Starting phenix.real_space_refine on Thu Aug 6 14:25:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evj_28631/08_2026/8evj_28631.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evj_28631/08_2026/8evj_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 { model { file = "/net/cci-nas-00/data/ceres_data/8evj_28631/08_2026/8evj_28631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evj_28631/08_2026/8evj_28631.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8evj_28631/08_2026/8evj_28631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evj_28631/08_2026/8evj_28631.map" } 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-2.2rc3-6140/lib/python3.11/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: 2.71, per 1000 atoms: 0.17 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: 1.00 Conformation dependent library (CDL) restraints added in 381.7 milliseconds 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: 1.95 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: 2.33 Time building geometry restraints manager: 1.41 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=" C3' DC J 88 " pdb=" C2' DC J 88 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.63e+01 bond pdb=" C3' DC I 111 " pdb=" C2' DC I 111 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.50e+01 bond pdb=" C5' DT I 161 " pdb=" C4' DT I 161 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.18e+01 bond pdb=" C3' DT J 131 " pdb=" C2' DT J 131 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG I 148 " pdb=" C2' DG I 148 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 16813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 23564 3.22 - 6.44: 276 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=" O4' DA J 114 " pdb=" C4' DA J 114 " pdb=" C3' DA J 114 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.57e+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=" O4' DT I 162 " pdb=" C4' DT I 162 " pdb=" C3' DT I 162 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.19e+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: 2334 0.077 - 0.155: 315 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.290 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16823 Z= 0.480 Angle : 1.032 16.093 23897 Z= 0.746 Chirality : 0.054 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 are 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/Z covalent geometry : bond 0.00600 / 0.48 (16818) covalent geometry : angle 1.03208 / 0.75 (23887) SS BOND : bond 0.00289 / 0.19 ( 5) SS BOND : angle 1.54019 / 3.10 ( 10) hydrogen bonds : bond 0.14205 / 15.66 ( 859) hydrogen bonds : angle 6.03303 / 8.14 ( 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 : 0.415 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: 0.9170 (pttm) REVERT: D 64 ASN cc_start: 0.9460 (m-40) cc_final: 0.9089 (m-40) REVERT: D 66 ILE cc_start: 0.9524 (mm) cc_final: 0.9248 (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: 0.8117 (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: 0.8046 (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: 0.8916 (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: 0.1203 time to fit residues: 46.9710 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 : 0.333 ------------------------------------------------------------------------------- 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: 30.0000 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... ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.056459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.036064 restraints weight = 114464.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.036188 restraints weight = 63520.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036490 restraints weight = 43720.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036868 restraints weight = 35211.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037017 restraints weight = 30444.458| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16823 Z= 0.239 Angle : 0.737 8.891 23897 Z= 0.417 Chirality : 0.045 0.245 2680 Planarity : 0.005 0.076 2052 Dihedral : 29.848 151.175 4500 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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 are not related in a simple way. whole: -0.36 (0.23), residues: 1275 helix: 0.43 (0.21), residues: 575 sheet: -0.21 (0.35), residues: 246 loop : -0.97 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.023 0.002 TYR H 80 PHE 0.011 0.002 PHE N 220 TRP 0.009 0.001 TRP M 193 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.24 (16818) covalent geometry : angle 0.73714 / 0.42 (23887) SS BOND : bond 0.00530 / 0.54 ( 5) SS BOND : angle 1.32524 / 2.81 ( 10) hydrogen bonds : bond 0.06527 / 7.39 ( 859) hydrogen bonds : angle 4.53648 / 6.08 ( 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 222 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.430 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: 0.9413 (pttm) cc_final: 0.9186 (pttm) REVERT: A 64 LYS cc_start: 0.9749 (mptt) cc_final: 0.9539 (mmtt) REVERT: A 106 ASP cc_start: 0.9132 (m-30) cc_final: 0.8890 (m-30) REVERT: B 54 THR cc_start: 0.9533 (m) cc_final: 0.9327 (m) REVERT: D 54 LYS cc_start: 0.9613 (mmmm) cc_final: 0.9261 (mtpt) REVERT: D 66 ILE cc_start: 0.9598 (mm) cc_final: 0.9344 (mm) REVERT: D 99 LEU cc_start: 0.9296 (mt) cc_final: 0.8871 (mp) REVERT: E 60 LEU cc_start: 0.9469 (mt) cc_final: 0.9163 (mt) REVERT: E 65 LEU cc_start: 0.9623 (tp) cc_final: 0.9127 (tp) REVERT: E 81 ASP cc_start: 0.8925 (t70) cc_final: 0.8718 (t70) REVERT: E 90 MET cc_start: 0.9195 (mmp) cc_final: 0.8995 (mmp) REVERT: E 93 GLN cc_start: 0.8538 (tm-30) cc_final: 0.6954 (tm-30) REVERT: E 105 GLU cc_start: 0.8836 (pp20) cc_final: 0.8298 (pp20) REVERT: E 106 ASP cc_start: 0.9263 (m-30) cc_final: 0.8769 (m-30) REVERT: E 109 LEU cc_start: 0.9831 (mm) cc_final: 0.9551 (mm) REVERT: E 125 GLN cc_start: 0.9563 (mt0) cc_final: 0.9260 (mt0) REVERT: F 49 LEU cc_start: 0.9667 (mt) cc_final: 0.9428 (mt) REVERT: F 74 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8819 (mm-30) REVERT: F 84 MET cc_start: 0.8761 (tpt) cc_final: 0.8171 (tpp) REVERT: F 93 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8104 (tm-30) REVERT: G 36 LYS cc_start: 0.9178 (mmtm) cc_final: 0.8792 (mmtm) REVERT: G 64 GLU cc_start: 0.8943 (tp30) cc_final: 0.8395 (tp30) REVERT: G 95 LYS cc_start: 0.9594 (tptt) cc_final: 0.9355 (ttmm) REVERT: H 56 MET cc_start: 0.9318 (tpp) cc_final: 0.9085 (tpp) REVERT: H 65 ASP cc_start: 0.8870 (t0) cc_final: 0.8224 (t0) REVERT: H 102 GLU cc_start: 0.8417 (pp20) cc_final: 0.8043 (pp20) REVERT: M 42 MET cc_start: 0.9200 (pmm) cc_final: 0.8923 (pmm) REVERT: M 103 MET cc_start: 0.9101 (tpt) cc_final: 0.8718 (tpt) REVERT: M 235 ASN cc_start: 0.9554 (t0) cc_final: 0.9220 (t0) REVERT: N 220 PHE cc_start: 0.9287 (m-80) cc_final: 0.8988 (m-80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1263 time to fit residues: 40.4326 Evaluate side-chains 175 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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: 50.0000 chunk 123 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 44 GLN M 249 HIS ** N 28 GLN ** 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 = 0.3366 r_free = 0.3366 target = 0.056289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.035847 restraints weight = 116936.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.036066 restraints weight = 63305.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.036536 restraints weight = 42407.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.036696 restraints weight = 32432.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036901 restraints weight = 28890.828| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16823 Z= 0.196 Angle : 0.664 9.856 23897 Z= 0.381 Chirality : 0.044 0.224 2680 Planarity : 0.004 0.066 2052 Dihedral : 29.905 148.018 4500 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1275 helix: 0.90 (0.21), residues: 575 sheet: -0.21 (0.35), residues: 248 loop : -0.84 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.016 0.001 TYR F 88 PHE 0.011 0.001 PHE D 67 TRP 0.031 0.002 TRP N 193 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.20 (16818) covalent geometry : angle 0.66351 / 0.38 (23887) SS BOND : bond 0.00419 / 0.48 ( 5) SS BOND : angle 1.23588 / 2.40 ( 10) hydrogen bonds : bond 0.05612 / 6.26 ( 859) hydrogen bonds : angle 4.27130 / 5.73 ( 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 225 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.351 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: 0.9401 (pttm) cc_final: 0.9155 (pttm) REVERT: A 64 LYS cc_start: 0.9728 (mptt) cc_final: 0.9524 (mmtt) REVERT: A 106 ASP cc_start: 0.9176 (m-30) cc_final: 0.8924 (m-30) REVERT: B 54 THR cc_start: 0.9548 (m) cc_final: 0.9335 (m) REVERT: B 98 TYR cc_start: 0.9302 (m-80) cc_final: 0.8885 (m-80) REVERT: C 51 MET cc_start: 0.9210 (tpp) cc_final: 0.8813 (mmm) REVERT: C 73 ASN cc_start: 0.9536 (OUTLIER) cc_final: 0.9258 (t0) REVERT: D 54 LYS cc_start: 0.9663 (mmmm) cc_final: 0.9289 (mtpt) REVERT: D 66 ILE cc_start: 0.9653 (mm) cc_final: 0.9391 (mm) REVERT: D 99 LEU cc_start: 0.9297 (mt) cc_final: 0.8802 (mp) REVERT: E 65 LEU cc_start: 0.9662 (tp) cc_final: 0.9179 (tp) REVERT: E 93 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8117 (tm-30) REVERT: E 97 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8584 (mt-10) REVERT: E 105 GLU cc_start: 0.8880 (pp20) cc_final: 0.8281 (pp20) REVERT: E 106 ASP cc_start: 0.9253 (m-30) cc_final: 0.8735 (m-30) REVERT: E 109 LEU cc_start: 0.9840 (mm) cc_final: 0.9527 (mm) REVERT: F 70 VAL cc_start: 0.9433 (p) cc_final: 0.9072 (p) REVERT: F 84 MET cc_start: 0.8886 (tpt) cc_final: 0.8187 (tpp) REVERT: F 93 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8138 (tm-30) REVERT: G 36 LYS cc_start: 0.9206 (mmtm) cc_final: 0.8844 (mmtm) REVERT: G 51 MET cc_start: 0.9606 (tpp) cc_final: 0.9337 (tpp) REVERT: G 61 GLU cc_start: 0.8932 (tp30) cc_final: 0.8621 (tt0) REVERT: G 64 GLU cc_start: 0.8927 (tp30) cc_final: 0.8432 (tp30) REVERT: G 95 LYS cc_start: 0.9606 (tptt) cc_final: 0.9361 (ttmm) REVERT: H 58 ILE cc_start: 0.9877 (mm) cc_final: 0.9635 (mt) REVERT: H 65 ASP cc_start: 0.8826 (t0) cc_final: 0.8138 (t0) REVERT: H 102 GLU cc_start: 0.8239 (pp20) cc_final: 0.7752 (pp20) REVERT: M 42 MET cc_start: 0.9194 (pmm) cc_final: 0.8973 (pmm) REVERT: M 235 ASN cc_start: 0.9575 (t0) cc_final: 0.9217 (t0) REVERT: M 262 LEU cc_start: 0.9275 (tp) cc_final: 0.9016 (tt) REVERT: N 42 MET cc_start: 0.9408 (pmm) cc_final: 0.9179 (pmm) REVERT: N 103 MET cc_start: 0.9147 (tpt) cc_final: 0.8915 (tpt) REVERT: N 220 PHE cc_start: 0.9315 (m-80) cc_final: 0.9062 (m-80) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.1241 time to fit residues: 39.9580 Evaluate side-chains 175 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 147 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN N 195 GLN N 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.056765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.036535 restraints weight = 115936.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036724 restraints weight = 62373.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.037213 restraints weight = 42057.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037377 restraints weight = 32231.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.037613 restraints weight = 28462.848| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1856 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= 0.150 Angle : 0.628 9.652 23897 Z= 0.363 Chirality : 0.043 0.208 2680 Planarity : 0.004 0.062 2052 Dihedral : 29.827 147.674 4500 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.24), residues: 1275 helix: 1.19 (0.21), residues: 575 sheet: -0.13 (0.35), residues: 256 loop : -0.74 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 32 TYR 0.011 0.001 TYR F 51 PHE 0.014 0.001 PHE E 104 TRP 0.010 0.001 TRP N 193 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (16818) covalent geometry : angle 0.62778 / 0.36 (23887) SS BOND : bond 0.00412 / 0.44 ( 5) SS BOND : angle 1.22170 / 2.50 ( 10) hydrogen bonds : bond 0.04911 / 5.43 ( 859) hydrogen bonds : angle 4.06784 / 5.49 ( 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 224 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.390 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 56 LYS cc_start: 0.9386 (pttm) cc_final: 0.9135 (pttm) REVERT: A 64 LYS cc_start: 0.9734 (mptt) cc_final: 0.9517 (mmtt) REVERT: A 106 ASP cc_start: 0.9170 (m-30) cc_final: 0.8924 (m-30) REVERT: B 54 THR cc_start: 0.9544 (m) cc_final: 0.9333 (m) REVERT: B 98 TYR cc_start: 0.9389 (m-80) cc_final: 0.9004 (m-80) REVERT: C 32 ARG cc_start: 0.9030 (tmm-80) cc_final: 0.8823 (tmm-80) REVERT: C 73 ASN cc_start: 0.9523 (t0) cc_final: 0.9223 (t0) REVERT: D 40 LYS cc_start: 0.9352 (mtmm) cc_final: 0.9032 (mttp) REVERT: D 66 ILE cc_start: 0.9694 (mm) cc_final: 0.9464 (mm) REVERT: D 93 THR cc_start: 0.9516 (m) cc_final: 0.9113 (p) REVERT: E 50 GLU cc_start: 0.9226 (pm20) cc_final: 0.8950 (pm20) REVERT: E 65 LEU cc_start: 0.9644 (tp) cc_final: 0.9126 (tp) REVERT: E 93 GLN cc_start: 0.8897 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 97 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8438 (mt-10) REVERT: E 105 GLU cc_start: 0.8852 (pp20) cc_final: 0.8382 (pp20) REVERT: E 106 ASP cc_start: 0.9252 (m-30) cc_final: 0.8791 (m-30) REVERT: E 109 LEU cc_start: 0.9845 (mm) cc_final: 0.9563 (mm) REVERT: F 59 LYS cc_start: 0.9606 (tmtt) cc_final: 0.8399 (tmtt) REVERT: F 63 GLU cc_start: 0.9137 (pt0) cc_final: 0.8423 (pt0) REVERT: F 84 MET cc_start: 0.8842 (tpt) cc_final: 0.8182 (tpp) REVERT: F 93 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8120 (tm-30) REVERT: G 36 LYS cc_start: 0.9217 (mmtm) cc_final: 0.8832 (mmtm) REVERT: G 61 GLU cc_start: 0.8873 (tp30) cc_final: 0.8533 (tt0) REVERT: G 64 GLU cc_start: 0.8804 (tp30) cc_final: 0.8287 (tp30) REVERT: G 95 LYS cc_start: 0.9587 (tptt) cc_final: 0.9368 (ttmm) REVERT: H 65 ASP cc_start: 0.8907 (t0) cc_final: 0.8452 (t0) REVERT: H 76 ARG cc_start: 0.9390 (ttm-80) cc_final: 0.9177 (ttm110) REVERT: H 99 LEU cc_start: 0.9355 (mm) cc_final: 0.9141 (mm) REVERT: H 102 GLU cc_start: 0.8279 (pp20) cc_final: 0.7971 (pp20) REVERT: M 103 MET cc_start: 0.9141 (tpt) cc_final: 0.8940 (tpt) REVERT: M 162 MET cc_start: 0.8127 (ppp) cc_final: 0.7759 (ppp) REVERT: M 235 ASN cc_start: 0.9567 (t0) cc_final: 0.9193 (t0) REVERT: M 262 LEU cc_start: 0.9265 (tp) cc_final: 0.9009 (tt) REVERT: N 220 PHE cc_start: 0.9357 (m-80) cc_final: 0.9128 (m-80) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1235 time to fit residues: 39.7661 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 : 0.450 ------------------------------------------------------------------------------- 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: 10.0000 chunk 8 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 30.0000 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 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 = 0.3360 r_free = 0.3360 target = 0.054580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.034381 restraints weight = 115503.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.034755 restraints weight = 58115.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.035257 restraints weight = 37598.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.035557 restraints weight = 28459.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.035748 restraints weight = 24516.449| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16823 Z= 0.191 Angle : 0.657 10.407 23897 Z= 0.376 Chirality : 0.043 0.208 2680 Planarity : 0.004 0.063 2052 Dihedral : 29.804 148.838 4500 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 are not related in a simple way. whole: 0.41 (0.24), residues: 1275 helix: 1.24 (0.21), residues: 574 sheet: -0.10 (0.35), residues: 256 loop : -0.66 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.022 0.001 TYR H 80 PHE 0.009 0.001 PHE H 62 TRP 0.014 0.001 TRP O 215 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (16818) covalent geometry : angle 0.65590 / 0.38 (23887) SS BOND : bond 0.00411 / 0.44 ( 5) SS BOND : angle 1.55714 / 3.14 ( 10) hydrogen bonds : bond 0.05502 / 6.17 ( 859) hydrogen bonds : angle 4.12510 / 5.49 ( 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 215 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.459 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 56 LYS cc_start: 0.9366 (pttm) cc_final: 0.9130 (pttm) REVERT: A 97 GLU cc_start: 0.9039 (mp0) cc_final: 0.8549 (mp0) REVERT: A 106 ASP cc_start: 0.9177 (m-30) cc_final: 0.8933 (m-30) REVERT: B 54 THR cc_start: 0.9520 (m) cc_final: 0.9303 (m) REVERT: B 98 TYR cc_start: 0.9354 (m-80) cc_final: 0.9021 (m-80) REVERT: C 73 ASN cc_start: 0.9565 (t0) cc_final: 0.9242 (t0) REVERT: D 40 LYS cc_start: 0.9362 (mtmm) cc_final: 0.9080 (mtmm) REVERT: D 65 ASP cc_start: 0.9171 (t70) cc_final: 0.8924 (t0) REVERT: D 66 ILE cc_start: 0.9727 (mm) cc_final: 0.9504 (mm) REVERT: E 50 GLU cc_start: 0.9241 (pm20) cc_final: 0.9002 (pm20) REVERT: E 65 LEU cc_start: 0.9681 (tp) cc_final: 0.9196 (tp) REVERT: E 93 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8718 (tm-30) REVERT: E 105 GLU cc_start: 0.8819 (pp20) cc_final: 0.8360 (pp20) REVERT: E 106 ASP cc_start: 0.9192 (m-30) cc_final: 0.8774 (m-30) REVERT: E 109 LEU cc_start: 0.9819 (mm) cc_final: 0.9516 (mm) REVERT: F 59 LYS cc_start: 0.9614 (tmtt) cc_final: 0.8381 (tmtt) REVERT: F 63 GLU cc_start: 0.9157 (pt0) cc_final: 0.8373 (pt0) REVERT: F 84 MET cc_start: 0.8668 (tpt) cc_final: 0.8021 (tpp) REVERT: F 93 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8137 (tm-30) REVERT: G 36 LYS cc_start: 0.9291 (mmtm) cc_final: 0.8930 (mmtm) REVERT: G 64 GLU cc_start: 0.8798 (tp30) cc_final: 0.8302 (tp30) REVERT: G 95 LYS cc_start: 0.9590 (tptt) cc_final: 0.9382 (ttmm) REVERT: H 65 ASP cc_start: 0.8983 (t0) cc_final: 0.8541 (t0) REVERT: H 76 ARG cc_start: 0.9353 (ttm-80) cc_final: 0.9040 (ttm110) REVERT: H 99 LEU cc_start: 0.9395 (mm) cc_final: 0.9166 (mm) REVERT: H 102 GLU cc_start: 0.8218 (pp20) cc_final: 0.7714 (pp20) REVERT: M 262 LEU cc_start: 0.9166 (tp) cc_final: 0.8915 (tt) REVERT: N 42 MET cc_start: 0.9388 (pmm) cc_final: 0.9140 (pmm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1304 time to fit residues: 39.9756 Evaluate side-chains 174 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 50.0000 chunk 23 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 82 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 249 HIS ** 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 = 0.3360 r_free = 0.3360 target = 0.054601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.034942 restraints weight = 115889.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.035283 restraints weight = 57664.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035787 restraints weight = 37057.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.036112 restraints weight = 28126.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.036231 restraints weight = 24127.028| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16823 Z= 0.177 Angle : 0.645 10.468 23897 Z= 0.368 Chirality : 0.043 0.208 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.786 148.946 4500 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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 are not related in a simple way. whole: 0.46 (0.24), residues: 1275 helix: 1.30 (0.22), residues: 575 sheet: -0.07 (0.35), residues: 256 loop : -0.68 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 67 TYR 0.014 0.001 TYR H 80 PHE 0.020 0.002 PHE A 78 TRP 0.008 0.001 TRP N 193 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (16818) covalent geometry : angle 0.64468 / 0.37 (23887) SS BOND : bond 0.00412 / 0.46 ( 5) SS BOND : angle 1.31825 / 2.69 ( 10) hydrogen bonds : bond 0.05168 / 5.76 ( 859) hydrogen bonds : angle 4.03805 / 5.36 ( 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 217 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.402 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 56 LYS cc_start: 0.9367 (pttm) cc_final: 0.9107 (ptpp) REVERT: A 59 GLU cc_start: 0.8819 (pp20) cc_final: 0.8614 (pm20) REVERT: A 106 ASP cc_start: 0.9196 (m-30) cc_final: 0.8957 (m-30) REVERT: B 54 THR cc_start: 0.9509 (m) cc_final: 0.9287 (m) REVERT: B 98 TYR cc_start: 0.9375 (m-10) cc_final: 0.9043 (m-80) REVERT: C 51 MET cc_start: 0.9383 (mmm) cc_final: 0.8920 (mmm) REVERT: C 55 LEU cc_start: 0.9792 (mt) cc_final: 0.9575 (mt) REVERT: C 73 ASN cc_start: 0.9566 (t0) cc_final: 0.9233 (t0) REVERT: D 30 ARG cc_start: 0.9050 (mmp80) cc_final: 0.8795 (mmp80) REVERT: D 40 LYS cc_start: 0.9331 (mtmm) cc_final: 0.9003 (mtmm) REVERT: D 66 ILE cc_start: 0.9706 (mm) cc_final: 0.9454 (mm) REVERT: E 50 GLU cc_start: 0.9221 (pm20) cc_final: 0.9011 (pm20) REVERT: E 65 LEU cc_start: 0.9675 (tp) cc_final: 0.9103 (tp) REVERT: E 93 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8726 (tm-30) REVERT: E 105 GLU cc_start: 0.8914 (pp20) cc_final: 0.8346 (pp20) REVERT: E 106 ASP cc_start: 0.9229 (m-30) cc_final: 0.8772 (m-30) REVERT: E 109 LEU cc_start: 0.9806 (mm) cc_final: 0.9450 (mm) REVERT: F 59 LYS cc_start: 0.9621 (tmtt) cc_final: 0.9198 (tmtt) REVERT: F 70 VAL cc_start: 0.9511 (p) cc_final: 0.9270 (p) REVERT: F 84 MET cc_start: 0.8740 (tpt) cc_final: 0.8054 (tpp) REVERT: F 93 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8206 (tm-30) REVERT: G 36 LYS cc_start: 0.9354 (mmtm) cc_final: 0.9012 (mmtm) REVERT: G 64 GLU cc_start: 0.8797 (tp30) cc_final: 0.8291 (tp30) REVERT: G 95 LYS cc_start: 0.9613 (tptt) cc_final: 0.9397 (ttmm) REVERT: H 65 ASP cc_start: 0.9030 (t0) cc_final: 0.8612 (t0) REVERT: H 76 ARG cc_start: 0.9397 (ttm-80) cc_final: 0.8972 (ttm110) REVERT: H 99 LEU cc_start: 0.9379 (mm) cc_final: 0.9162 (mm) REVERT: H 102 GLU cc_start: 0.8144 (pp20) cc_final: 0.7662 (pp20) REVERT: M 76 TYR cc_start: 0.8656 (t80) cc_final: 0.8426 (t80) REVERT: M 162 MET cc_start: 0.8178 (ppp) cc_final: 0.7708 (ppp) REVERT: M 262 LEU cc_start: 0.9242 (tp) cc_final: 0.8972 (tt) REVERT: N 42 MET cc_start: 0.9430 (pmm) cc_final: 0.9178 (pmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1354 time to fit residues: 41.6371 Evaluate side-chains 177 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 11 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 100 optimal weight: 0.0670 overall best weight: 5.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 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 = 0.3332 r_free = 0.3332 target = 0.053412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.033457 restraints weight = 118824.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033819 restraints weight = 59063.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.034296 restraints weight = 37946.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.034467 restraints weight = 28627.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.034700 restraints weight = 25269.276| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16823 Z= 0.254 Angle : 0.717 11.096 23897 Z= 0.401 Chirality : 0.044 0.213 2680 Planarity : 0.005 0.062 2052 Dihedral : 29.882 150.742 4500 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 are not related in a simple way. whole: 0.29 (0.24), residues: 1275 helix: 1.10 (0.21), residues: 575 sheet: -0.23 (0.35), residues: 258 loop : -0.63 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 23 TYR 0.018 0.002 TYR M 76 PHE 0.016 0.002 PHE N 220 TRP 0.007 0.001 TRP N 58 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.25 (16818) covalent geometry : angle 0.71690 / 0.40 (23887) SS BOND : bond 0.00553 / 0.64 ( 5) SS BOND : angle 1.42559 / 2.91 ( 10) hydrogen bonds : bond 0.06630 / 7.52 ( 859) hydrogen bonds : angle 4.28766 / 5.59 ( 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 206 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.478 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: A 106 ASP cc_start: 0.9206 (m-30) cc_final: 0.8993 (m-30) REVERT: B 54 THR cc_start: 0.9492 (m) cc_final: 0.9280 (m) REVERT: B 98 TYR cc_start: 0.9353 (m-10) cc_final: 0.9076 (m-80) REVERT: C 51 MET cc_start: 0.9300 (mmm) cc_final: 0.9049 (mmm) REVERT: C 73 ASN cc_start: 0.9624 (t0) cc_final: 0.9277 (t0) REVERT: C 104 GLN cc_start: 0.8612 (mp10) cc_final: 0.8310 (mp10) REVERT: D 66 ILE cc_start: 0.9723 (mm) cc_final: 0.9499 (mm) REVERT: D 68 GLU cc_start: 0.8644 (mp0) cc_final: 0.8385 (mp0) REVERT: D 99 LEU cc_start: 0.9286 (mt) cc_final: 0.8989 (mp) REVERT: E 90 MET cc_start: 0.9291 (mmp) cc_final: 0.9028 (mmm) REVERT: E 93 GLN cc_start: 0.8937 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 97 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8074 (mt-10) REVERT: E 105 GLU cc_start: 0.8884 (pp20) cc_final: 0.8589 (pp20) REVERT: E 106 ASP cc_start: 0.9225 (m-30) cc_final: 0.8816 (m-30) REVERT: F 84 MET cc_start: 0.8938 (tpt) cc_final: 0.8284 (tpp) REVERT: F 93 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8274 (tm-30) REVERT: G 36 LYS cc_start: 0.9380 (mmtm) cc_final: 0.9093 (mmtm) REVERT: G 64 GLU cc_start: 0.8796 (tp30) cc_final: 0.8257 (tp30) REVERT: G 89 ASN cc_start: 0.9546 (m-40) cc_final: 0.9208 (m-40) REVERT: G 95 LYS cc_start: 0.9617 (tptt) cc_final: 0.9402 (ttmm) REVERT: H 65 ASP cc_start: 0.9057 (t0) cc_final: 0.8737 (t0) REVERT: H 76 ARG cc_start: 0.9299 (ttm-80) cc_final: 0.8938 (ttm110) REVERT: H 99 LEU cc_start: 0.9502 (mm) cc_final: 0.9269 (mm) REVERT: H 102 GLU cc_start: 0.8092 (pp20) cc_final: 0.7892 (pp20) REVERT: M 162 MET cc_start: 0.8192 (ppp) cc_final: 0.7758 (ppp) REVERT: M 262 LEU cc_start: 0.9206 (tp) cc_final: 0.8933 (tt) REVERT: N 42 MET cc_start: 0.9437 (pmm) cc_final: 0.9169 (pmm) REVERT: N 193 TRP cc_start: 0.8920 (m100) cc_final: 0.8514 (m100) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1252 time to fit residues: 37.3069 Evaluate side-chains 165 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 1.9990 chunk 138 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 28 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 50.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 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 = 0.3347 r_free = 0.3347 target = 0.055492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.035293 restraints weight = 115642.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035569 restraints weight = 60287.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036045 restraints weight = 39521.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.036302 restraints weight = 30466.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.036470 restraints weight = 26532.760| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16823 Z= 0.199 Angle : 0.699 15.410 23897 Z= 0.390 Chirality : 0.044 0.212 2680 Planarity : 0.004 0.061 2052 Dihedral : 29.883 149.782 4500 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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 are not related in a simple way. whole: 0.35 (0.24), residues: 1275 helix: 1.16 (0.21), residues: 575 sheet: -0.20 (0.35), residues: 258 loop : -0.59 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.029 0.002 TYR C 57 PHE 0.019 0.002 PHE A 67 TRP 0.011 0.001 TRP M 58 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 (16818) covalent geometry : angle 0.69753 / 0.39 (23887) SS BOND : bond 0.00535 / 0.55 ( 5) SS BOND : angle 2.21688 / 4.85 ( 10) hydrogen bonds : bond 0.05578 / 6.27 ( 859) hydrogen bonds : angle 4.23791 / 5.63 ( 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 218 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.340 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: 0.9192 (m-30) cc_final: 0.8971 (m-30) REVERT: B 54 THR cc_start: 0.9479 (m) cc_final: 0.9262 (m) REVERT: B 98 TYR cc_start: 0.9332 (m-10) cc_final: 0.9061 (m-80) REVERT: C 51 MET cc_start: 0.9380 (mmm) cc_final: 0.9098 (mmm) REVERT: C 73 ASN cc_start: 0.9619 (t0) cc_final: 0.9298 (t0) REVERT: C 75 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9141 (mmmm) REVERT: C 104 GLN cc_start: 0.8605 (mp10) cc_final: 0.8308 (mp10) REVERT: D 30 ARG cc_start: 0.9018 (mmp80) cc_final: 0.8781 (mmp80) REVERT: D 40 LYS cc_start: 0.9327 (mtmm) cc_final: 0.9016 (mtmm) REVERT: D 66 ILE cc_start: 0.9723 (mm) cc_final: 0.9483 (mm) REVERT: D 99 LEU cc_start: 0.9308 (mt) cc_final: 0.9028 (mp) REVERT: E 65 LEU cc_start: 0.9652 (tp) cc_final: 0.9099 (tp) REVERT: E 90 MET cc_start: 0.9289 (mmp) cc_final: 0.9050 (mmm) REVERT: E 93 GLN cc_start: 0.8890 (tm-30) cc_final: 0.7086 (tm-30) REVERT: E 97 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8345 (mt-10) REVERT: E 105 GLU cc_start: 0.8895 (pp20) cc_final: 0.8468 (pp20) REVERT: E 106 ASP cc_start: 0.9198 (m-30) cc_final: 0.8801 (m-30) REVERT: E 109 LEU cc_start: 0.9834 (mm) cc_final: 0.9470 (mm) REVERT: F 59 LYS cc_start: 0.9602 (tmtt) cc_final: 0.9137 (tmtt) REVERT: F 84 MET cc_start: 0.8792 (tpt) cc_final: 0.8131 (tpp) REVERT: F 93 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8252 (tm-30) REVERT: G 36 LYS cc_start: 0.9383 (mmtm) cc_final: 0.9081 (mmtm) REVERT: G 61 GLU cc_start: 0.8919 (tp30) cc_final: 0.8569 (tp30) REVERT: G 64 GLU cc_start: 0.8781 (tp30) cc_final: 0.8188 (tp30) REVERT: G 89 ASN cc_start: 0.9499 (m-40) cc_final: 0.9212 (m-40) REVERT: G 95 LYS cc_start: 0.9631 (tptt) cc_final: 0.9414 (ttmm) REVERT: H 65 ASP cc_start: 0.9011 (t0) cc_final: 0.8750 (t0) REVERT: H 73 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8879 (mm-30) REVERT: H 99 LEU cc_start: 0.9494 (mm) cc_final: 0.9256 (mm) REVERT: H 102 GLU cc_start: 0.8113 (pp20) cc_final: 0.7674 (pp20) REVERT: M 262 LEU cc_start: 0.9226 (tp) cc_final: 0.8957 (tt) REVERT: N 42 MET cc_start: 0.9468 (pmm) cc_final: 0.9237 (pmm) REVERT: N 162 MET cc_start: 0.8709 (tpt) cc_final: 0.8456 (tpp) REVERT: N 193 TRP cc_start: 0.8673 (m100) cc_final: 0.8286 (m100) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1304 time to fit residues: 40.1026 Evaluate side-chains 170 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 5.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 50.0000 chunk 110 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 50.0000 chunk 111 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 HIS ** 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 = 0.3356 r_free = 0.3356 target = 0.055899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.035731 restraints weight = 115530.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.036048 restraints weight = 61540.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.036467 restraints weight = 39867.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036606 restraints weight = 31369.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.036793 restraints weight = 28055.548| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16823 Z= 0.160 Angle : 0.681 14.293 23897 Z= 0.381 Chirality : 0.044 0.226 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.811 149.149 4500 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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 are not related in a simple way. whole: 0.41 (0.24), residues: 1275 helix: 1.19 (0.21), residues: 575 sheet: -0.13 (0.35), residues: 256 loop : -0.57 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 76 TYR 0.030 0.002 TYR H 80 PHE 0.015 0.002 PHE A 67 TRP 0.007 0.001 TRP N 58 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (16818) covalent geometry : angle 0.67999 / 0.38 (23887) SS BOND : bond 0.00336 / 0.37 ( 5) SS BOND : angle 1.75234 / 3.68 ( 10) hydrogen bonds : bond 0.04970 / 5.50 ( 859) hydrogen bonds : angle 4.16941 / 5.51 ( 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 219 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.469 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 106 ASP cc_start: 0.9169 (m-30) cc_final: 0.8925 (m-30) REVERT: B 54 THR cc_start: 0.9481 (m) cc_final: 0.9267 (m) REVERT: B 98 TYR cc_start: 0.9350 (m-10) cc_final: 0.9084 (m-80) REVERT: C 51 MET cc_start: 0.9364 (mmm) cc_final: 0.8888 (mmm) REVERT: C 55 LEU cc_start: 0.9812 (mt) cc_final: 0.9512 (mt) REVERT: C 73 ASN cc_start: 0.9609 (t0) cc_final: 0.9287 (t0) REVERT: C 75 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9161 (mmmm) REVERT: C 104 GLN cc_start: 0.8632 (mp10) cc_final: 0.8341 (mp10) REVERT: D 30 ARG cc_start: 0.9018 (mmp80) cc_final: 0.8791 (mmp80) REVERT: D 40 LYS cc_start: 0.9314 (mtmm) cc_final: 0.9008 (mtmm) REVERT: D 66 ILE cc_start: 0.9691 (mm) cc_final: 0.9411 (mm) REVERT: D 68 GLU cc_start: 0.8716 (mp0) cc_final: 0.8431 (mp0) REVERT: D 99 LEU cc_start: 0.9301 (mt) cc_final: 0.9000 (mp) REVERT: D 105 LYS cc_start: 0.9421 (ptmt) cc_final: 0.9192 (ptmm) REVERT: E 65 LEU cc_start: 0.9650 (tp) cc_final: 0.9103 (tp) REVERT: E 90 MET cc_start: 0.9286 (mmp) cc_final: 0.9037 (mmm) REVERT: E 93 GLN cc_start: 0.8860 (tm-30) cc_final: 0.7103 (tm-30) REVERT: E 97 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8333 (mt-10) REVERT: E 105 GLU cc_start: 0.8904 (pp20) cc_final: 0.8471 (pp20) REVERT: E 106 ASP cc_start: 0.9197 (m-30) cc_final: 0.8864 (m-30) REVERT: E 109 LEU cc_start: 0.9825 (mm) cc_final: 0.9429 (mm) REVERT: F 59 LYS cc_start: 0.9614 (tmtt) cc_final: 0.9192 (tmtt) REVERT: F 84 MET cc_start: 0.8876 (tpt) cc_final: 0.8206 (tpp) REVERT: F 93 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8251 (tm-30) REVERT: G 36 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9042 (mmtm) REVERT: G 57 TYR cc_start: 0.9091 (t80) cc_final: 0.8794 (t80) REVERT: G 61 GLU cc_start: 0.8914 (tp30) cc_final: 0.8496 (tp30) REVERT: G 64 GLU cc_start: 0.8770 (tp30) cc_final: 0.8231 (tp30) REVERT: G 89 ASN cc_start: 0.9477 (m-40) cc_final: 0.9168 (m-40) REVERT: G 95 LYS cc_start: 0.9619 (tptt) cc_final: 0.9395 (ttmm) REVERT: H 76 ARG cc_start: 0.9344 (mtm110) cc_final: 0.8889 (mtp-110) REVERT: H 99 LEU cc_start: 0.9450 (mm) cc_final: 0.9231 (mm) REVERT: H 102 GLU cc_start: 0.8063 (pp20) cc_final: 0.7617 (pp20) REVERT: M 162 MET cc_start: 0.8194 (ppp) cc_final: 0.7716 (ppp) REVERT: M 262 LEU cc_start: 0.9255 (tp) cc_final: 0.8997 (tt) REVERT: N 42 MET cc_start: 0.9528 (pmm) cc_final: 0.9285 (pmm) REVERT: N 193 TRP cc_start: 0.8710 (m100) cc_final: 0.8493 (m100) REVERT: N 256 PHE cc_start: 0.8873 (m-80) cc_final: 0.8515 (m-80) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1276 time to fit residues: 39.9183 Evaluate side-chains 184 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 0.8980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 50.0000 chunk 57 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 62 optimal weight: 0.0060 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 50.0000 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 44 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 = 0.3382 r_free = 0.3382 target = 0.056927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.036282 restraints weight = 118410.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036471 restraints weight = 62301.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.036914 restraints weight = 41729.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037211 restraints weight = 32389.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.037317 restraints weight = 27603.902| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16823 Z= 0.142 Angle : 0.677 13.995 23897 Z= 0.377 Chirality : 0.043 0.221 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.678 148.666 4500 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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 are not related in a simple way. whole: 0.42 (0.24), residues: 1275 helix: 1.21 (0.21), residues: 575 sheet: -0.14 (0.35), residues: 256 loop : -0.57 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 76 TYR 0.017 0.001 TYR O 252 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP N 58 HIS 0.010 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (16818) covalent geometry : angle 0.67659 / 0.38 (23887) SS BOND : bond 0.00246 / 0.24 ( 5) SS BOND : angle 1.75804 / 3.70 ( 10) hydrogen bonds : bond 0.04537 / 4.99 ( 859) hydrogen bonds : angle 4.06790 / 5.36 ( 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 230 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.299 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 106 ASP cc_start: 0.9160 (m-30) cc_final: 0.8898 (m-30) REVERT: B 52 GLU cc_start: 0.9042 (mp0) cc_final: 0.8746 (mp0) REVERT: B 54 THR cc_start: 0.9497 (m) cc_final: 0.9285 (m) REVERT: B 98 TYR cc_start: 0.9326 (m-10) cc_final: 0.8907 (m-80) REVERT: C 32 ARG cc_start: 0.8972 (tmm-80) cc_final: 0.8740 (tmm-80) REVERT: C 51 MET cc_start: 0.9393 (mmm) cc_final: 0.8917 (mmm) REVERT: C 55 LEU cc_start: 0.9797 (mt) cc_final: 0.9545 (mt) REVERT: C 73 ASN cc_start: 0.9575 (t0) cc_final: 0.9256 (t0) REVERT: C 75 LYS cc_start: 0.9474 (mmmm) cc_final: 0.9140 (mmmm) REVERT: C 89 ASN cc_start: 0.9354 (m-40) cc_final: 0.9118 (m-40) REVERT: C 104 GLN cc_start: 0.8617 (mp10) cc_final: 0.8206 (mp10) REVERT: D 40 LYS cc_start: 0.9292 (mtmm) cc_final: 0.8979 (mtmm) REVERT: D 54 LYS cc_start: 0.9657 (mmmm) cc_final: 0.9375 (mmmm) REVERT: D 66 ILE cc_start: 0.9683 (mm) cc_final: 0.9425 (mm) REVERT: D 68 GLU cc_start: 0.8649 (mp0) cc_final: 0.8413 (mp0) REVERT: D 99 LEU cc_start: 0.9254 (mt) cc_final: 0.8970 (mp) REVERT: E 65 LEU cc_start: 0.9660 (tp) cc_final: 0.9067 (tp) REVERT: E 90 MET cc_start: 0.9255 (mmp) cc_final: 0.8952 (mmm) REVERT: E 105 GLU cc_start: 0.8875 (pp20) cc_final: 0.8418 (pp20) REVERT: E 106 ASP cc_start: 0.9222 (m-30) cc_final: 0.8868 (m-30) REVERT: E 109 LEU cc_start: 0.9826 (mm) cc_final: 0.9470 (mm) REVERT: F 59 LYS cc_start: 0.9629 (tmtt) cc_final: 0.8438 (tmtt) REVERT: F 63 GLU cc_start: 0.9199 (pt0) cc_final: 0.8363 (pt0) REVERT: F 84 MET cc_start: 0.8817 (tpt) cc_final: 0.8239 (tpp) REVERT: F 93 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8171 (tm-30) REVERT: G 36 LYS cc_start: 0.9370 (mmtm) cc_final: 0.9031 (mmtm) REVERT: G 57 TYR cc_start: 0.9024 (t80) cc_final: 0.8804 (t80) REVERT: G 64 GLU cc_start: 0.8691 (tp30) cc_final: 0.8161 (tp30) REVERT: G 89 ASN cc_start: 0.9429 (m-40) cc_final: 0.9193 (m-40) REVERT: G 95 LYS cc_start: 0.9585 (tptt) cc_final: 0.9348 (ttmm) REVERT: H 65 ASP cc_start: 0.9150 (t70) cc_final: 0.8902 (t0) REVERT: H 99 LEU cc_start: 0.9363 (mm) cc_final: 0.9148 (mm) REVERT: H 102 GLU cc_start: 0.8052 (pp20) cc_final: 0.7635 (pp20) REVERT: M 162 MET cc_start: 0.8183 (ppp) cc_final: 0.7773 (ppp) REVERT: M 262 LEU cc_start: 0.9233 (tp) cc_final: 0.8983 (tt) REVERT: N 42 MET cc_start: 0.9503 (pmm) cc_final: 0.9259 (pmm) REVERT: N 103 MET cc_start: 0.8272 (mmm) cc_final: 0.8068 (mmp) REVERT: N 256 PHE cc_start: 0.8828 (m-80) cc_final: 0.8449 (m-80) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1174 time to fit residues: 38.7749 Evaluate side-chains 191 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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: 40.0000 chunk 96 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 44 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 = 0.3336 r_free = 0.3336 target = 0.055042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.035046 restraints weight = 115571.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.035258 restraints weight = 62341.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035674 restraints weight = 41882.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035886 restraints weight = 32681.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.036104 restraints weight = 28637.812| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2810 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= 0.233 Angle : 0.722 13.994 23897 Z= 0.398 Chirality : 0.044 0.213 2680 Planarity : 0.005 0.062 2052 Dihedral : 29.766 151.335 4500 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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 are not related in a simple way. whole: 0.46 (0.24), residues: 1275 helix: 1.19 (0.21), residues: 575 sheet: -0.02 (0.35), residues: 250 loop : -0.54 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 30 TYR 0.021 0.002 TYR F 51 PHE 0.015 0.002 PHE N 220 TRP 0.072 0.002 TRP N 193 HIS 0.009 0.002 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.23 (16818) covalent geometry : angle 0.72131 / 0.40 (23887) SS BOND : bond 0.00440 / 0.51 ( 5) SS BOND : angle 1.86630 / 3.98 ( 10) hydrogen bonds : bond 0.06184 / 7.03 ( 859) hydrogen bonds : angle 4.22560 / 5.52 ( 2167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2405.45 seconds wall clock time: 42 minutes 24.02 seconds (2544.02 seconds total)