Starting phenix.real_space_refine on Fri Jun 13 15:57:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8syp_40889/06_2025/8syp_40889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8syp_40889/06_2025/8syp_40889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8syp_40889/06_2025/8syp_40889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8syp_40889/06_2025/8syp_40889.map" model { file = "/net/cci-nas-00/data/ceres_data/8syp_40889/06_2025/8syp_40889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8syp_40889/06_2025/8syp_40889.cif" } resolution = 2.6 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= -0.000 sd= 0.068 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 8814 2.51 5 N 2809 2.21 5 O 3523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 15472 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: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 8.50, per 1000 atoms: 0.55 Number of scatterers: 15472 At special positions: 0 Unit cell: (141.504, 125.664, 126.72, 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 3523 8.00 N 2809 7.00 C 8814 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: 3.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 22 sheets defined 47.2% alpha, 19.3% beta 134 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 7.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.918A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.780A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.901A 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 45 through 73 removed outlier: 4.405A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 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: 3.793A 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 77 removed outlier: 3.751A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.689A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.859A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.783A 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 45 through 73 removed outlier: 4.348A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 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: 3.729A 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 84 through 87 removed outlier: 4.004A pdb=" N LYS M 87 " --> pdb=" O GLU M 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 84 through 87' Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.877A pdb=" N SER M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.577A pdb=" N ASP M 240 " --> pdb=" O GLU M 237 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 237 through 241' 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 84 through 87 removed outlier: 3.966A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.927A 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: 6.666A 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: 6.524A 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: 7.216A 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 83 through 84 removed outlier: 6.903A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.212A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.513A pdb=" N GLY M 71 " --> pdb=" O TRP M 58 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS M 60 " --> pdb=" O TRP M 69 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP M 69 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR M 62 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU M 67 " --> pdb=" O THR M 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 32 through 34 removed outlier: 4.077A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.519A pdb=" N VAL M 40 " --> pdb=" O LEU M 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 163 through 164 removed outlier: 3.637A pdb=" N VAL M 177 " --> pdb=" O ILE M 233 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE M 229 " --> pdb=" O CYS M 181 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.665A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.766A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY N 71 " --> pdb=" O TRP N 58 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.959A 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: 6.766A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 removed outlier: 3.513A pdb=" N MET N 42 " --> pdb=" O MET N 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 163 through 164 Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.757A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 662 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3177 1.33 - 1.46: 5535 1.46 - 1.58: 7031 1.58 - 1.70: 572 1.70 - 1.83: 52 Bond restraints: 16367 Sorted by residual: bond pdb=" O3' DT J 91 " pdb=" P DT J 92 " ideal model delta sigma weight residual 1.607 1.386 0.221 1.50e-02 4.44e+03 2.18e+02 bond pdb=" O3' DT J 92 " pdb=" P DG J 93 " ideal model delta sigma weight residual 1.607 1.392 0.215 1.50e-02 4.44e+03 2.05e+02 bond pdb=" O3' DG I 75 " pdb=" P DA I 76 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.50e-02 4.44e+03 5.95e+01 bond pdb=" O3' DA I 72 " pdb=" P DT I 73 " ideal model delta sigma weight residual 1.607 1.517 0.090 1.50e-02 4.44e+03 3.61e+01 bond pdb=" O3' DT I 66 " pdb=" P DT I 67 " ideal model delta sigma weight residual 1.607 1.535 0.072 1.50e-02 4.44e+03 2.28e+01 ... (remaining 16362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.76: 23308 5.76 - 11.52: 59 11.52 - 17.29: 3 17.29 - 23.05: 3 23.05 - 28.81: 3 Bond angle restraints: 23376 Sorted by residual: angle pdb=" C3' DT J 92 " pdb=" O3' DT J 92 " pdb=" P DG J 93 " ideal model delta sigma weight residual 120.20 91.39 28.81 1.50e+00 4.44e-01 3.69e+02 angle pdb=" C3' DT J 91 " pdb=" O3' DT J 91 " pdb=" P DT J 92 " ideal model delta sigma weight residual 120.20 147.08 -26.88 1.50e+00 4.44e-01 3.21e+02 angle pdb=" O3' DT J 92 " pdb=" P DG J 93 " pdb=" O5' DG J 93 " ideal model delta sigma weight residual 104.00 77.82 26.18 1.50e+00 4.44e-01 3.05e+02 angle pdb=" O3' DT J 91 " pdb=" P DT J 92 " pdb=" O5' DT J 92 " ideal model delta sigma weight residual 104.00 125.36 -21.36 1.50e+00 4.44e-01 2.03e+02 angle pdb=" O3' DT J 92 " pdb=" P DG J 93 " pdb=" OP2 DG J 93 " ideal model delta sigma weight residual 108.00 130.70 -22.70 3.00e+00 1.11e-01 5.72e+01 ... (remaining 23371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7439 35.46 - 70.92: 1625 70.92 - 106.37: 23 106.37 - 141.83: 1 141.83 - 177.29: 4 Dihedral angle restraints: 9092 sinusoidal: 5611 harmonic: 3481 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 37.29 -177.29 1 3.50e+01 8.16e-04 1.57e+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 -140.00 36.59 -176.59 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 53 " pdb=" C3' DG I 53 " pdb=" O3' DG I 53 " pdb=" P DC I 54 " ideal model delta sinusoidal sigma weight residual -140.00 34.03 -174.03 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 9089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2300 0.069 - 0.138: 290 0.138 - 0.207: 34 0.207 - 0.277: 8 0.277 - 0.346: 1 Chirality restraints: 2633 Sorted by residual: chirality pdb=" P DA I 76 " pdb=" OP1 DA I 76 " pdb=" OP2 DA I 76 " pdb=" O5' DA I 76 " both_signs ideal model delta sigma weight residual True 2.35 -2.00 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" P DA I 72 " pdb=" OP1 DA I 72 " pdb=" OP2 DA I 72 " pdb=" O5' DA I 72 " both_signs ideal model delta sigma weight residual True 2.35 -2.10 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2630 not shown) Planarity restraints: 1931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 62 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO N 63 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO N 63 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO N 63 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 111 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C GLU N 111 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU N 111 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP N 112 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASP F 24 " -0.059 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.019 2.00e-02 2.50e+03 ... (remaining 1928 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3382 2.80 - 3.32: 12276 3.32 - 3.85: 29836 3.85 - 4.37: 35468 4.37 - 4.90: 52364 Nonbonded interactions: 133326 Sorted by model distance: nonbonded pdb=" OG1 THR A 118 " pdb=" CD ARG B 45 " model vdw 2.273 3.440 nonbonded pdb=" O2 DC I 134 " pdb=" N2 DG J 29 " model vdw 2.288 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.289 3.040 nonbonded pdb=" N2 DG I 25 " pdb=" O2 DC J 138 " model vdw 2.301 2.496 nonbonded pdb=" CG LYS B 77 " pdb=" NH2 ARG D 89 " model vdw 2.325 3.520 ... (remaining 133321 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' } 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: 1.080 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.700 Find NCS groups from input model: 0.370 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:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.006 0.221 16371 Z= 0.318 Angle : 0.983 28.811 23384 Z= 0.560 Chirality : 0.049 0.346 2633 Planarity : 0.008 0.124 1931 Dihedral : 27.373 177.288 6850 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.59 % Allowed : 24.80 % Favored : 74.61 % 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: -0.62 (0.22), residues: 1175 helix: 0.09 (0.20), residues: 538 sheet: -0.13 (0.35), residues: 238 loop : -1.08 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 199 HIS 0.007 0.001 HIS M 249 PHE 0.009 0.002 PHE A 67 TYR 0.018 0.002 TYR N 72 ARG 0.020 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.13295 ( 856) hydrogen bonds : angle 6.15185 ( 2156) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.33386 ( 8) covalent geometry : bond 0.00624 (16367) covalent geometry : angle 0.98239 (23376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 241 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: D 39 TYR cc_start: 0.8305 (t80) cc_final: 0.7890 (t80) REVERT: M 34 VAL cc_start: 0.9151 (t) cc_final: 0.8902 (p) REVERT: M 64 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8005 (ttp80) REVERT: M 65 GLN cc_start: 0.8614 (mt0) cc_final: 0.8248 (mt0) REVERT: N 172 SER cc_start: 0.8915 (m) cc_final: 0.8570 (p) outliers start: 6 outliers final: 5 residues processed: 245 average time/residue: 1.7459 time to fit residues: 460.5993 Evaluate side-chains 223 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 163 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN F 75 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067635 restraints weight = 25594.020| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.84 r_work: 0.2625 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16371 Z= 0.285 Angle : 0.631 9.383 23384 Z= 0.367 Chirality : 0.040 0.165 2633 Planarity : 0.005 0.080 1931 Dihedral : 29.926 179.263 4567 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.94 % Allowed : 22.15 % Favored : 73.92 % 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: 0.71 (0.24), residues: 1175 helix: 1.70 (0.21), residues: 540 sheet: 0.16 (0.35), residues: 222 loop : -0.98 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 58 HIS 0.004 0.001 HIS N 249 PHE 0.010 0.002 PHE H 67 TYR 0.016 0.002 TYR N 72 ARG 0.006 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.05298 ( 856) hydrogen bonds : angle 3.65480 ( 2156) SS BOND : bond 0.00692 ( 4) SS BOND : angle 1.18176 ( 8) covalent geometry : bond 0.00655 (16367) covalent geometry : angle 0.63100 (23376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8796 (pt0) cc_final: 0.8487 (pm20) REVERT: B 84 MET cc_start: 0.9025 (mmm) cc_final: 0.8695 (mmm) REVERT: D 65 ASP cc_start: 0.9179 (t0) cc_final: 0.8871 (t0) REVERT: E 52 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8365 (ttm-80) REVERT: E 76 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8669 (pt0) REVERT: H 65 ASP cc_start: 0.9371 (t70) cc_final: 0.9037 (t0) REVERT: H 90 GLU cc_start: 0.9164 (mp0) cc_final: 0.8924 (mp0) REVERT: M 34 VAL cc_start: 0.9278 (t) cc_final: 0.8930 (p) REVERT: M 84 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: M 240 ASP cc_start: 0.8861 (m-30) cc_final: 0.8213 (m-30) REVERT: N 25 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8346 (mm-40) REVERT: N 64 ARG cc_start: 0.8776 (ttt-90) cc_final: 0.8265 (tmm-80) REVERT: N 95 ASP cc_start: 0.8427 (t0) cc_final: 0.8194 (t0) REVERT: N 172 SER cc_start: 0.8506 (m) cc_final: 0.8148 (p) outliers start: 40 outliers final: 11 residues processed: 232 average time/residue: 1.6613 time to fit residues: 414.7503 Evaluate side-chains 216 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 104 GLN N 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.068892 restraints weight = 25442.780| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.80 r_work: 0.2651 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16371 Z= 0.185 Angle : 0.585 6.791 23384 Z= 0.345 Chirality : 0.037 0.155 2633 Planarity : 0.004 0.061 1931 Dihedral : 29.904 179.715 4562 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.76 % Allowed : 22.93 % Favored : 74.31 % 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: 1.24 (0.25), residues: 1175 helix: 2.27 (0.22), residues: 542 sheet: 0.31 (0.36), residues: 222 loop : -0.89 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 58 HIS 0.003 0.001 HIS N 249 PHE 0.008 0.001 PHE N 220 TYR 0.014 0.001 TYR N 72 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 856) hydrogen bonds : angle 3.47249 ( 2156) SS BOND : bond 0.00593 ( 4) SS BOND : angle 0.91935 ( 8) covalent geometry : bond 0.00416 (16367) covalent geometry : angle 0.58487 (23376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9014 (mmm) cc_final: 0.8685 (mmm) REVERT: D 65 ASP cc_start: 0.9217 (t0) cc_final: 0.8875 (t0) REVERT: H 65 ASP cc_start: 0.9360 (t70) cc_final: 0.8914 (t0) REVERT: H 90 GLU cc_start: 0.9190 (mp0) cc_final: 0.8906 (mp0) REVERT: M 34 VAL cc_start: 0.9229 (t) cc_final: 0.8897 (p) REVERT: M 240 ASP cc_start: 0.8898 (m-30) cc_final: 0.8255 (m-30) REVERT: N 25 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8337 (mm-40) REVERT: N 64 ARG cc_start: 0.8816 (ttt-90) cc_final: 0.8281 (tmm-80) REVERT: N 95 ASP cc_start: 0.8476 (t0) cc_final: 0.8035 (t0) REVERT: N 172 SER cc_start: 0.8433 (m) cc_final: 0.8075 (p) REVERT: N 176 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7685 (ttm-80) REVERT: N 233 ILE cc_start: 0.8212 (mm) cc_final: 0.7599 (mm) REVERT: N 261 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8895 (tttp) outliers start: 28 outliers final: 16 residues processed: 223 average time/residue: 1.6174 time to fit residues: 389.0892 Evaluate side-chains 222 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 176 ARG Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.111036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.068821 restraints weight = 25417.706| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.81 r_work: 0.2650 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16371 Z= 0.207 Angle : 0.575 6.928 23384 Z= 0.338 Chirality : 0.037 0.158 2633 Planarity : 0.004 0.053 1931 Dihedral : 29.768 179.409 4562 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.54 % Allowed : 21.85 % Favored : 74.61 % 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: 1.46 (0.25), residues: 1175 helix: 2.49 (0.22), residues: 544 sheet: 0.45 (0.36), residues: 222 loop : -0.85 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 58 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.015 0.001 TYR N 72 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 856) hydrogen bonds : angle 3.32409 ( 2156) SS BOND : bond 0.00477 ( 4) SS BOND : angle 0.92269 ( 8) covalent geometry : bond 0.00473 (16367) covalent geometry : angle 0.57493 (23376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9330 (ttmm) cc_final: 0.9105 (ttpp) REVERT: B 77 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9108 (mtmt) REVERT: B 84 MET cc_start: 0.9098 (mmm) cc_final: 0.8761 (mmm) REVERT: C 71 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8780 (ttp-110) REVERT: D 39 TYR cc_start: 0.8709 (t80) cc_final: 0.7947 (t80) REVERT: D 65 ASP cc_start: 0.9255 (t0) cc_final: 0.8795 (t0) REVERT: E 52 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8376 (ttm-80) REVERT: E 76 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8685 (pt0) REVERT: F 24 ASP cc_start: 0.7578 (t70) cc_final: 0.7010 (t70) REVERT: G 76 THR cc_start: 0.9168 (p) cc_final: 0.8960 (t) REVERT: G 91 GLU cc_start: 0.9058 (tp30) cc_final: 0.8836 (tp30) REVERT: H 65 ASP cc_start: 0.9373 (t70) cc_final: 0.9042 (t0) REVERT: H 90 GLU cc_start: 0.9202 (mp0) cc_final: 0.8996 (mp0) REVERT: M 34 VAL cc_start: 0.9217 (t) cc_final: 0.8912 (p) REVERT: M 57 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8363 (mm-40) REVERT: M 84 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: M 134 GLN cc_start: 0.8808 (pm20) cc_final: 0.8578 (pm20) REVERT: M 176 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7240 (tpm-80) REVERT: M 240 ASP cc_start: 0.8896 (m-30) cc_final: 0.8233 (m-30) REVERT: N 25 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8341 (mm-40) REVERT: N 64 ARG cc_start: 0.8801 (ttt-90) cc_final: 0.8427 (ttp-170) REVERT: N 95 ASP cc_start: 0.8568 (t0) cc_final: 0.8165 (t0) REVERT: N 172 SER cc_start: 0.8399 (m) cc_final: 0.7905 (p) outliers start: 36 outliers final: 13 residues processed: 234 average time/residue: 1.6880 time to fit residues: 425.1770 Evaluate side-chains 224 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 57 GLN Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 100 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN N 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.111835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.069861 restraints weight = 25591.450| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.84 r_work: 0.2669 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16371 Z= 0.148 Angle : 0.568 7.275 23384 Z= 0.334 Chirality : 0.036 0.181 2633 Planarity : 0.004 0.048 1931 Dihedral : 29.758 179.405 4562 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.15 % Allowed : 22.44 % Favored : 74.41 % 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: 1.63 (0.25), residues: 1175 helix: 2.64 (0.22), residues: 544 sheet: 0.51 (0.36), residues: 222 loop : -0.77 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 58 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR N 72 ARG 0.007 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 856) hydrogen bonds : angle 3.27550 ( 2156) SS BOND : bond 0.00451 ( 4) SS BOND : angle 0.90789 ( 8) covalent geometry : bond 0.00324 (16367) covalent geometry : angle 0.56814 (23376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9334 (ttmm) cc_final: 0.9112 (ttpp) REVERT: B 77 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9120 (mtmt) REVERT: B 84 MET cc_start: 0.9092 (mmm) cc_final: 0.8774 (mmm) REVERT: C 71 ARG cc_start: 0.9030 (ttm-80) cc_final: 0.8796 (ttp-110) REVERT: D 39 TYR cc_start: 0.8679 (t80) cc_final: 0.7927 (t80) REVERT: D 65 ASP cc_start: 0.9264 (t0) cc_final: 0.8795 (t0) REVERT: E 52 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8375 (ttm-80) REVERT: E 122 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8524 (ptpt) REVERT: G 76 THR cc_start: 0.9162 (p) cc_final: 0.8933 (t) REVERT: G 91 GLU cc_start: 0.9081 (tp30) cc_final: 0.8877 (tp30) REVERT: H 65 ASP cc_start: 0.9383 (t70) cc_final: 0.8947 (t0) REVERT: M 34 VAL cc_start: 0.9219 (t) cc_final: 0.8909 (p) REVERT: M 134 GLN cc_start: 0.8810 (pm20) cc_final: 0.8566 (pm20) REVERT: M 169 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8482 (ptp) REVERT: M 176 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7210 (tpm-80) REVERT: M 240 ASP cc_start: 0.8907 (m-30) cc_final: 0.8220 (m-30) REVERT: N 25 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8346 (mm-40) REVERT: N 45 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8221 (tttm) REVERT: N 64 ARG cc_start: 0.8814 (ttt-90) cc_final: 0.8344 (tmm-80) REVERT: N 95 ASP cc_start: 0.8588 (t0) cc_final: 0.8134 (t0) REVERT: N 103 MET cc_start: 0.8574 (ttt) cc_final: 0.8322 (ttt) outliers start: 32 outliers final: 12 residues processed: 223 average time/residue: 1.6588 time to fit residues: 399.1709 Evaluate side-chains 221 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 169 MET Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 25 GLN N 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.111753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069604 restraints weight = 25559.008| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.84 r_work: 0.2667 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16371 Z= 0.180 Angle : 0.565 7.278 23384 Z= 0.332 Chirality : 0.036 0.156 2633 Planarity : 0.004 0.043 1931 Dihedral : 29.634 179.247 4562 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.66 % Allowed : 22.74 % Favored : 74.61 % 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: 1.73 (0.25), residues: 1175 helix: 2.70 (0.22), residues: 546 sheet: 0.59 (0.36), residues: 222 loop : -0.74 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 199 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.014 0.001 TYR N 72 ARG 0.014 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 856) hydrogen bonds : angle 3.20293 ( 2156) SS BOND : bond 0.00380 ( 4) SS BOND : angle 0.80220 ( 8) covalent geometry : bond 0.00407 (16367) covalent geometry : angle 0.56515 (23376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9338 (ttmm) cc_final: 0.9116 (ttpp) REVERT: B 77 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9090 (mtmt) REVERT: B 84 MET cc_start: 0.9089 (mmm) cc_final: 0.8751 (mmm) REVERT: C 71 ARG cc_start: 0.9055 (ttm-80) cc_final: 0.8801 (ttp-110) REVERT: D 39 TYR cc_start: 0.8681 (t80) cc_final: 0.7915 (t80) REVERT: D 65 ASP cc_start: 0.9267 (t0) cc_final: 0.8805 (t0) REVERT: E 52 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8372 (ttm-80) REVERT: E 122 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8522 (ptpt) REVERT: G 76 THR cc_start: 0.9128 (p) cc_final: 0.8885 (t) REVERT: G 91 GLU cc_start: 0.9078 (tp30) cc_final: 0.8874 (tp30) REVERT: H 65 ASP cc_start: 0.9363 (t70) cc_final: 0.8914 (t0) REVERT: H 87 THR cc_start: 0.9076 (p) cc_final: 0.8771 (p) REVERT: H 90 GLU cc_start: 0.9121 (mp0) cc_final: 0.8586 (mp0) REVERT: M 34 VAL cc_start: 0.9249 (t) cc_final: 0.8941 (p) REVERT: M 134 GLN cc_start: 0.8821 (pm20) cc_final: 0.8569 (pm20) REVERT: M 240 ASP cc_start: 0.8916 (m-30) cc_final: 0.8218 (m-30) REVERT: N 25 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8361 (mm-40) REVERT: N 45 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8232 (tttm) REVERT: N 64 ARG cc_start: 0.8824 (ttt-90) cc_final: 0.8323 (tmm-80) REVERT: N 95 ASP cc_start: 0.8574 (t0) cc_final: 0.8150 (t0) REVERT: N 103 MET cc_start: 0.8561 (ttt) cc_final: 0.8302 (ttt) outliers start: 27 outliers final: 12 residues processed: 234 average time/residue: 1.6807 time to fit residues: 423.7356 Evaluate side-chains 224 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN N 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.112534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070507 restraints weight = 25694.227| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.83 r_work: 0.2686 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16371 Z= 0.144 Angle : 0.564 8.597 23384 Z= 0.331 Chirality : 0.035 0.152 2633 Planarity : 0.004 0.041 1931 Dihedral : 29.618 179.416 4562 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.56 % Allowed : 23.03 % Favored : 74.41 % 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: 1.81 (0.25), residues: 1175 helix: 2.74 (0.22), residues: 548 sheet: 0.65 (0.36), residues: 222 loop : -0.68 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 199 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR N 72 ARG 0.008 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 856) hydrogen bonds : angle 3.18941 ( 2156) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.82819 ( 8) covalent geometry : bond 0.00316 (16367) covalent geometry : angle 0.56436 (23376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9325 (ttmm) cc_final: 0.9102 (ttpp) REVERT: B 77 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9099 (mtmt) REVERT: B 84 MET cc_start: 0.9073 (mmm) cc_final: 0.8736 (mmm) REVERT: C 71 ARG cc_start: 0.9055 (ttm-80) cc_final: 0.8801 (ttp-110) REVERT: D 39 TYR cc_start: 0.8653 (t80) cc_final: 0.7873 (t80) REVERT: D 65 ASP cc_start: 0.9250 (t0) cc_final: 0.8746 (t0) REVERT: E 122 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8512 (ptpt) REVERT: G 76 THR cc_start: 0.9117 (p) cc_final: 0.8878 (t) REVERT: G 91 GLU cc_start: 0.9089 (tp30) cc_final: 0.8872 (tp30) REVERT: H 65 ASP cc_start: 0.9359 (t70) cc_final: 0.8898 (t0) REVERT: H 87 THR cc_start: 0.9068 (p) cc_final: 0.8794 (p) REVERT: H 90 GLU cc_start: 0.9126 (mp0) cc_final: 0.8589 (mp0) REVERT: M 34 VAL cc_start: 0.9250 (t) cc_final: 0.8937 (p) REVERT: M 134 GLN cc_start: 0.8834 (pm20) cc_final: 0.8577 (pm20) REVERT: M 240 ASP cc_start: 0.8913 (m-30) cc_final: 0.8193 (m-30) REVERT: N 25 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8356 (mm-40) REVERT: N 45 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8232 (tttm) REVERT: N 95 ASP cc_start: 0.8568 (t0) cc_final: 0.8130 (t0) REVERT: N 103 MET cc_start: 0.8533 (ttt) cc_final: 0.8316 (ttt) REVERT: N 172 SER cc_start: 0.8377 (m) cc_final: 0.8035 (p) outliers start: 26 outliers final: 11 residues processed: 229 average time/residue: 1.7484 time to fit residues: 432.1653 Evaluate side-chains 227 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 138 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.112710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.070883 restraints weight = 25608.069| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.82 r_work: 0.2697 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16371 Z= 0.145 Angle : 0.567 9.423 23384 Z= 0.331 Chirality : 0.035 0.153 2633 Planarity : 0.004 0.057 1931 Dihedral : 29.584 179.516 4562 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.36 % Allowed : 23.13 % Favored : 74.51 % 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: 1.86 (0.25), residues: 1175 helix: 2.81 (0.22), residues: 546 sheet: 0.68 (0.36), residues: 222 loop : -0.68 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 199 HIS 0.003 0.001 HIS M 249 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR N 72 ARG 0.015 0.001 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 856) hydrogen bonds : angle 3.17287 ( 2156) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.80491 ( 8) covalent geometry : bond 0.00318 (16367) covalent geometry : angle 0.56723 (23376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9325 (ttmm) cc_final: 0.9103 (ttpp) REVERT: B 77 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9068 (mtmt) REVERT: B 84 MET cc_start: 0.9072 (mmm) cc_final: 0.8740 (mmm) REVERT: C 71 ARG cc_start: 0.9051 (ttm-80) cc_final: 0.8798 (ttp-110) REVERT: D 39 TYR cc_start: 0.8650 (t80) cc_final: 0.7858 (t80) REVERT: D 65 ASP cc_start: 0.9245 (t0) cc_final: 0.8743 (t0) REVERT: E 122 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8501 (ptpt) REVERT: G 76 THR cc_start: 0.9116 (p) cc_final: 0.8877 (t) REVERT: G 91 GLU cc_start: 0.9089 (tp30) cc_final: 0.8800 (tp30) REVERT: H 65 ASP cc_start: 0.9360 (t70) cc_final: 0.8910 (t0) REVERT: H 87 THR cc_start: 0.9064 (p) cc_final: 0.8825 (p) REVERT: H 90 GLU cc_start: 0.9126 (mp0) cc_final: 0.8657 (mp0) REVERT: M 34 VAL cc_start: 0.9251 (t) cc_final: 0.8937 (p) REVERT: M 134 GLN cc_start: 0.8839 (pm20) cc_final: 0.8579 (pm20) REVERT: M 240 ASP cc_start: 0.8907 (m-30) cc_final: 0.8199 (m-30) REVERT: N 25 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8357 (mm-40) REVERT: N 45 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8214 (tttm) REVERT: N 95 ASP cc_start: 0.8555 (t0) cc_final: 0.8113 (t0) REVERT: N 103 MET cc_start: 0.8529 (ttt) cc_final: 0.8319 (ttt) REVERT: N 172 SER cc_start: 0.8382 (m) cc_final: 0.8020 (p) REVERT: N 261 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8886 (ttmm) outliers start: 24 outliers final: 12 residues processed: 226 average time/residue: 1.6410 time to fit residues: 399.7904 Evaluate side-chains 227 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.069936 restraints weight = 25661.947| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.82 r_work: 0.2677 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16371 Z= 0.181 Angle : 0.576 9.944 23384 Z= 0.335 Chirality : 0.036 0.156 2633 Planarity : 0.004 0.039 1931 Dihedral : 29.556 179.232 4562 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.97 % Allowed : 24.02 % Favored : 74.02 % 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: 1.86 (0.25), residues: 1175 helix: 2.75 (0.22), residues: 548 sheet: 0.73 (0.36), residues: 222 loop : -0.66 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 199 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.014 0.001 TYR N 72 ARG 0.010 0.000 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 856) hydrogen bonds : angle 3.19119 ( 2156) SS BOND : bond 0.00388 ( 4) SS BOND : angle 0.80881 ( 8) covalent geometry : bond 0.00410 (16367) covalent geometry : angle 0.57553 (23376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.928 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9346 (ttmm) cc_final: 0.9123 (ttpp) REVERT: B 77 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9104 (mtmt) REVERT: B 84 MET cc_start: 0.9119 (mmm) cc_final: 0.8907 (mmm) REVERT: C 71 ARG cc_start: 0.9078 (ttm-80) cc_final: 0.8830 (ttp-110) REVERT: D 39 TYR cc_start: 0.8706 (t80) cc_final: 0.7990 (t80) REVERT: D 65 ASP cc_start: 0.9300 (t0) cc_final: 0.8822 (t0) REVERT: E 83 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7861 (mtp85) REVERT: E 122 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8610 (ptpt) REVERT: G 76 THR cc_start: 0.9101 (p) cc_final: 0.8860 (t) REVERT: H 65 ASP cc_start: 0.9389 (t70) cc_final: 0.8949 (t0) REVERT: H 90 GLU cc_start: 0.9156 (mp0) cc_final: 0.8889 (mp0) REVERT: M 134 GLN cc_start: 0.8815 (pm20) cc_final: 0.8549 (pm20) REVERT: M 169 MET cc_start: 0.8805 (mtm) cc_final: 0.8567 (ptm) REVERT: M 240 ASP cc_start: 0.8913 (m-30) cc_final: 0.8248 (m-30) REVERT: N 25 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8392 (mm-40) REVERT: N 45 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8277 (tttm) REVERT: N 64 ARG cc_start: 0.8844 (ttt-90) cc_final: 0.8516 (ttp-170) REVERT: N 95 ASP cc_start: 0.8587 (t0) cc_final: 0.8191 (t0) REVERT: N 103 MET cc_start: 0.8612 (ttt) cc_final: 0.8379 (ttt) REVERT: N 172 SER cc_start: 0.8402 (m) cc_final: 0.7999 (p) REVERT: N 261 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8893 (ttmm) outliers start: 20 outliers final: 9 residues processed: 224 average time/residue: 1.8650 time to fit residues: 452.1332 Evaluate side-chains 222 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 40 optimal weight: 0.0770 chunk 124 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.112419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.070573 restraints weight = 25660.706| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.87 r_work: 0.2684 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16371 Z= 0.148 Angle : 0.579 10.168 23384 Z= 0.336 Chirality : 0.035 0.164 2633 Planarity : 0.004 0.037 1931 Dihedral : 29.570 179.188 4562 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.48 % Allowed : 25.20 % Favored : 73.33 % 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: 1.90 (0.26), residues: 1175 helix: 2.79 (0.22), residues: 548 sheet: 0.75 (0.37), residues: 222 loop : -0.63 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 199 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.001 TYR N 76 ARG 0.013 0.000 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 856) hydrogen bonds : angle 3.18424 ( 2156) SS BOND : bond 0.00371 ( 4) SS BOND : angle 0.84766 ( 8) covalent geometry : bond 0.00327 (16367) covalent geometry : angle 0.57918 (23376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9329 (ttmm) cc_final: 0.9102 (ttpp) REVERT: B 77 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9101 (mtmt) REVERT: B 84 MET cc_start: 0.9109 (mmm) cc_final: 0.8893 (mmm) REVERT: C 71 ARG cc_start: 0.9061 (ttm-80) cc_final: 0.8808 (ttp-110) REVERT: D 39 TYR cc_start: 0.8664 (t80) cc_final: 0.7941 (t80) REVERT: D 65 ASP cc_start: 0.9280 (t0) cc_final: 0.8803 (t0) REVERT: E 122 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8547 (ptpt) REVERT: G 76 THR cc_start: 0.9094 (p) cc_final: 0.8855 (t) REVERT: H 65 ASP cc_start: 0.9375 (t70) cc_final: 0.8913 (t0) REVERT: H 90 GLU cc_start: 0.9138 (mp0) cc_final: 0.8863 (mp0) REVERT: M 134 GLN cc_start: 0.8812 (pm20) cc_final: 0.8594 (pm20) REVERT: M 240 ASP cc_start: 0.8894 (m-30) cc_final: 0.8120 (m-30) REVERT: N 25 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8361 (mm-40) REVERT: N 45 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8229 (tttm) REVERT: N 64 ARG cc_start: 0.8854 (ttt-90) cc_final: 0.8529 (ttp-170) REVERT: N 95 ASP cc_start: 0.8558 (t0) cc_final: 0.8154 (t0) REVERT: N 103 MET cc_start: 0.8554 (ttt) cc_final: 0.8353 (ttt) REVERT: N 172 SER cc_start: 0.8373 (m) cc_final: 0.7976 (p) REVERT: N 261 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8879 (ttmm) outliers start: 15 outliers final: 9 residues processed: 218 average time/residue: 1.7975 time to fit residues: 421.6058 Evaluate side-chains 221 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 99 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.068984 restraints weight = 25450.138| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.81 r_work: 0.2655 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16371 Z= 0.216 Angle : 0.594 9.901 23384 Z= 0.343 Chirality : 0.037 0.159 2633 Planarity : 0.004 0.037 1931 Dihedral : 29.674 179.581 4562 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.77 % Allowed : 24.80 % Favored : 73.43 % 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: 1.81 (0.26), residues: 1175 helix: 2.68 (0.22), residues: 544 sheet: 0.76 (0.37), residues: 222 loop : -0.62 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 199 HIS 0.003 0.001 HIS M 249 PHE 0.008 0.001 PHE F 61 TYR 0.015 0.001 TYR N 72 ARG 0.012 0.001 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 856) hydrogen bonds : angle 3.26268 ( 2156) SS BOND : bond 0.00498 ( 4) SS BOND : angle 0.87268 ( 8) covalent geometry : bond 0.00495 (16367) covalent geometry : angle 0.59373 (23376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15329.74 seconds wall clock time: 265 minutes 23.29 seconds (15923.29 seconds total)