Starting phenix.real_space_refine on Sun Aug 24 00:30:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evj_28631/08_2025/8evj_28631.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evj_28631/08_2025/8evj_28631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evj_28631/08_2025/8evj_28631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evj_28631/08_2025/8evj_28631.map" model { file = "/net/cci-nas-00/data/ceres_data/8evj_28631/08_2025/8evj_28631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evj_28631/08_2025/8evj_28631.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 275 5.49 5 S 38 5.16 5 C 9198 2.51 5 N 2889 2.21 5 O 3551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15951 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2830 Classifications: {'DNA': 138} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 137} Chain: "I" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2825 Classifications: {'DNA': 138} Link IDs: {'rna3p': 137} 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: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 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: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 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: "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 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 748 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Time building chain proxies: 3.60, per 1000 atoms: 0.23 Number of scatterers: 15951 At special positions: 0 Unit cell: (140.448, 121.44, 187.968, 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 38 16.00 P 275 15.00 O 3551 8.00 N 2889 7.00 C 9198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS O 220 " distance=2.03 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: 1.27 Conformation dependent library (CDL) restraints added in 527.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 22 sheets defined 46.7% alpha, 17.1% beta 132 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.771A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.459A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.803A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 83 through 93 removed outlier: 4.153A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.488A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.658A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.549A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.720A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.232A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.663A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.072A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.706A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.613A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.804A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.061A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.386A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.774A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) 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 121 removed outlier: 3.658A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 54 removed outlier: 3.971A pdb=" N TYR M 54 " --> pdb=" O PHE M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 113 removed outlier: 4.104A pdb=" N SER M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix 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 237 through 241 removed outlier: 3.993A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 185 removed outlier: 4.221A pdb=" N GLN O 176 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU O 182 " --> pdb=" O LEU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 220 Processing helix chain 'O' and resid 226 through 235 removed outlier: 3.637A pdb=" N ARG O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 241 removed outlier: 3.987A pdb=" N LYS O 239 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR O 240 " --> pdb=" O ASN O 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.670A 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 'B' and resid 96 through 97 removed outlier: 6.823A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.684A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.589A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.517A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'M' and resid 25 through 28 Processing sheet with id=AB1, first strand: chain 'M' and resid 32 through 34 removed outlier: 5.957A pdb=" N GLU M 32 " --> pdb=" O THR M 139 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 5.957A pdb=" N GLU M 32 " --> pdb=" O THR M 139 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 40 through 42 Processing sheet with id=AB4, first strand: chain 'M' and resid 168 through 171 removed outlier: 7.049A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 177 through 180 removed outlier: 4.013A pdb=" N VAL M 177 " --> pdb=" O ILE M 233 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE M 233 " --> pdb=" O VAL M 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB7, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.254A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR N 54 " --> pdb=" O TYR N 74 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR N 74 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.254A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC1, first strand: chain 'N' and resid 162 through 164 removed outlier: 4.083A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE N 233 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.447A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 206 through 207 Processing sheet with id=AC4, first strand: chain 'O' and resid 191 through 195 removed outlier: 6.162A pdb=" N TRP O 193 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN O 202 " --> pdb=" O TRP O 193 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP O 195 " --> pdb=" O THR O 200 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 324 hydrogen bonds 640 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3957 1.34 - 1.46: 5327 1.46 - 1.58: 6924 1.58 - 1.70: 549 1.70 - 1.83: 61 Bond restraints: 16818 Sorted by residual: bond pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.24e+00 bond pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CG LEU F 62 " pdb=" CD2 LEU F 62 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CG GLN A 76 " pdb=" CD GLN A 76 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.27e+00 bond pdb=" C SER M 252 " pdb=" N PRO M 253 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.13e+00 ... (remaining 16813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 23591 3.22 - 6.44: 249 6.44 - 9.66: 36 9.66 - 12.87: 8 12.87 - 16.09: 3 Bond angle restraints: 23887 Sorted by residual: angle pdb=" CA MET O 187 " pdb=" CB MET O 187 " pdb=" CG MET O 187 " ideal model delta sigma weight residual 114.10 125.32 -11.22 2.00e+00 2.50e-01 3.15e+01 angle pdb=" CB MET O 187 " pdb=" CG MET O 187 " pdb=" SD MET O 187 " ideal model delta sigma weight residual 112.70 128.79 -16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" N GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 110.40 118.15 -7.75 1.63e+00 3.76e-01 2.26e+01 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" CA LYS H 31 " pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 ... (remaining 23882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 7593 29.05 - 58.10: 1712 58.10 - 87.14: 151 87.14 - 116.19: 3 116.19 - 145.24: 1 Dihedral angle restraints: 9460 sinusoidal: 5682 harmonic: 3778 Sorted by residual: dihedral pdb=" C4' DT J 87 " pdb=" C3' DT J 87 " pdb=" O3' DT J 87 " pdb=" P DC J 88 " ideal model delta sinusoidal sigma weight residual 220.00 74.76 145.24 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA MET M 162 " pdb=" C MET M 162 " pdb=" N THR M 163 " pdb=" CA THR M 163 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU B 97 " pdb=" C LEU B 97 " pdb=" N TYR B 98 " pdb=" CA TYR B 98 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 9457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2385 0.077 - 0.155: 264 0.155 - 0.232: 26 0.232 - 0.309: 4 0.309 - 0.387: 1 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CB ILE M 56 " pdb=" CA ILE M 56 " pdb=" CG1 ILE M 56 " pdb=" CG2 ILE M 56 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB THR N 241 " pdb=" CA THR N 241 " pdb=" OG1 THR N 241 " pdb=" CG2 THR N 241 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2677 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.029 2.00e-02 2.50e+03 2.84e-02 1.62e+01 pdb=" CG TYR F 88 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO G 80 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO C 80 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.046 5.00e-02 4.00e+02 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3746 2.81 - 3.33: 14002 3.33 - 3.85: 31572 3.85 - 4.38: 34727 4.38 - 4.90: 51143 Nonbonded interactions: 135190 Sorted by model distance: nonbonded pdb=" OG1 THR N 128 " pdb=" OH TYR N 194 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU D 102 " pdb=" OH TYR N 54 " model vdw 2.287 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.300 3.040 nonbonded pdb=" O2 DC J 120 " pdb=" N2 DG I 43 " model vdw 2.305 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.305 3.040 ... (remaining 135185 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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 : 0.005 0.063 16823 Z= 0.217 Angle : 0.936 16.093 23897 Z= 0.511 Chirality : 0.050 0.387 2680 Planarity : 0.007 0.089 2052 Dihedral : 26.053 145.237 7023 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.22), residues: 1275 helix: -0.97 (0.20), residues: 555 sheet: -0.02 (0.36), residues: 246 loop : -1.40 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 129 TYR 0.068 0.002 TYR F 88 PHE 0.020 0.002 PHE M 220 TRP 0.020 0.001 TRP N 199 HIS 0.017 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00464 (16818) covalent geometry : angle 0.93549 (23887) SS BOND : bond 0.00289 ( 5) SS BOND : angle 1.54019 ( 10) hydrogen bonds : bond 0.14205 ( 859) hydrogen bonds : angle 6.03303 ( 2167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9407 (pttm) cc_final: 0.9194 (pttm) REVERT: A 106 ASP cc_start: 0.9099 (m-30) cc_final: 0.8793 (m-30) REVERT: C 74 LYS cc_start: 0.9574 (mptt) cc_final: 0.9299 (mmtt) REVERT: D 40 LYS cc_start: 0.9405 (mtmm) cc_final: 0.9163 (pttm) REVERT: D 64 ASN cc_start: 0.9460 (m-40) cc_final: 0.9090 (m-40) REVERT: D 66 ILE cc_start: 0.9524 (mm) cc_final: 0.9247 (mm) REVERT: D 68 GLU cc_start: 0.8786 (mp0) cc_final: 0.8485 (mp0) REVERT: D 99 LEU cc_start: 0.9420 (mt) cc_final: 0.9187 (mp) REVERT: E 50 GLU cc_start: 0.9213 (pm20) cc_final: 0.8990 (pm20) REVERT: E 65 LEU cc_start: 0.9549 (tp) cc_final: 0.8959 (tp) REVERT: E 79 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8900 (ptmm) REVERT: E 105 GLU cc_start: 0.8905 (pp20) cc_final: 0.8495 (pp20) REVERT: E 106 ASP cc_start: 0.9347 (m-30) cc_final: 0.8730 (m-30) REVERT: F 49 LEU cc_start: 0.9637 (mt) cc_final: 0.9373 (mp) REVERT: F 59 LYS cc_start: 0.9449 (tmtt) cc_final: 0.8987 (tmtt) REVERT: F 84 MET cc_start: 0.8846 (tpt) cc_final: 0.8476 (tpp) REVERT: F 93 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 64 GLU cc_start: 0.8742 (tp30) cc_final: 0.8195 (tp30) REVERT: G 101 THR cc_start: 0.9455 (m) cc_final: 0.9186 (p) REVERT: H 65 ASP cc_start: 0.8914 (t0) cc_final: 0.8462 (t0) REVERT: H 68 GLU cc_start: 0.8777 (pp20) cc_final: 0.8565 (pp20) REVERT: H 73 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8045 (mm-30) REVERT: H 76 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8380 (ttp-110) REVERT: M 235 ASN cc_start: 0.9510 (t0) cc_final: 0.9200 (t0) REVERT: N 42 MET cc_start: 0.9219 (pmm) cc_final: 0.8915 (pmm) REVERT: N 220 PHE cc_start: 0.9314 (m-80) cc_final: 0.8980 (m-80) REVERT: N 256 PHE cc_start: 0.8922 (m-80) cc_final: 0.8679 (m-80) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.1436 time to fit residues: 55.2912 Evaluate side-chains 200 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.053849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.034143 restraints weight = 117763.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.034521 restraints weight = 59655.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035005 restraints weight = 38208.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035188 restraints weight = 28950.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035426 restraints weight = 25581.760| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16823 Z= 0.264 Angle : 0.658 8.742 23897 Z= 0.380 Chirality : 0.038 0.156 2680 Planarity : 0.005 0.073 2052 Dihedral : 29.725 145.422 4500 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.23), residues: 1275 helix: 0.60 (0.21), residues: 576 sheet: -0.20 (0.35), residues: 248 loop : -1.08 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 63 TYR 0.034 0.002 TYR F 88 PHE 0.015 0.002 PHE H 62 TRP 0.005 0.001 TRP N 132 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00562 (16818) covalent geometry : angle 0.65803 (23887) SS BOND : bond 0.00625 ( 5) SS BOND : angle 1.35601 ( 10) hydrogen bonds : bond 0.06254 ( 859) hydrogen bonds : angle 4.33659 ( 2167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9377 (pttm) cc_final: 0.9140 (pttm) REVERT: A 106 ASP cc_start: 0.9198 (m-30) cc_final: 0.8943 (m-30) REVERT: B 49 LEU cc_start: 0.9451 (mp) cc_final: 0.9140 (tp) REVERT: B 98 TYR cc_start: 0.9278 (m-80) cc_final: 0.8897 (m-80) REVERT: C 73 ASN cc_start: 0.9580 (OUTLIER) cc_final: 0.9341 (t0) REVERT: D 66 ILE cc_start: 0.9643 (mm) cc_final: 0.9409 (mm) REVERT: D 99 LEU cc_start: 0.9301 (mt) cc_final: 0.8908 (mp) REVERT: D 105 LYS cc_start: 0.9389 (ptmm) cc_final: 0.9156 (ptmm) REVERT: E 60 LEU cc_start: 0.9356 (mt) cc_final: 0.8720 (mt) REVERT: E 65 LEU cc_start: 0.9668 (tp) cc_final: 0.9197 (tp) REVERT: E 79 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8631 (tmmt) REVERT: E 93 GLN cc_start: 0.8612 (tm-30) cc_final: 0.6366 (tm-30) REVERT: E 97 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7193 (mt-10) REVERT: E 105 GLU cc_start: 0.8907 (pp20) cc_final: 0.8461 (pp20) REVERT: E 106 ASP cc_start: 0.9306 (m-30) cc_final: 0.8826 (m-30) REVERT: F 59 LYS cc_start: 0.9401 (tmtt) cc_final: 0.8931 (tmtt) REVERT: F 74 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9066 (mm-30) REVERT: F 84 MET cc_start: 0.8944 (tpt) cc_final: 0.8279 (tpp) REVERT: F 93 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8271 (tm-30) REVERT: G 61 GLU cc_start: 0.9001 (tp30) cc_final: 0.8570 (tp30) REVERT: G 64 GLU cc_start: 0.8914 (tp30) cc_final: 0.8363 (tp30) REVERT: G 95 LYS cc_start: 0.9612 (tptt) cc_final: 0.9406 (ttmm) REVERT: H 58 ILE cc_start: 0.9868 (mm) cc_final: 0.9652 (mt) REVERT: H 65 ASP cc_start: 0.8934 (t0) cc_final: 0.8150 (t0) REVERT: H 102 GLU cc_start: 0.8213 (pp20) cc_final: 0.7986 (pp20) REVERT: M 42 MET cc_start: 0.9273 (pmm) cc_final: 0.9058 (pmm) REVERT: M 235 ASN cc_start: 0.9580 (t0) cc_final: 0.9247 (t0) REVERT: M 262 LEU cc_start: 0.9238 (tp) cc_final: 0.8950 (tt) REVERT: N 220 PHE cc_start: 0.9375 (m-80) cc_final: 0.9080 (m-80) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1587 time to fit residues: 48.6943 Evaluate side-chains 173 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 146 optimal weight: 40.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 HIS N 28 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.054602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034911 restraints weight = 116083.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.035276 restraints weight = 57281.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035797 restraints weight = 36396.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036120 restraints weight = 27390.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036201 restraints weight = 23501.794| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16823 Z= 0.183 Angle : 0.598 9.365 23897 Z= 0.346 Chirality : 0.036 0.150 2680 Planarity : 0.004 0.065 2052 Dihedral : 29.568 145.190 4500 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.24), residues: 1275 helix: 1.09 (0.21), residues: 577 sheet: -0.18 (0.34), residues: 258 loop : -0.86 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.030 0.001 TYR H 80 PHE 0.009 0.001 PHE H 62 TRP 0.024 0.001 TRP N 193 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (16818) covalent geometry : angle 0.59776 (23887) SS BOND : bond 0.00542 ( 5) SS BOND : angle 1.33876 ( 10) hydrogen bonds : bond 0.04698 ( 859) hydrogen bonds : angle 3.97754 ( 2167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9363 (pttm) cc_final: 0.9145 (pttm) REVERT: A 106 ASP cc_start: 0.9207 (m-30) cc_final: 0.8988 (m-30) REVERT: B 49 LEU cc_start: 0.9427 (mp) cc_final: 0.9110 (tp) REVERT: B 98 TYR cc_start: 0.9402 (m-80) cc_final: 0.8988 (m-80) REVERT: C 73 ASN cc_start: 0.9608 (t0) cc_final: 0.9340 (t0) REVERT: D 66 ILE cc_start: 0.9690 (mm) cc_final: 0.9439 (mm) REVERT: E 50 GLU cc_start: 0.9195 (pm20) cc_final: 0.8952 (pm20) REVERT: E 79 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8771 (ttpp) REVERT: E 93 GLN cc_start: 0.9058 (tm-30) cc_final: 0.7795 (tm-30) REVERT: E 105 GLU cc_start: 0.8932 (pp20) cc_final: 0.8483 (pp20) REVERT: E 106 ASP cc_start: 0.9253 (m-30) cc_final: 0.8910 (m-30) REVERT: E 109 LEU cc_start: 0.9841 (mm) cc_final: 0.9539 (mm) REVERT: F 59 LYS cc_start: 0.9513 (tmtt) cc_final: 0.9124 (tmtt) REVERT: F 63 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8861 (mt-10) REVERT: F 70 VAL cc_start: 0.9462 (p) cc_final: 0.9176 (p) REVERT: F 84 MET cc_start: 0.8924 (tpt) cc_final: 0.8188 (tpp) REVERT: F 93 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8260 (tm-30) REVERT: G 36 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8788 (mmtm) REVERT: G 51 MET cc_start: 0.9573 (tpp) cc_final: 0.9294 (tpp) REVERT: G 56 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8730 (mm-30) REVERT: G 61 GLU cc_start: 0.8982 (tp30) cc_final: 0.8514 (tp30) REVERT: G 64 GLU cc_start: 0.8851 (tp30) cc_final: 0.8373 (tp30) REVERT: G 89 ASN cc_start: 0.9424 (m-40) cc_final: 0.9154 (m-40) REVERT: G 95 LYS cc_start: 0.9618 (tptt) cc_final: 0.9399 (ttmm) REVERT: H 65 ASP cc_start: 0.9041 (t0) cc_final: 0.8565 (t0) REVERT: H 99 LEU cc_start: 0.9395 (mm) cc_final: 0.9190 (mm) REVERT: H 102 GLU cc_start: 0.8095 (pp20) cc_final: 0.7649 (pp20) REVERT: M 103 MET cc_start: 0.9215 (tpt) cc_final: 0.8953 (tpt) REVERT: M 162 MET cc_start: 0.8129 (ppp) cc_final: 0.7855 (ppp) REVERT: M 235 ASN cc_start: 0.9575 (t0) cc_final: 0.9182 (t0) REVERT: M 262 LEU cc_start: 0.9242 (tp) cc_final: 0.8971 (tt) REVERT: N 220 PHE cc_start: 0.9363 (m-80) cc_final: 0.9136 (m-80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1676 time to fit residues: 53.4290 Evaluate side-chains 180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN M 65 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.034303 restraints weight = 116190.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034719 restraints weight = 57762.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.035211 restraints weight = 36387.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035519 restraints weight = 27452.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.035605 restraints weight = 23546.114| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16823 Z= 0.206 Angle : 0.611 9.639 23897 Z= 0.353 Chirality : 0.037 0.151 2680 Planarity : 0.004 0.062 2052 Dihedral : 29.519 146.103 4500 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.24), residues: 1275 helix: 1.28 (0.21), residues: 578 sheet: 0.02 (0.35), residues: 252 loop : -0.82 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 64 TYR 0.025 0.001 TYR D 37 PHE 0.011 0.001 PHE E 67 TRP 0.022 0.001 TRP O 215 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00442 (16818) covalent geometry : angle 0.61034 (23887) SS BOND : bond 0.00536 ( 5) SS BOND : angle 1.28884 ( 10) hydrogen bonds : bond 0.05100 ( 859) hydrogen bonds : angle 3.95487 ( 2167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9207 (m-30) cc_final: 0.8966 (m-30) REVERT: B 49 LEU cc_start: 0.9406 (mp) cc_final: 0.9196 (mp) REVERT: B 52 GLU cc_start: 0.9124 (mp0) cc_final: 0.8838 (mp0) REVERT: B 98 TYR cc_start: 0.9341 (m-10) cc_final: 0.9008 (m-80) REVERT: C 73 ASN cc_start: 0.9661 (t0) cc_final: 0.9381 (t0) REVERT: C 75 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9140 (mmmm) REVERT: D 66 ILE cc_start: 0.9715 (mm) cc_final: 0.9484 (mm) REVERT: D 99 LEU cc_start: 0.9277 (mt) cc_final: 0.8892 (mp) REVERT: E 50 GLU cc_start: 0.9193 (pm20) cc_final: 0.8961 (pm20) REVERT: E 81 ASP cc_start: 0.8946 (t70) cc_final: 0.8711 (t70) REVERT: E 90 MET cc_start: 0.9251 (mmp) cc_final: 0.8988 (mmm) REVERT: E 105 GLU cc_start: 0.8911 (pp20) cc_final: 0.8634 (pp20) REVERT: E 106 ASP cc_start: 0.9248 (m-30) cc_final: 0.8904 (m-30) REVERT: F 59 LYS cc_start: 0.9553 (tmtt) cc_final: 0.9138 (tmtt) REVERT: F 63 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8813 (mt-10) REVERT: F 84 MET cc_start: 0.8933 (tpt) cc_final: 0.8096 (tpp) REVERT: F 93 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8375 (tm-30) REVERT: G 36 LYS cc_start: 0.9278 (mmtm) cc_final: 0.9050 (mmtm) REVERT: G 56 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8780 (mm-30) REVERT: G 64 GLU cc_start: 0.8739 (tp30) cc_final: 0.8295 (tp30) REVERT: G 89 ASN cc_start: 0.9462 (m-40) cc_final: 0.9162 (m-40) REVERT: G 95 LYS cc_start: 0.9671 (tptt) cc_final: 0.9470 (ttmm) REVERT: H 65 ASP cc_start: 0.9066 (t0) cc_final: 0.8733 (t0) REVERT: H 76 ARG cc_start: 0.9399 (ttm-80) cc_final: 0.8921 (ttm110) REVERT: H 99 LEU cc_start: 0.9413 (mm) cc_final: 0.9204 (mm) REVERT: H 102 GLU cc_start: 0.8111 (pp20) cc_final: 0.7739 (pp20) REVERT: M 262 LEU cc_start: 0.9258 (tp) cc_final: 0.8988 (tt) REVERT: N 220 PHE cc_start: 0.9393 (m-80) cc_final: 0.9135 (m-80) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1339 time to fit residues: 41.7241 Evaluate side-chains 172 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.053611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.034052 restraints weight = 117123.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.034404 restraints weight = 57936.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.034897 restraints weight = 37029.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035073 restraints weight = 27971.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035265 restraints weight = 24724.156| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16823 Z= 0.213 Angle : 0.616 9.828 23897 Z= 0.354 Chirality : 0.037 0.239 2680 Planarity : 0.004 0.061 2052 Dihedral : 29.552 145.767 4500 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.24), residues: 1275 helix: 1.30 (0.21), residues: 577 sheet: -0.00 (0.35), residues: 252 loop : -0.73 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.023 0.002 TYR C 57 PHE 0.009 0.001 PHE N 220 TRP 0.012 0.001 TRP N 193 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00459 (16818) covalent geometry : angle 0.61544 (23887) SS BOND : bond 0.00471 ( 5) SS BOND : angle 1.22137 ( 10) hydrogen bonds : bond 0.05065 ( 859) hydrogen bonds : angle 3.93327 ( 2167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 CYS cc_start: 0.9297 (p) cc_final: 0.8752 (p) REVERT: A 97 GLU cc_start: 0.8846 (mp0) cc_final: 0.8469 (mp0) REVERT: A 106 ASP cc_start: 0.9213 (m-30) cc_final: 0.8969 (m-30) REVERT: B 52 GLU cc_start: 0.9150 (mp0) cc_final: 0.8823 (mp0) REVERT: B 98 TYR cc_start: 0.9323 (m-10) cc_final: 0.9030 (m-80) REVERT: C 73 ASN cc_start: 0.9666 (t0) cc_final: 0.9366 (t0) REVERT: C 75 LYS cc_start: 0.9475 (mmmm) cc_final: 0.9199 (mmmm) REVERT: D 65 ASP cc_start: 0.9224 (t70) cc_final: 0.9022 (t0) REVERT: D 66 ILE cc_start: 0.9711 (mm) cc_final: 0.9460 (mm) REVERT: E 50 GLU cc_start: 0.9250 (pm20) cc_final: 0.9028 (pm20) REVERT: E 90 MET cc_start: 0.9268 (mmp) cc_final: 0.8991 (mmp) REVERT: E 105 GLU cc_start: 0.8933 (pp20) cc_final: 0.8584 (pp20) REVERT: E 106 ASP cc_start: 0.9221 (m-30) cc_final: 0.8840 (m-30) REVERT: E 109 LEU cc_start: 0.9822 (mm) cc_final: 0.9474 (mm) REVERT: E 120 MET cc_start: 0.8762 (mpp) cc_final: 0.8331 (mpp) REVERT: F 59 LYS cc_start: 0.9543 (tmmt) cc_final: 0.9138 (tmtt) REVERT: F 63 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8879 (mt-10) REVERT: F 70 VAL cc_start: 0.9481 (p) cc_final: 0.8907 (p) REVERT: F 74 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8939 (mt-10) REVERT: F 84 MET cc_start: 0.8977 (tpt) cc_final: 0.8140 (tpp) REVERT: F 93 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8497 (tm-30) REVERT: G 56 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8708 (mm-30) REVERT: G 64 GLU cc_start: 0.8778 (tp30) cc_final: 0.8356 (tp30) REVERT: G 89 ASN cc_start: 0.9470 (m-40) cc_final: 0.9171 (m-40) REVERT: G 95 LYS cc_start: 0.9666 (tptt) cc_final: 0.9453 (ttmm) REVERT: H 65 ASP cc_start: 0.9044 (t0) cc_final: 0.8783 (t0) REVERT: H 76 ARG cc_start: 0.9460 (ttm-80) cc_final: 0.9257 (ttm110) REVERT: H 99 LEU cc_start: 0.9499 (mm) cc_final: 0.9259 (mm) REVERT: H 102 GLU cc_start: 0.8056 (pp20) cc_final: 0.7826 (pp20) REVERT: M 162 MET cc_start: 0.8193 (ppp) cc_final: 0.7848 (ppp) REVERT: M 262 LEU cc_start: 0.9271 (tp) cc_final: 0.9007 (tt) REVERT: N 103 MET cc_start: 0.9282 (tpt) cc_final: 0.9062 (tpt) REVERT: N 220 PHE cc_start: 0.9450 (m-80) cc_final: 0.9138 (m-80) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1522 time to fit residues: 48.1949 Evaluate side-chains 176 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 82 optimal weight: 0.0020 chunk 125 optimal weight: 0.0770 chunk 72 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 44 GLN M 249 HIS ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.057584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.037060 restraints weight = 116353.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.037178 restraints weight = 58195.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.037476 restraints weight = 37441.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.037846 restraints weight = 29981.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.038100 restraints weight = 25858.107| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16823 Z= 0.141 Angle : 0.604 8.869 23897 Z= 0.344 Chirality : 0.037 0.152 2680 Planarity : 0.004 0.058 2052 Dihedral : 29.240 143.153 4500 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.09 % Allowed : 1.44 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.24), residues: 1275 helix: 1.37 (0.22), residues: 572 sheet: 0.17 (0.36), residues: 254 loop : -0.69 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.018 0.001 TYR D 37 PHE 0.009 0.001 PHE A 67 TRP 0.009 0.001 TRP N 193 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00295 (16818) covalent geometry : angle 0.60331 (23887) SS BOND : bond 0.00229 ( 5) SS BOND : angle 1.06593 ( 10) hydrogen bonds : bond 0.04069 ( 859) hydrogen bonds : angle 3.76341 ( 2167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9165 (m-30) cc_final: 0.8905 (m-30) REVERT: B 52 GLU cc_start: 0.9048 (mp0) cc_final: 0.8728 (mp0) REVERT: B 98 TYR cc_start: 0.9314 (m-10) cc_final: 0.8936 (m-80) REVERT: C 73 ASN cc_start: 0.9610 (t0) cc_final: 0.9280 (t0) REVERT: C 75 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9166 (mmmm) REVERT: C 104 GLN cc_start: 0.8609 (mp10) cc_final: 0.8283 (mp10) REVERT: D 65 ASP cc_start: 0.9174 (t70) cc_final: 0.8917 (t0) REVERT: D 66 ILE cc_start: 0.9698 (mm) cc_final: 0.9451 (mm) REVERT: E 65 LEU cc_start: 0.9624 (tp) cc_final: 0.8975 (tp) REVERT: E 105 GLU cc_start: 0.8859 (pp20) cc_final: 0.8508 (pp20) REVERT: E 106 ASP cc_start: 0.9215 (m-30) cc_final: 0.8921 (m-30) REVERT: E 109 LEU cc_start: 0.9824 (mm) cc_final: 0.9486 (mm) REVERT: E 120 MET cc_start: 0.8869 (mpp) cc_final: 0.8446 (mpp) REVERT: E 126 LEU cc_start: 0.9723 (tp) cc_final: 0.9404 (tp) REVERT: F 59 LYS cc_start: 0.9537 (tmmt) cc_final: 0.9061 (tmtt) REVERT: F 63 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8897 (mt-10) REVERT: F 70 VAL cc_start: 0.9492 (p) cc_final: 0.8765 (p) REVERT: F 74 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8914 (mm-30) REVERT: F 84 MET cc_start: 0.8813 (tpt) cc_final: 0.7992 (tpp) REVERT: F 93 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8309 (tm-30) REVERT: F 98 TYR cc_start: 0.9169 (m-10) cc_final: 0.8921 (m-10) REVERT: G 56 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8410 (mm-30) REVERT: G 64 GLU cc_start: 0.8718 (tp30) cc_final: 0.8280 (tp30) REVERT: G 89 ASN cc_start: 0.9367 (m-40) cc_final: 0.9120 (m-40) REVERT: G 95 LYS cc_start: 0.9597 (tptt) cc_final: 0.9372 (ttmm) REVERT: H 58 ILE cc_start: 0.9706 (mt) cc_final: 0.9499 (mm) REVERT: H 99 LEU cc_start: 0.9357 (mm) cc_final: 0.9076 (mm) REVERT: M 247 LEU cc_start: 0.9371 (tp) cc_final: 0.9128 (tp) REVERT: M 262 LEU cc_start: 0.9225 (tp) cc_final: 0.8992 (tt) REVERT: N 130 ASP cc_start: 0.9477 (p0) cc_final: 0.9259 (p0) REVERT: N 220 PHE cc_start: 0.9413 (m-80) cc_final: 0.9112 (m-80) REVERT: N 256 PHE cc_start: 0.8697 (m-80) cc_final: 0.8381 (m-80) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1347 time to fit residues: 48.1949 Evaluate side-chains 197 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 105 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.055453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035099 restraints weight = 117519.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035411 restraints weight = 59042.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.035905 restraints weight = 38355.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.036217 restraints weight = 29195.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036388 restraints weight = 25125.115| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16823 Z= 0.155 Angle : 0.605 9.065 23897 Z= 0.345 Chirality : 0.036 0.162 2680 Planarity : 0.004 0.057 2052 Dihedral : 29.177 144.933 4500 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.24), residues: 1275 helix: 1.40 (0.22), residues: 572 sheet: 0.17 (0.35), residues: 256 loop : -0.59 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.019 0.001 TYR F 51 PHE 0.017 0.001 PHE H 62 TRP 0.007 0.001 TRP M 58 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00332 (16818) covalent geometry : angle 0.60497 (23887) SS BOND : bond 0.00315 ( 5) SS BOND : angle 1.08517 ( 10) hydrogen bonds : bond 0.04294 ( 859) hydrogen bonds : angle 3.77028 ( 2167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9193 (m-30) cc_final: 0.8937 (m-30) REVERT: B 52 GLU cc_start: 0.9143 (mp0) cc_final: 0.8800 (mp0) REVERT: B 98 TYR cc_start: 0.9250 (m-10) cc_final: 0.9019 (m-80) REVERT: C 73 ASN cc_start: 0.9618 (t0) cc_final: 0.9223 (t0) REVERT: D 66 ILE cc_start: 0.9719 (mm) cc_final: 0.9485 (mm) REVERT: E 64 LYS cc_start: 0.9570 (mppt) cc_final: 0.9216 (mmtm) REVERT: E 79 LYS cc_start: 0.9281 (ptmm) cc_final: 0.8846 (ptmm) REVERT: E 93 GLN cc_start: 0.9415 (mm-40) cc_final: 0.9202 (mm-40) REVERT: E 97 GLU cc_start: 0.8996 (mp0) cc_final: 0.8635 (mp0) REVERT: E 105 GLU cc_start: 0.8884 (pp20) cc_final: 0.8646 (pp20) REVERT: E 106 ASP cc_start: 0.9250 (m-30) cc_final: 0.8856 (m-30) REVERT: E 109 LEU cc_start: 0.9821 (mm) cc_final: 0.9572 (mm) REVERT: E 120 MET cc_start: 0.8892 (mpp) cc_final: 0.8409 (mpp) REVERT: F 63 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8980 (mt-10) REVERT: F 70 VAL cc_start: 0.9522 (p) cc_final: 0.9117 (p) REVERT: F 84 MET cc_start: 0.8912 (tpt) cc_final: 0.8601 (tpp) REVERT: F 88 TYR cc_start: 0.8953 (m-10) cc_final: 0.8363 (m-10) REVERT: F 93 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8282 (tm-30) REVERT: G 56 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8516 (mm-30) REVERT: G 64 GLU cc_start: 0.8721 (tp30) cc_final: 0.8304 (tp30) REVERT: G 89 ASN cc_start: 0.9406 (m-40) cc_final: 0.9130 (m-40) REVERT: G 95 LYS cc_start: 0.9573 (tptt) cc_final: 0.9355 (ttmm) REVERT: H 73 GLU cc_start: 0.9373 (tp30) cc_final: 0.9122 (mm-30) REVERT: H 76 ARG cc_start: 0.9399 (ttm110) cc_final: 0.9186 (ttp-110) REVERT: H 99 LEU cc_start: 0.9395 (mm) cc_final: 0.9154 (mm) REVERT: M 162 MET cc_start: 0.8013 (ppp) cc_final: 0.7758 (ppp) REVERT: M 262 LEU cc_start: 0.9207 (tp) cc_final: 0.8983 (tt) REVERT: N 42 MET cc_start: 0.9430 (pmm) cc_final: 0.9158 (pmm) REVERT: N 130 ASP cc_start: 0.9498 (p0) cc_final: 0.9214 (p0) REVERT: N 220 PHE cc_start: 0.9400 (m-80) cc_final: 0.9092 (m-80) REVERT: N 256 PHE cc_start: 0.8709 (m-80) cc_final: 0.8361 (m-80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1337 time to fit residues: 44.3533 Evaluate side-chains 192 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 144 optimal weight: 50.0000 chunk 42 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.053640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.033886 restraints weight = 115739.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.034264 restraints weight = 58375.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034770 restraints weight = 37276.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035081 restraints weight = 27957.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.035169 restraints weight = 23849.949| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16823 Z= 0.228 Angle : 0.647 10.338 23897 Z= 0.366 Chirality : 0.038 0.167 2680 Planarity : 0.004 0.058 2052 Dihedral : 29.384 145.740 4500 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.24), residues: 1275 helix: 1.41 (0.22), residues: 577 sheet: 0.15 (0.36), residues: 252 loop : -0.58 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.024 0.002 TYR D 37 PHE 0.019 0.002 PHE E 67 TRP 0.008 0.001 TRP O 215 HIS 0.015 0.002 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00494 (16818) covalent geometry : angle 0.64670 (23887) SS BOND : bond 0.00510 ( 5) SS BOND : angle 1.22450 ( 10) hydrogen bonds : bond 0.05279 ( 859) hydrogen bonds : angle 3.91192 ( 2167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9204 (m-30) cc_final: 0.8957 (m-30) REVERT: B 98 TYR cc_start: 0.9308 (m-10) cc_final: 0.9020 (m-80) REVERT: C 73 ASN cc_start: 0.9681 (t0) cc_final: 0.9308 (t0) REVERT: D 66 ILE cc_start: 0.9725 (mm) cc_final: 0.9474 (mm) REVERT: D 83 ARG cc_start: 0.8736 (mmp80) cc_final: 0.8440 (mmp80) REVERT: D 99 LEU cc_start: 0.9400 (mt) cc_final: 0.9154 (mp) REVERT: E 64 LYS cc_start: 0.9566 (mppt) cc_final: 0.9300 (mmtm) REVERT: E 65 LEU cc_start: 0.9646 (tp) cc_final: 0.9110 (tp) REVERT: E 105 GLU cc_start: 0.8969 (pp20) cc_final: 0.8709 (pp20) REVERT: E 106 ASP cc_start: 0.9278 (m-30) cc_final: 0.8875 (m-30) REVERT: E 109 LEU cc_start: 0.9831 (mm) cc_final: 0.9580 (mm) REVERT: F 63 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8893 (mt-10) REVERT: F 84 MET cc_start: 0.9074 (tpt) cc_final: 0.8668 (tpp) REVERT: F 88 TYR cc_start: 0.8945 (m-10) cc_final: 0.8268 (m-10) REVERT: F 93 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8425 (tm-30) REVERT: G 42 ARG cc_start: 0.9273 (mmm-85) cc_final: 0.8638 (tpt170) REVERT: G 56 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8526 (mm-30) REVERT: G 64 GLU cc_start: 0.8782 (tp30) cc_final: 0.8365 (tp30) REVERT: G 95 LYS cc_start: 0.9644 (tptt) cc_final: 0.9427 (ttmm) REVERT: H 65 ASP cc_start: 0.9052 (t0) cc_final: 0.8842 (t0) REVERT: H 76 ARG cc_start: 0.9542 (ttm110) cc_final: 0.9231 (ttp-110) REVERT: M 162 MET cc_start: 0.8242 (ppp) cc_final: 0.7912 (ppp) REVERT: M 262 LEU cc_start: 0.9275 (tp) cc_final: 0.9025 (tt) REVERT: N 42 MET cc_start: 0.9483 (pmm) cc_final: 0.9204 (pmm) REVERT: N 220 PHE cc_start: 0.9429 (m-80) cc_final: 0.9117 (m-80) REVERT: N 256 PHE cc_start: 0.8884 (m-80) cc_final: 0.8483 (m-80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1379 time to fit residues: 43.5272 Evaluate side-chains 179 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.053541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.034025 restraints weight = 117639.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034440 restraints weight = 58623.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034937 restraints weight = 37397.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035262 restraints weight = 28084.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.035421 restraints weight = 23860.726| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16823 Z= 0.220 Angle : 0.654 9.864 23897 Z= 0.370 Chirality : 0.038 0.167 2680 Planarity : 0.004 0.059 2052 Dihedral : 29.444 145.095 4500 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.24), residues: 1275 helix: 1.19 (0.22), residues: 580 sheet: 0.02 (0.35), residues: 252 loop : -0.63 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 235 TYR 0.026 0.002 TYR C 57 PHE 0.028 0.002 PHE E 67 TRP 0.007 0.001 TRP O 215 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00477 (16818) covalent geometry : angle 0.65374 (23887) SS BOND : bond 0.00538 ( 5) SS BOND : angle 1.26982 ( 10) hydrogen bonds : bond 0.05123 ( 859) hydrogen bonds : angle 4.03800 ( 2167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9188 (m-30) cc_final: 0.8930 (m-30) REVERT: B 23 ARG cc_start: 0.8616 (tpt90) cc_final: 0.8330 (tpt170) REVERT: B 98 TYR cc_start: 0.9251 (m-10) cc_final: 0.8979 (m-80) REVERT: C 73 ASN cc_start: 0.9684 (t0) cc_final: 0.9320 (t0) REVERT: C 104 GLN cc_start: 0.8700 (mp10) cc_final: 0.8256 (mp10) REVERT: D 66 ILE cc_start: 0.9726 (mm) cc_final: 0.9478 (mm) REVERT: D 68 GLU cc_start: 0.8657 (mp0) cc_final: 0.8367 (mp0) REVERT: D 83 ARG cc_start: 0.8738 (mmp80) cc_final: 0.8434 (mmp80) REVERT: D 99 LEU cc_start: 0.9377 (mt) cc_final: 0.9115 (mp) REVERT: E 64 LYS cc_start: 0.9564 (mppt) cc_final: 0.9327 (mmtm) REVERT: E 90 MET cc_start: 0.9309 (mmp) cc_final: 0.9109 (mmp) REVERT: E 93 GLN cc_start: 0.9448 (mm-40) cc_final: 0.9188 (mm-40) REVERT: E 97 GLU cc_start: 0.9163 (mp0) cc_final: 0.8767 (mp0) REVERT: E 105 GLU cc_start: 0.8978 (pp20) cc_final: 0.8596 (pp20) REVERT: E 106 ASP cc_start: 0.9216 (m-30) cc_final: 0.8789 (m-30) REVERT: E 109 LEU cc_start: 0.9828 (mm) cc_final: 0.9557 (mm) REVERT: F 63 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8890 (mt-10) REVERT: F 84 MET cc_start: 0.8993 (tpt) cc_final: 0.8582 (tpp) REVERT: F 88 TYR cc_start: 0.8929 (m-10) cc_final: 0.8237 (m-10) REVERT: F 93 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8413 (tm-30) REVERT: G 42 ARG cc_start: 0.9319 (mmm-85) cc_final: 0.8669 (tpt170) REVERT: G 51 MET cc_start: 0.9532 (tpp) cc_final: 0.9297 (tpp) REVERT: G 56 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8503 (mm-30) REVERT: G 64 GLU cc_start: 0.8760 (tp30) cc_final: 0.8290 (tp30) REVERT: G 95 LYS cc_start: 0.9683 (tptt) cc_final: 0.9473 (ttmm) REVERT: H 76 ARG cc_start: 0.9550 (ttm110) cc_final: 0.9250 (ttp-110) REVERT: H 92 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8794 (tp40) REVERT: M 76 TYR cc_start: 0.8764 (t80) cc_final: 0.8491 (t80) REVERT: M 262 LEU cc_start: 0.9270 (tp) cc_final: 0.9018 (tt) REVERT: N 42 MET cc_start: 0.9370 (pmm) cc_final: 0.9113 (pmm) REVERT: N 103 MET cc_start: 0.8733 (mmp) cc_final: 0.8498 (mmm) REVERT: N 220 PHE cc_start: 0.9415 (m-80) cc_final: 0.9121 (m-80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1455 time to fit residues: 46.3000 Evaluate side-chains 183 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.055556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.035596 restraints weight = 113929.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035776 restraints weight = 61192.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036267 restraints weight = 40973.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036428 restraints weight = 31224.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.036623 restraints weight = 27593.191| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16823 Z= 0.181 Angle : 0.647 11.397 23897 Z= 0.365 Chirality : 0.038 0.185 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.373 144.299 4500 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1275 helix: 1.31 (0.22), residues: 576 sheet: 0.06 (0.35), residues: 252 loop : -0.59 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.021 0.001 TYR D 37 PHE 0.033 0.002 PHE E 67 TRP 0.007 0.001 TRP N 199 HIS 0.013 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (16818) covalent geometry : angle 0.64671 (23887) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.15706 ( 10) hydrogen bonds : bond 0.04618 ( 859) hydrogen bonds : angle 3.97476 ( 2167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8683 (mp0) cc_final: 0.8450 (mp0) REVERT: A 106 ASP cc_start: 0.9183 (m-30) cc_final: 0.8918 (m-30) REVERT: B 98 TYR cc_start: 0.9312 (m-10) cc_final: 0.8964 (m-80) REVERT: C 73 ASN cc_start: 0.9687 (t0) cc_final: 0.9322 (t0) REVERT: D 66 ILE cc_start: 0.9716 (mm) cc_final: 0.9480 (mm) REVERT: D 68 GLU cc_start: 0.8626 (mp0) cc_final: 0.8368 (mp0) REVERT: D 83 ARG cc_start: 0.8717 (mmp80) cc_final: 0.8411 (mmp80) REVERT: E 65 LEU cc_start: 0.9641 (tp) cc_final: 0.9122 (tp) REVERT: E 68 GLN cc_start: 0.9069 (pp30) cc_final: 0.8850 (pp30) REVERT: E 93 GLN cc_start: 0.9412 (mm-40) cc_final: 0.9200 (mm-40) REVERT: E 105 GLU cc_start: 0.8936 (pp20) cc_final: 0.8558 (pp20) REVERT: E 106 ASP cc_start: 0.9188 (m-30) cc_final: 0.8764 (m-30) REVERT: E 109 LEU cc_start: 0.9831 (mm) cc_final: 0.9576 (mm) REVERT: E 126 LEU cc_start: 0.9726 (tp) cc_final: 0.9454 (tp) REVERT: F 63 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8893 (mt-10) REVERT: F 84 MET cc_start: 0.8953 (tpt) cc_final: 0.8561 (tpp) REVERT: F 88 TYR cc_start: 0.8893 (m-10) cc_final: 0.8161 (m-10) REVERT: F 93 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8333 (tm-30) REVERT: G 42 ARG cc_start: 0.9292 (mmm-85) cc_final: 0.8610 (tpt170) REVERT: G 56 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8513 (mm-30) REVERT: G 64 GLU cc_start: 0.8741 (tp30) cc_final: 0.8322 (tp30) REVERT: G 95 LYS cc_start: 0.9663 (tptt) cc_final: 0.9420 (ttmm) REVERT: H 76 ARG cc_start: 0.9475 (ttm110) cc_final: 0.9274 (ttp-110) REVERT: H 92 GLN cc_start: 0.9128 (tp-100) cc_final: 0.8800 (tp40) REVERT: M 262 LEU cc_start: 0.9271 (tp) cc_final: 0.9035 (tt) REVERT: N 42 MET cc_start: 0.9364 (pmm) cc_final: 0.9099 (pmm) REVERT: N 220 PHE cc_start: 0.9416 (m-80) cc_final: 0.9117 (m-80) REVERT: N 256 PHE cc_start: 0.8839 (m-80) cc_final: 0.8442 (m-80) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1405 time to fit residues: 45.1086 Evaluate side-chains 193 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 146 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 147 optimal weight: 0.1980 chunk 120 optimal weight: 0.0470 chunk 135 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.057788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.037897 restraints weight = 110377.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038164 restraints weight = 58463.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.038656 restraints weight = 38432.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.038828 restraints weight = 29001.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039077 restraints weight = 25538.976| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16823 Z= 0.144 Angle : 0.631 10.670 23897 Z= 0.354 Chirality : 0.038 0.219 2680 Planarity : 0.004 0.061 2052 Dihedral : 29.004 142.513 4500 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.24), residues: 1275 helix: 1.26 (0.22), residues: 578 sheet: 0.14 (0.35), residues: 254 loop : -0.61 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.022 0.001 TYR C 57 PHE 0.034 0.002 PHE E 67 TRP 0.008 0.001 TRP M 58 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00308 (16818) covalent geometry : angle 0.63082 (23887) SS BOND : bond 0.00310 ( 5) SS BOND : angle 0.99402 ( 10) hydrogen bonds : bond 0.04114 ( 859) hydrogen bonds : angle 3.81140 ( 2167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.88 seconds wall clock time: 47 minutes 46.58 seconds (2866.58 seconds total)