.044 1948 Dihedral : 29.786 178.363 4573 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.94 % Allowed : 26.43 % 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: 1.48 (0.25), residues: 1188 helix: 2.66 (0.22), residues: 543 sheet: 0.30 (0.35), residues: 220 loop : -0.91 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.004 0.001 HIS M 249 PHE 0.011 0.001 PHE A 67 TYR 0.015 0.001 TYR H 37 ARG 0.009 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 796) hydrogen bonds : angle 3.27962 ( 2028) SS BOND : bond 0.00327 ( 4) SS BOND : angle 1.02043 ( 8) covalent geometry : bond 0.00340 (16474) covalent geometry : angle 0.58835 (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 203 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8383 (mp) cc_final: 0.8161 (mt) REVERT: B 44 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8282 (mttm) REVERT: C 91 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: D 39 TYR cc_start: 0.8087 (t80) cc_final: 0.7189 (t80) REVERT: D 46 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.6234 (m90) REVERT: D 68 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7921 (mt-10) REVERT: E 39 HIS cc_start: 0.6812 (t70) cc_final: 0.6396 (t70) REVERT: E 90 MET cc_start: 0.8740 (mmm) cc_final: 0.8438 (tpp) REVERT: E 97 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: E 115 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8830 (mtmm) REVERT: F 44 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8455 (mtmm) REVERT: G 90 ASP cc_start: 0.8544 (t0) cc_final: 0.8082 (t0) REVERT: H 60 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8525 (m110) REVERT: M 34 VAL cc_start: 0.8477 (t) cc_final: 0.8074 (p) REVERT: M 45 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8393 (tptp) REVERT: M 64 ARG cc_start: 0.8795 (ttm110) cc_final: 0.8116 (tmm160) REVERT: M 95 ASP cc_start: 0.7934 (t0) cc_final: 0.7602 (t70) REVERT: M 112 ASP cc_start: 0.7683 (m-30) cc_final: 0.7276 (m-30) REVERT: M 176 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8378 (ttm110) REVERT: M 234 ASN cc_start: 0.7972 (p0) cc_final: 0.7558 (m-40) REVERT: N 32 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7738 (mm-30) REVERT: N 95 ASP cc_start: 0.8450 (t70) cc_final: 0.7991 (t0) REVERT: N 104 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8228 (tp30) REVERT: N 111 GLU cc_start: 0.9123 (pt0) cc_final: 0.8808 (pp20) REVERT: N 237 GLU cc_start: 0.7700 (pm20) cc_final: 0.7253 (mp0) outliers start: 20 outliers final: 12 residues processed: 195 average time/residue: 1.7002 time to fit residues: 358.3516 Evaluate side-chains 194 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 24 ASP 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 39 SER Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 59 VAL 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 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 123 optimal weight: 0.0270 chunk 135 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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** M 57 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 = 0.3709 r_free = 0.3709 target = 0.105315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068335 restraints weight = 30732.822| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.02 r_work: 0.2895 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16478 Z= 0.143 Angle : 0.582 11.134 23529 Z= 0.334 Chirality : 0.035 0.143 2652 Planarity : 0.004 0.042 1948 Dihedral : 29.663 178.430 4573 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.46 % Allowed : 27.02 % Favored : 71.53 % 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: 1.58 (0.25), residues: 1188 helix: 2.72 (0.22), residues: 543 sheet: 0.34 (0.36), residues: 220 loop : -0.83 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.004 0.001 HIS M 249 PHE 0.010 0.001 PHE A 67 TYR 0.014 0.001 TYR H 37 ARG 0.012 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 796) hydrogen bonds : angle 3.22085 ( 2028) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.91825 ( 8) covalent geometry : bond 0.00315 (16474) covalent geometry : angle 0.58161 (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 201 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8697 (pt0) cc_final: 0.8181 (pm20) REVERT: B 44 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8291 (mttm) REVERT: C 91 GLU cc_start: 0.8879 (tp30) cc_final: 0.8579 (tp30) REVERT: D 68 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7971 (mt-10) REVERT: D 76 ARG cc_start: 0.8239 (mtm180) cc_final: 0.7805 (mtm-85) REVERT: E 39 HIS cc_start: 0.6908 (t70) cc_final: 0.6496 (t70) REVERT: E 90 MET cc_start: 0.8748 (mmm) cc_final: 0.8483 (tpp) REVERT: E 97 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: E 115 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8871 (mtpp) REVERT: F 44 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8380 (mttm) REVERT: G 90 ASP cc_start: 0.8519 (t0) cc_final: 0.8159 (t0) REVERT: H 60 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8555 (m110) REVERT: M 34 VAL cc_start: 0.8443 (t) cc_final: 0.8053 (p) REVERT: M 45 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8449 (tptp) REVERT: M 64 ARG cc_start: 0.8779 (ttm110) cc_final: 0.8111 (tmm160) REVERT: M 95 ASP cc_start: 0.7980 (t0) cc_final: 0.7672 (t70) REVERT: M 112 ASP cc_start: 0.7863 (m-30) cc_final: 0.7440 (m-30) REVERT: M 176 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8335 (ttm110) REVERT: M 219 ARG cc_start: 0.8679 (mtp180) cc_final: 0.7965 (ttp80) REVERT: N 32 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7852 (mm-30) REVERT: N 95 ASP cc_start: 0.8510 (t70) cc_final: 0.8077 (t0) REVERT: N 104 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8209 (tp30) REVERT: N 111 GLU cc_start: 0.9105 (pt0) cc_final: 0.8827 (pp20) REVERT: N 112 ASP cc_start: 0.8007 (m-30) cc_final: 0.7750 (m-30) REVERT: N 237 GLU cc_start: 0.7792 (pm20) cc_final: 0.7359 (mp0) outliers start: 15 outliers final: 10 residues processed: 198 average time/residue: 2.3161 time to fit residues: 496.4165 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 : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 97 GLU 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 45 LYS Chi-restraints excluded: chain M residue 59 VAL 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 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** H 44 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 = 0.3710 r_free = 0.3710 target = 0.105458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068218 restraints weight = 30599.847| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.08 r_work: 0.2896 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5125 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= 0.153 Angle : 0.586 12.075 23529 Z= 0.334 Chirality : 0.035 0.135 2652 Planarity : 0.004 0.039 1948 Dihedral : 29.609 178.412 4573 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.65 % Allowed : 27.02 % Favored : 71.33 % 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: 1.60 (0.25), residues: 1188 helix: 2.70 (0.22), residues: 543 sheet: 0.40 (0.36), residues: 220 loop : -0.79 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 69 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 0.011 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 796) hydrogen bonds : angle 3.22557 ( 2028) SS BOND : bond 0.00305 ( 4) SS BOND : angle 0.98379 ( 8) covalent geometry : bond 0.00344 (16474) covalent geometry : angle 0.58534 (23521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11598.05 seconds wall clock time: 202 minutes 28.75 seconds (12148.75 seconds total)