Starting phenix.real_space_refine on Sat Jun 14 03:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evj_28631/06_2025/8evj_28631.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evj_28631/06_2025/8evj_28631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evj_28631/06_2025/8evj_28631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evj_28631/06_2025/8evj_28631.map" model { file = "/net/cci-nas-00/data/ceres_data/8evj_28631/06_2025/8evj_28631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evj_28631/06_2025/8evj_28631.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.75, per 1000 atoms: 0.61 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: 4.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 7.33 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: 6.88 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3957 1.34 - 1.46: 5327 1.46 - 1.58: 6924 1.58 - 1.70: 549 1.70 - 1.83: 61 Bond restraints: 16818 Sorted by residual: bond pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.24e+00 bond pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CG LEU F 62 " pdb=" CD2 LEU F 62 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CG GLN A 76 " pdb=" CD GLN A 76 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.27e+00 bond pdb=" C SER M 252 " pdb=" N PRO M 253 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.13e+00 ... (remaining 16813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 23591 3.22 - 6.44: 249 6.44 - 9.66: 36 9.66 - 12.87: 8 12.87 - 16.09: 3 Bond angle restraints: 23887 Sorted by residual: angle pdb=" CA MET O 187 " pdb=" CB MET O 187 " pdb=" CG MET O 187 " ideal model delta sigma weight residual 114.10 125.32 -11.22 2.00e+00 2.50e-01 3.15e+01 angle pdb=" CB MET O 187 " pdb=" CG MET O 187 " pdb=" SD MET O 187 " ideal model delta sigma weight residual 112.70 128.79 -16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" N GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 110.40 118.15 -7.75 1.63e+00 3.76e-01 2.26e+01 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" CA LYS H 31 " pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 ... (remaining 23882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 7593 29.05 - 58.10: 1712 58.10 - 87.14: 151 87.14 - 116.19: 3 116.19 - 145.24: 1 Dihedral angle restraints: 9460 sinusoidal: 5682 harmonic: 3778 Sorted by residual: dihedral pdb=" C4' DT J 87 " pdb=" C3' DT J 87 " pdb=" O3' DT J 87 " pdb=" P DC J 88 " ideal model delta sinusoidal sigma weight residual 220.00 74.76 145.24 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA MET M 162 " pdb=" C MET M 162 " pdb=" N THR M 163 " pdb=" CA THR M 163 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU B 97 " pdb=" C LEU B 97 " pdb=" N TYR B 98 " pdb=" CA TYR B 98 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 9457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2385 0.077 - 0.155: 264 0.155 - 0.232: 26 0.232 - 0.309: 4 0.309 - 0.387: 1 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CB ILE M 56 " pdb=" CA ILE M 56 " pdb=" CG1 ILE M 56 " pdb=" CG2 ILE M 56 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB THR N 241 " pdb=" CA THR N 241 " pdb=" OG1 THR N 241 " pdb=" CG2 THR N 241 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2677 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.029 2.00e-02 2.50e+03 2.84e-02 1.62e+01 pdb=" CG TYR F 88 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO G 80 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO C 80 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.046 5.00e-02 4.00e+02 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3746 2.81 - 3.33: 14002 3.33 - 3.85: 31572 3.85 - 4.38: 34727 4.38 - 4.90: 51143 Nonbonded interactions: 135190 Sorted by model distance: nonbonded pdb=" OG1 THR N 128 " pdb=" OH TYR N 194 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU D 102 " pdb=" OH TYR N 54 " model vdw 2.287 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.300 3.040 nonbonded pdb=" O2 DC J 120 " pdb=" N2 DG I 43 " model vdw 2.305 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.305 3.040 ... (remaining 135185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 44.730 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16823 Z= 0.217 Angle : 0.936 16.093 23897 Z= 0.511 Chirality : 0.050 0.387 2680 Planarity : 0.007 0.089 2052 Dihedral : 26.053 145.237 7023 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (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 TRP 0.020 0.001 TRP N 199 HIS 0.017 0.001 HIS B 75 PHE 0.020 0.002 PHE M 220 TYR 0.068 0.002 TYR F 88 ARG 0.015 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.14205 ( 859) hydrogen bonds : angle 6.03303 ( 2167) SS BOND : bond 0.00289 ( 5) SS BOND : angle 1.54019 ( 10) covalent geometry : bond 0.00464 (16818) covalent geometry : angle 0.93549 (23887) *********************** 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 : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9407 (pttm) cc_final: 0.9194 (pttm) REVERT: A 106 ASP cc_start: 0.9099 (m-30) cc_final: 0.8793 (m-30) REVERT: C 74 LYS cc_start: 0.9574 (mptt) cc_final: 0.9299 (mmtt) REVERT: D 40 LYS cc_start: 0.9405 (mtmm) cc_final: 0.9163 (pttm) REVERT: D 64 ASN cc_start: 0.9460 (m-40) cc_final: 0.9090 (m-40) REVERT: D 66 ILE cc_start: 0.9524 (mm) cc_final: 0.9247 (mm) REVERT: D 68 GLU cc_start: 0.8786 (mp0) cc_final: 0.8485 (mp0) REVERT: D 99 LEU cc_start: 0.9420 (mt) cc_final: 0.9187 (mp) REVERT: E 50 GLU cc_start: 0.9213 (pm20) cc_final: 0.8990 (pm20) REVERT: E 65 LEU cc_start: 0.9549 (tp) cc_final: 0.8959 (tp) REVERT: E 79 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8900 (ptmm) REVERT: E 105 GLU cc_start: 0.8905 (pp20) cc_final: 0.8495 (pp20) REVERT: E 106 ASP cc_start: 0.9347 (m-30) cc_final: 0.8730 (m-30) REVERT: F 49 LEU cc_start: 0.9637 (mt) cc_final: 0.9373 (mp) REVERT: F 59 LYS cc_start: 0.9449 (tmtt) cc_final: 0.8987 (tmtt) REVERT: F 84 MET cc_start: 0.8846 (tpt) cc_final: 0.8476 (tpp) REVERT: F 93 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 64 GLU cc_start: 0.8742 (tp30) cc_final: 0.8195 (tp30) REVERT: G 101 THR cc_start: 0.9455 (m) cc_final: 0.9186 (p) REVERT: H 65 ASP cc_start: 0.8914 (t0) cc_final: 0.8462 (t0) REVERT: H 68 GLU cc_start: 0.8777 (pp20) cc_final: 0.8565 (pp20) REVERT: H 73 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8045 (mm-30) REVERT: H 76 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8380 (ttp-110) REVERT: M 235 ASN cc_start: 0.9510 (t0) cc_final: 0.9200 (t0) REVERT: N 42 MET cc_start: 0.9219 (pmm) cc_final: 0.8915 (pmm) REVERT: N 220 PHE cc_start: 0.9314 (m-80) cc_final: 0.8980 (m-80) REVERT: N 256 PHE cc_start: 0.8922 (m-80) cc_final: 0.8679 (m-80) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.3061 time to fit residues: 117.2541 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 : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.0060 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN N 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.059244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.038517 restraints weight = 117239.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038939 restraints weight = 60013.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039433 restraints weight = 38063.179| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16823 Z= 0.144 Angle : 0.583 7.330 23897 Z= 0.340 Chirality : 0.036 0.161 2680 Planarity : 0.005 0.069 2052 Dihedral : 29.316 143.583 4500 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1275 helix: 0.41 (0.21), residues: 571 sheet: 0.17 (0.36), residues: 240 loop : -1.16 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.030 0.001 TYR F 88 ARG 0.005 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 859) hydrogen bonds : angle 4.16898 ( 2167) SS BOND : bond 0.00364 ( 5) SS BOND : angle 1.12806 ( 10) covalent geometry : bond 0.00299 (16818) covalent geometry : angle 0.58233 (23887) *********************** 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 251 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9398 (pttm) cc_final: 0.9162 (pttm) REVERT: A 64 LYS cc_start: 0.9688 (mptt) cc_final: 0.9481 (mmtm) REVERT: A 106 ASP cc_start: 0.9152 (m-30) cc_final: 0.8936 (m-30) REVERT: B 49 LEU cc_start: 0.9291 (mp) cc_final: 0.8922 (tp) REVERT: D 54 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9223 (mtpt) REVERT: D 65 ASP cc_start: 0.9289 (t70) cc_final: 0.9050 (t0) REVERT: D 66 ILE cc_start: 0.9538 (mm) cc_final: 0.9250 (mm) REVERT: E 56 LYS cc_start: 0.9618 (ptpp) cc_final: 0.9396 (ptpp) REVERT: E 60 LEU cc_start: 0.9352 (mt) cc_final: 0.9035 (mt) REVERT: E 65 LEU cc_start: 0.9617 (tp) cc_final: 0.9033 (tp) REVERT: E 79 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8823 (tmmt) REVERT: E 89 VAL cc_start: 0.9616 (t) cc_final: 0.9163 (p) REVERT: E 90 MET cc_start: 0.9085 (mmp) cc_final: 0.8851 (mmm) REVERT: E 93 GLN cc_start: 0.8367 (tm-30) cc_final: 0.6798 (tm-30) REVERT: E 105 GLU cc_start: 0.8914 (pp20) cc_final: 0.8300 (pp20) REVERT: E 106 ASP cc_start: 0.9311 (m-30) cc_final: 0.8779 (m-30) REVERT: E 109 LEU cc_start: 0.9826 (mm) cc_final: 0.9546 (mm) REVERT: F 70 VAL cc_start: 0.9427 (p) cc_final: 0.8998 (p) REVERT: F 84 MET cc_start: 0.8794 (tpt) cc_final: 0.8193 (tpp) REVERT: F 93 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7978 (tm-30) REVERT: G 36 LYS cc_start: 0.9224 (mmtm) cc_final: 0.8835 (mmtm) REVERT: G 64 GLU cc_start: 0.8738 (tp30) cc_final: 0.8176 (tp30) REVERT: G 95 LYS cc_start: 0.9574 (tptt) cc_final: 0.9341 (ttmm) REVERT: H 56 MET cc_start: 0.9198 (tpp) cc_final: 0.8974 (tpp) REVERT: H 65 ASP cc_start: 0.8808 (t0) cc_final: 0.8247 (t0) REVERT: H 90 GLU cc_start: 0.9284 (mp0) cc_final: 0.9061 (mp0) REVERT: H 99 LEU cc_start: 0.9160 (mm) cc_final: 0.8937 (mm) REVERT: H 102 GLU cc_start: 0.8504 (pp20) cc_final: 0.8013 (pp20) REVERT: M 235 ASN cc_start: 0.9511 (t0) cc_final: 0.9178 (t0) REVERT: N 130 ASP cc_start: 0.9477 (p0) cc_final: 0.9163 (p0) REVERT: N 220 PHE cc_start: 0.9220 (m-80) cc_final: 0.8959 (m-80) REVERT: N 256 PHE cc_start: 0.8802 (m-80) cc_final: 0.8493 (m-80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3141 time to fit residues: 111.9863 Evaluate side-chains 197 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 73 ASN ** D 44 GLN ** 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 = 0.3352 r_free = 0.3352 target = 0.054076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.034303 restraints weight = 117426.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034689 restraints weight = 58892.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.035181 restraints weight = 37686.167| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16823 Z= 0.242 Angle : 0.640 11.030 23897 Z= 0.368 Chirality : 0.037 0.146 2680 Planarity : 0.005 0.064 2052 Dihedral : 29.482 146.768 4500 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.18 % Allowed : 5.14 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1275 helix: 0.95 (0.21), residues: 577 sheet: -0.11 (0.35), residues: 258 loop : -0.95 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 193 HIS 0.007 0.001 HIS F 75 PHE 0.016 0.002 PHE A 67 TYR 0.032 0.002 TYR D 37 ARG 0.006 0.001 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.05727 ( 859) hydrogen bonds : angle 4.11168 ( 2167) SS BOND : bond 0.00479 ( 5) SS BOND : angle 1.61932 ( 10) covalent geometry : bond 0.00519 (16818) covalent geometry : angle 0.63947 (23887) *********************** 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 218 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9391 (pttm) cc_final: 0.9161 (pttm) REVERT: A 106 ASP cc_start: 0.9203 (m-30) cc_final: 0.8935 (m-30) REVERT: B 49 LEU cc_start: 0.9413 (mp) cc_final: 0.9134 (tp) REVERT: B 63 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: B 98 TYR cc_start: 0.9311 (m-80) cc_final: 0.8933 (m-80) REVERT: C 73 ASN cc_start: 0.9596 (OUTLIER) cc_final: 0.9258 (t0) REVERT: D 65 ASP cc_start: 0.9244 (t70) cc_final: 0.9043 (t0) REVERT: D 66 ILE cc_start: 0.9706 (mm) cc_final: 0.9465 (mm) REVERT: E 81 ASP cc_start: 0.9018 (t70) cc_final: 0.8787 (t70) REVERT: E 93 GLN cc_start: 0.9028 (tm-30) cc_final: 0.7885 (tm-30) REVERT: E 97 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8400 (mt-10) REVERT: E 105 GLU cc_start: 0.8970 (pp20) cc_final: 0.8526 (pp20) REVERT: E 106 ASP cc_start: 0.9304 (m-30) cc_final: 0.8832 (m-30) REVERT: E 109 LEU cc_start: 0.9842 (mm) cc_final: 0.9510 (mm) REVERT: F 59 LYS cc_start: 0.9499 (tmtt) cc_final: 0.9125 (tmtt) REVERT: F 84 MET cc_start: 0.9134 (tpt) cc_final: 0.8550 (tpp) REVERT: F 93 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8217 (tm-30) REVERT: G 36 LYS cc_start: 0.9336 (mmtm) cc_final: 0.9030 (mmtm) REVERT: G 51 MET cc_start: 0.9584 (tpt) cc_final: 0.9366 (tpp) REVERT: G 56 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8996 (mm-30) REVERT: G 61 GLU cc_start: 0.9040 (tp30) cc_final: 0.8786 (tt0) REVERT: G 64 GLU cc_start: 0.8864 (tp30) cc_final: 0.8302 (tp30) REVERT: G 95 LYS cc_start: 0.9618 (tptt) cc_final: 0.9406 (ttmm) REVERT: H 65 ASP cc_start: 0.9145 (t0) cc_final: 0.8675 (t0) REVERT: H 99 LEU cc_start: 0.9377 (mm) cc_final: 0.9162 (mm) REVERT: H 102 GLU cc_start: 0.8092 (pp20) cc_final: 0.7853 (pp20) REVERT: M 235 ASN cc_start: 0.9609 (t0) cc_final: 0.9251 (t0) REVERT: M 262 LEU cc_start: 0.9268 (tp) cc_final: 0.8987 (tt) outliers start: 2 outliers final: 0 residues processed: 217 average time/residue: 0.3303 time to fit residues: 101.8007 Evaluate side-chains 170 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 70.0000 chunk 102 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 overall best weight: 2.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN ** 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 = 0.3377 r_free = 0.3377 target = 0.055218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.035242 restraints weight = 112205.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.035661 restraints weight = 56344.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036165 restraints weight = 36016.681| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16823 Z= 0.163 Angle : 0.593 9.214 23897 Z= 0.343 Chirality : 0.036 0.150 2680 Planarity : 0.004 0.061 2052 Dihedral : 29.309 144.743 4500 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.09 % Allowed : 2.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1275 helix: 1.30 (0.22), residues: 577 sheet: -0.01 (0.35), residues: 258 loop : -0.81 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 193 HIS 0.007 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.023 0.001 TYR D 37 ARG 0.004 0.000 ARG M 64 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 859) hydrogen bonds : angle 3.84598 ( 2167) SS BOND : bond 0.00371 ( 5) SS BOND : angle 1.06667 ( 10) covalent geometry : bond 0.00350 (16818) covalent geometry : angle 0.59231 (23887) *********************** 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 250 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9800 (mp) cc_final: 0.9562 (mp) REVERT: A 106 ASP cc_start: 0.9201 (m-30) cc_final: 0.8920 (m-30) REVERT: B 49 LEU cc_start: 0.9369 (mp) cc_final: 0.8960 (tp) REVERT: B 98 TYR cc_start: 0.9359 (m-10) cc_final: 0.9069 (m-80) REVERT: C 73 ASN cc_start: 0.9568 (t0) cc_final: 0.9296 (t0) REVERT: C 75 LYS cc_start: 0.9470 (mmmm) cc_final: 0.9080 (mmmm) REVERT: D 66 ILE cc_start: 0.9697 (mm) cc_final: 0.9443 (mm) REVERT: E 50 GLU cc_start: 0.9222 (pm20) cc_final: 0.8983 (pm20) REVERT: E 56 LYS cc_start: 0.9609 (ptpp) cc_final: 0.9375 (ptpp) REVERT: E 60 LEU cc_start: 0.9586 (mt) cc_final: 0.8950 (mp) REVERT: E 65 LEU cc_start: 0.9679 (tp) cc_final: 0.9049 (tp) REVERT: E 93 GLN cc_start: 0.8865 (tm-30) cc_final: 0.6993 (tm-30) REVERT: E 97 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8284 (mt-10) REVERT: E 105 GLU cc_start: 0.8959 (pp20) cc_final: 0.8503 (pp20) REVERT: E 106 ASP cc_start: 0.9319 (m-30) cc_final: 0.8954 (m-30) REVERT: E 109 LEU cc_start: 0.9849 (mm) cc_final: 0.9543 (mm) REVERT: F 59 LYS cc_start: 0.9706 (tmtt) cc_final: 0.9352 (tmtt) REVERT: F 84 MET cc_start: 0.8882 (tpt) cc_final: 0.8046 (tpp) REVERT: F 93 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8238 (tm-30) REVERT: G 36 LYS cc_start: 0.9387 (mmtm) cc_final: 0.9059 (mmtm) REVERT: G 61 GLU cc_start: 0.8974 (tp30) cc_final: 0.8607 (tt0) REVERT: G 64 GLU cc_start: 0.8843 (tp30) cc_final: 0.8366 (tp30) REVERT: G 89 ASN cc_start: 0.9422 (m-40) cc_final: 0.9173 (m-40) REVERT: G 95 LYS cc_start: 0.9621 (tptt) cc_final: 0.9405 (ttmm) REVERT: H 65 ASP cc_start: 0.9066 (t0) cc_final: 0.8672 (t0) REVERT: H 76 ARG cc_start: 0.9378 (ttm-80) cc_final: 0.9076 (ttm110) REVERT: H 99 LEU cc_start: 0.9319 (mm) cc_final: 0.9064 (mm) REVERT: H 102 GLU cc_start: 0.8155 (pp20) cc_final: 0.7679 (pp20) REVERT: M 76 TYR cc_start: 0.8701 (t80) cc_final: 0.8463 (t80) REVERT: M 162 MET cc_start: 0.8179 (ppp) cc_final: 0.7782 (ppp) REVERT: M 235 ASN cc_start: 0.9571 (t0) cc_final: 0.9169 (t0) REVERT: M 262 LEU cc_start: 0.9240 (tp) cc_final: 0.8968 (tt) REVERT: N 256 PHE cc_start: 0.8867 (m-80) cc_final: 0.8485 (m-80) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.4403 time to fit residues: 154.0235 Evaluate side-chains 187 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 146 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.033043 restraints weight = 119892.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.033336 restraints weight = 59768.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.033840 restraints weight = 38415.037| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16823 Z= 0.289 Angle : 0.678 11.871 23897 Z= 0.386 Chirality : 0.039 0.162 2680 Planarity : 0.005 0.063 2052 Dihedral : 29.583 147.288 4500 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1275 helix: 1.21 (0.21), residues: 575 sheet: 0.10 (0.36), residues: 250 loop : -0.70 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 215 HIS 0.011 0.002 HIS G 82 PHE 0.017 0.002 PHE N 220 TYR 0.026 0.002 TYR D 37 ARG 0.008 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.06294 ( 859) hydrogen bonds : angle 4.17729 ( 2167) SS BOND : bond 0.00645 ( 5) SS BOND : angle 1.46332 ( 10) covalent geometry : bond 0.00621 (16818) covalent geometry : angle 0.67744 (23887) *********************** 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 209 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 2.059 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 106 ASP cc_start: 0.9222 (m-30) cc_final: 0.8978 (m-30) REVERT: B 63 GLU cc_start: 0.9362 (pm20) cc_final: 0.9112 (pm20) REVERT: B 98 TYR cc_start: 0.9308 (m-10) cc_final: 0.9026 (m-80) REVERT: C 73 ASN cc_start: 0.9686 (t0) cc_final: 0.9430 (t0) REVERT: C 75 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9194 (mmmm) REVERT: D 65 ASP cc_start: 0.9339 (t0) cc_final: 0.9129 (t0) REVERT: D 66 ILE cc_start: 0.9760 (mm) cc_final: 0.9542 (mm) REVERT: D 83 ARG cc_start: 0.8821 (mmp80) cc_final: 0.8475 (mmp80) REVERT: D 99 LEU cc_start: 0.9380 (mt) cc_final: 0.9074 (mp) REVERT: D 105 LYS cc_start: 0.9482 (ptmt) cc_final: 0.9254 (ptmm) REVERT: E 50 GLU cc_start: 0.9289 (pm20) cc_final: 0.9050 (pm20) REVERT: E 64 LYS cc_start: 0.9679 (mppt) cc_final: 0.9439 (mmtm) REVERT: E 68 GLN cc_start: 0.9073 (pp30) cc_final: 0.8859 (pp30) REVERT: E 90 MET cc_start: 0.9286 (mmp) cc_final: 0.9081 (mmp) REVERT: E 93 GLN cc_start: 0.8773 (tm-30) cc_final: 0.7275 (tm-30) REVERT: E 97 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7899 (mt-10) REVERT: E 105 GLU cc_start: 0.9005 (pp20) cc_final: 0.8629 (pp20) REVERT: E 106 ASP cc_start: 0.9264 (m-30) cc_final: 0.8832 (m-30) REVERT: E 109 LEU cc_start: 0.9830 (mm) cc_final: 0.9493 (mm) REVERT: F 59 LYS cc_start: 0.9647 (tmtt) cc_final: 0.9230 (tmtt) REVERT: F 84 MET cc_start: 0.9169 (tpt) cc_final: 0.8853 (tpp) REVERT: F 88 TYR cc_start: 0.8950 (m-10) cc_final: 0.8341 (m-10) REVERT: F 93 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8443 (tm-30) REVERT: G 64 GLU cc_start: 0.8791 (tp30) cc_final: 0.8345 (tp30) REVERT: G 89 ASN cc_start: 0.9530 (m-40) cc_final: 0.9205 (m-40) REVERT: H 65 ASP cc_start: 0.9211 (t0) cc_final: 0.8816 (t0) REVERT: H 73 GLU cc_start: 0.9433 (tp30) cc_final: 0.9127 (mm-30) REVERT: H 76 ARG cc_start: 0.9398 (ttm-80) cc_final: 0.9091 (ttp-110) REVERT: H 99 LEU cc_start: 0.9536 (mm) cc_final: 0.9299 (mm) REVERT: M 42 MET cc_start: 0.9274 (pmm) cc_final: 0.9050 (pmm) REVERT: M 262 LEU cc_start: 0.9282 (tp) cc_final: 0.9000 (tt) REVERT: N 193 TRP cc_start: 0.8783 (m100) cc_final: 0.8315 (m100) REVERT: N 220 PHE cc_start: 0.9293 (m-80) cc_final: 0.9088 (m-80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.4516 time to fit residues: 134.9646 Evaluate side-chains 168 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 118 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** 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 = 0.3337 r_free = 0.3337 target = 0.053543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.033808 restraints weight = 117422.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034163 restraints weight = 57883.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034490 restraints weight = 36747.237| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2993 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= 0.215 Angle : 0.636 10.356 23897 Z= 0.364 Chirality : 0.038 0.220 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.564 145.340 4500 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1275 helix: 1.34 (0.21), residues: 575 sheet: 0.08 (0.36), residues: 250 loop : -0.66 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 215 HIS 0.011 0.002 HIS F 75 PHE 0.011 0.001 PHE N 220 TYR 0.027 0.002 TYR C 57 ARG 0.004 0.000 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.05091 ( 859) hydrogen bonds : angle 4.02069 ( 2167) SS BOND : bond 0.00428 ( 5) SS BOND : angle 1.24927 ( 10) covalent geometry : bond 0.00465 (16818) covalent geometry : angle 0.63533 (23887) *********************** 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 228 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9198 (m-30) cc_final: 0.8947 (m-30) REVERT: B 98 TYR cc_start: 0.9296 (m-10) cc_final: 0.9028 (m-80) REVERT: C 73 ASN cc_start: 0.9686 (t0) cc_final: 0.9422 (t0) REVERT: C 75 LYS cc_start: 0.9492 (mmmm) cc_final: 0.9216 (mmmm) REVERT: C 104 GLN cc_start: 0.8733 (mp10) cc_final: 0.8257 (mp10) REVERT: D 66 ILE cc_start: 0.9742 (mm) cc_final: 0.9507 (mm) REVERT: D 99 LEU cc_start: 0.9407 (mt) cc_final: 0.9105 (mp) REVERT: E 64 LYS cc_start: 0.9664 (mppt) cc_final: 0.9438 (mmtm) REVERT: E 65 LEU cc_start: 0.9686 (tp) cc_final: 0.9132 (tp) REVERT: E 90 MET cc_start: 0.9293 (mmp) cc_final: 0.9073 (mmp) REVERT: E 93 GLN cc_start: 0.8711 (tm-30) cc_final: 0.7587 (tm-30) REVERT: E 97 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7680 (mt-10) REVERT: E 105 GLU cc_start: 0.8947 (pp20) cc_final: 0.8679 (pp20) REVERT: E 106 ASP cc_start: 0.9286 (m-30) cc_final: 0.8906 (m-30) REVERT: F 59 LYS cc_start: 0.9646 (tmtt) cc_final: 0.8569 (tmtt) REVERT: F 63 GLU cc_start: 0.9191 (pt0) cc_final: 0.8220 (pt0) REVERT: F 84 MET cc_start: 0.9023 (tpt) cc_final: 0.8577 (tpp) REVERT: F 88 TYR cc_start: 0.8933 (m-10) cc_final: 0.8282 (m-10) REVERT: F 93 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8491 (tm-30) REVERT: G 64 GLU cc_start: 0.8763 (tp30) cc_final: 0.8293 (tp30) REVERT: G 89 ASN cc_start: 0.9490 (m-40) cc_final: 0.9145 (m-40) REVERT: H 65 ASP cc_start: 0.9090 (t0) cc_final: 0.8763 (t0) REVERT: H 76 ARG cc_start: 0.9457 (ttm-80) cc_final: 0.9181 (ttm110) REVERT: H 99 LEU cc_start: 0.9530 (mm) cc_final: 0.9326 (mm) REVERT: H 102 GLU cc_start: 0.8025 (pp20) cc_final: 0.7699 (pp20) REVERT: M 162 MET cc_start: 0.8374 (ppp) cc_final: 0.7965 (ppp) REVERT: M 262 LEU cc_start: 0.9314 (tp) cc_final: 0.9044 (tt) REVERT: N 42 MET cc_start: 0.9456 (pmm) cc_final: 0.9216 (pmm) REVERT: N 193 TRP cc_start: 0.8654 (m100) cc_final: 0.8438 (m100) REVERT: N 220 PHE cc_start: 0.9361 (m-80) cc_final: 0.9110 (m-80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3278 time to fit residues: 105.2288 Evaluate side-chains 172 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 146 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.053567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.033864 restraints weight = 117907.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034233 restraints weight = 58524.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.034735 restraints weight = 37280.758| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16823 Z= 0.204 Angle : 0.644 10.567 23897 Z= 0.366 Chirality : 0.038 0.183 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.517 145.391 4500 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1275 helix: 1.34 (0.22), residues: 571 sheet: 0.04 (0.35), residues: 250 loop : -0.62 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 215 HIS 0.012 0.002 HIS F 75 PHE 0.013 0.001 PHE A 67 TYR 0.019 0.001 TYR D 37 ARG 0.005 0.000 ARG M 64 Details of bonding type rmsd hydrogen bonds : bond 0.04990 ( 859) hydrogen bonds : angle 4.05833 ( 2167) SS BOND : bond 0.00582 ( 5) SS BOND : angle 2.06973 ( 10) covalent geometry : bond 0.00440 (16818) covalent geometry : angle 0.64304 (23887) *********************** 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 223 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9411 (pttm) cc_final: 0.9192 (ptpp) REVERT: A 106 ASP cc_start: 0.9191 (m-30) cc_final: 0.8951 (m-30) REVERT: B 58 LEU cc_start: 0.9792 (tt) cc_final: 0.9585 (tt) REVERT: B 62 LEU cc_start: 0.9773 (mp) cc_final: 0.9546 (mp) REVERT: B 98 TYR cc_start: 0.9294 (m-10) cc_final: 0.9027 (m-80) REVERT: C 73 ASN cc_start: 0.9660 (t0) cc_final: 0.9298 (t0) REVERT: D 66 ILE cc_start: 0.9739 (mm) cc_final: 0.9493 (mm) REVERT: D 83 ARG cc_start: 0.8761 (mmp80) cc_final: 0.8464 (mmp80) REVERT: D 99 LEU cc_start: 0.9375 (mt) cc_final: 0.9014 (mp) REVERT: E 60 LEU cc_start: 0.9491 (mp) cc_final: 0.8750 (mt) REVERT: E 64 LYS cc_start: 0.9686 (mppt) cc_final: 0.9409 (mmtm) REVERT: E 65 LEU cc_start: 0.9676 (tp) cc_final: 0.9155 (tp) REVERT: E 90 MET cc_start: 0.9298 (mmp) cc_final: 0.9077 (mmp) REVERT: E 93 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7470 (tm-30) REVERT: E 105 GLU cc_start: 0.8983 (pp20) cc_final: 0.8749 (pp20) REVERT: E 106 ASP cc_start: 0.9291 (m-30) cc_final: 0.8949 (m-30) REVERT: F 59 LYS cc_start: 0.9659 (tmtt) cc_final: 0.9229 (tmtt) REVERT: F 84 MET cc_start: 0.9012 (tpt) cc_final: 0.8548 (tpp) REVERT: F 88 TYR cc_start: 0.8940 (m-10) cc_final: 0.8244 (m-10) REVERT: F 93 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8444 (tm-30) REVERT: G 61 GLU cc_start: 0.8971 (tp30) cc_final: 0.8619 (tp30) REVERT: G 64 GLU cc_start: 0.8747 (tp30) cc_final: 0.8247 (tp30) REVERT: G 89 ASN cc_start: 0.9477 (m-40) cc_final: 0.9143 (m-40) REVERT: H 65 ASP cc_start: 0.9105 (t0) cc_final: 0.8701 (t0) REVERT: H 99 LEU cc_start: 0.9524 (mm) cc_final: 0.9275 (mm) REVERT: H 102 GLU cc_start: 0.8056 (pp20) cc_final: 0.7786 (pp20) REVERT: M 262 LEU cc_start: 0.9297 (tp) cc_final: 0.9034 (tt) REVERT: N 42 MET cc_start: 0.9507 (pmm) cc_final: 0.9246 (pmm) REVERT: N 220 PHE cc_start: 0.9362 (m-80) cc_final: 0.9040 (m-80) REVERT: N 256 PHE cc_start: 0.8831 (m-80) cc_final: 0.8341 (m-80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3354 time to fit residues: 105.4629 Evaluate side-chains 181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 100 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036839 restraints weight = 113164.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037098 restraints weight = 60427.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037573 restraints weight = 40161.934| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16823 Z= 0.150 Angle : 0.633 12.279 23897 Z= 0.356 Chirality : 0.038 0.186 2680 Planarity : 0.004 0.059 2052 Dihedral : 29.248 143.590 4500 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.09 % Allowed : 1.62 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1275 helix: 1.42 (0.22), residues: 569 sheet: -0.04 (0.35), residues: 256 loop : -0.54 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP N 193 HIS 0.010 0.001 HIS F 75 PHE 0.016 0.001 PHE A 67 TYR 0.025 0.001 TYR C 57 ARG 0.006 0.000 ARG M 64 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 859) hydrogen bonds : angle 3.91756 ( 2167) SS BOND : bond 0.00870 ( 5) SS BOND : angle 1.83306 ( 10) covalent geometry : bond 0.00322 (16818) covalent geometry : angle 0.63199 (23887) *********************** 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 235 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9152 (m-30) cc_final: 0.8909 (m-30) REVERT: B 98 TYR cc_start: 0.9276 (m-10) cc_final: 0.8968 (m-80) REVERT: C 73 ASN cc_start: 0.9594 (t0) cc_final: 0.9215 (t0) REVERT: C 104 GLN cc_start: 0.8601 (mp10) cc_final: 0.8347 (mp10) REVERT: D 66 ILE cc_start: 0.9689 (mm) cc_final: 0.9465 (mm) REVERT: D 68 GLU cc_start: 0.8621 (mp0) cc_final: 0.8346 (mp0) REVERT: E 50 GLU cc_start: 0.9348 (pm20) cc_final: 0.9142 (pm20) REVERT: E 64 LYS cc_start: 0.9670 (mppt) cc_final: 0.9402 (mmtm) REVERT: E 65 LEU cc_start: 0.9661 (tp) cc_final: 0.9121 (tp) REVERT: E 68 GLN cc_start: 0.9021 (pp30) cc_final: 0.8803 (pp30) REVERT: E 105 GLU cc_start: 0.8937 (pp20) cc_final: 0.8691 (pp20) REVERT: E 106 ASP cc_start: 0.9252 (m-30) cc_final: 0.8848 (m-30) REVERT: E 109 LEU cc_start: 0.9830 (mm) cc_final: 0.9594 (mm) REVERT: F 59 LYS cc_start: 0.9679 (tmtt) cc_final: 0.8527 (tmtt) REVERT: F 63 GLU cc_start: 0.9233 (pt0) cc_final: 0.8465 (pt0) REVERT: F 84 MET cc_start: 0.8876 (tpt) cc_final: 0.8438 (tpp) REVERT: F 88 TYR cc_start: 0.8873 (m-10) cc_final: 0.8099 (m-10) REVERT: F 93 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8288 (tm-30) REVERT: G 64 GLU cc_start: 0.8752 (tp30) cc_final: 0.8338 (tp30) REVERT: G 89 ASN cc_start: 0.9353 (m-40) cc_final: 0.9124 (m-40) REVERT: H 65 ASP cc_start: 0.9065 (t0) cc_final: 0.8613 (t0) REVERT: H 102 GLU cc_start: 0.8157 (pp20) cc_final: 0.7859 (pp20) REVERT: M 262 LEU cc_start: 0.9264 (tp) cc_final: 0.9027 (tt) REVERT: N 42 MET cc_start: 0.9362 (pmm) cc_final: 0.9145 (pmm) REVERT: N 220 PHE cc_start: 0.9343 (m-80) cc_final: 0.9035 (m-80) REVERT: N 256 PHE cc_start: 0.8746 (m-80) cc_final: 0.8263 (m-80) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.3100 time to fit residues: 103.5845 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 : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.051828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.031732 restraints weight = 119467.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.032099 restraints weight = 59583.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.032577 restraints weight = 38185.560| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16823 Z= 0.324 Angle : 0.736 12.049 23897 Z= 0.414 Chirality : 0.041 0.186 2680 Planarity : 0.005 0.058 2052 Dihedral : 29.695 147.295 4500 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1275 helix: 1.14 (0.21), residues: 576 sheet: -0.24 (0.34), residues: 252 loop : -0.73 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP N 193 HIS 0.014 0.002 HIS G 82 PHE 0.022 0.002 PHE H 62 TYR 0.030 0.002 TYR M 76 ARG 0.008 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.06762 ( 859) hydrogen bonds : angle 4.34835 ( 2167) SS BOND : bond 0.00594 ( 5) SS BOND : angle 2.24047 ( 10) covalent geometry : bond 0.00700 (16818) covalent geometry : angle 0.73466 (23887) *********************** 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 209 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.479 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 97 GLU cc_start: 0.8866 (mp0) cc_final: 0.8543 (mp0) REVERT: A 106 ASP cc_start: 0.9227 (m-30) cc_final: 0.8984 (m-30) REVERT: C 36 LYS cc_start: 0.9239 (mptt) cc_final: 0.8995 (mmtm) REVERT: C 73 ASN cc_start: 0.9719 (t0) cc_final: 0.9389 (t0) REVERT: C 104 GLN cc_start: 0.8790 (mp10) cc_final: 0.8545 (mp10) REVERT: D 66 ILE cc_start: 0.9742 (mm) cc_final: 0.9491 (mm) REVERT: D 68 GLU cc_start: 0.8686 (mp0) cc_final: 0.8356 (mp0) REVERT: D 83 ARG cc_start: 0.8802 (mmp80) cc_final: 0.8549 (mmp80) REVERT: E 64 LYS cc_start: 0.9668 (mppt) cc_final: 0.9412 (pttt) REVERT: E 90 MET cc_start: 0.9366 (mmp) cc_final: 0.9132 (mmp) REVERT: E 105 GLU cc_start: 0.9051 (pp20) cc_final: 0.8808 (pp20) REVERT: E 106 ASP cc_start: 0.9345 (m-30) cc_final: 0.8996 (m-30) REVERT: F 84 MET cc_start: 0.9101 (tpt) cc_final: 0.8421 (tpp) REVERT: F 93 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8547 (tm-30) REVERT: G 64 GLU cc_start: 0.8812 (tp30) cc_final: 0.8360 (tp30) REVERT: G 89 ASN cc_start: 0.9525 (m-40) cc_final: 0.9310 (m-40) REVERT: H 40 LYS cc_start: 0.9766 (ttmt) cc_final: 0.9454 (ttpp) REVERT: H 64 ASN cc_start: 0.9514 (m-40) cc_final: 0.9123 (m110) REVERT: H 65 ASP cc_start: 0.9148 (t0) cc_final: 0.8557 (t0) REVERT: H 76 ARG cc_start: 0.9480 (ttm-80) cc_final: 0.9219 (ttm110) REVERT: H 90 GLU cc_start: 0.9271 (mp0) cc_final: 0.8944 (mp0) REVERT: M 42 MET cc_start: 0.9330 (pmm) cc_final: 0.9080 (pmm) REVERT: M 262 LEU cc_start: 0.9358 (tp) cc_final: 0.9084 (tt) REVERT: N 42 MET cc_start: 0.9454 (pmm) cc_final: 0.9192 (pmm) REVERT: N 103 MET cc_start: 0.9062 (mmm) cc_final: 0.8818 (mmm) REVERT: N 220 PHE cc_start: 0.9450 (m-80) cc_final: 0.9220 (m-80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3452 time to fit residues: 102.7844 Evaluate side-chains 162 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 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 = 0.3332 r_free = 0.3332 target = 0.053324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.033303 restraints weight = 118539.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.033609 restraints weight = 59502.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.034122 restraints weight = 38123.750| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16823 Z= 0.203 Angle : 0.683 10.955 23897 Z= 0.382 Chirality : 0.039 0.254 2680 Planarity : 0.004 0.059 2052 Dihedral : 29.616 144.159 4500 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1275 helix: 1.16 (0.22), residues: 576 sheet: -0.19 (0.34), residues: 252 loop : -0.63 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 193 HIS 0.015 0.002 HIS G 82 PHE 0.023 0.002 PHE E 67 TYR 0.031 0.002 TYR C 57 ARG 0.005 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04954 ( 859) hydrogen bonds : angle 4.13641 ( 2167) SS BOND : bond 0.00403 ( 5) SS BOND : angle 1.89938 ( 10) covalent geometry : bond 0.00442 (16818) covalent geometry : angle 0.68158 (23887) ********************** 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 221 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8951 (mp0) cc_final: 0.8543 (mp0) REVERT: A 106 ASP cc_start: 0.9162 (m-30) cc_final: 0.8923 (m-30) REVERT: C 73 ASN cc_start: 0.9715 (t0) cc_final: 0.9358 (t0) REVERT: C 104 GLN cc_start: 0.8735 (mp10) cc_final: 0.8451 (mp10) REVERT: D 66 ILE cc_start: 0.9747 (mm) cc_final: 0.9518 (mm) REVERT: D 83 ARG cc_start: 0.8769 (mmp80) cc_final: 0.8454 (mmp80) REVERT: D 99 LEU cc_start: 0.9390 (mt) cc_final: 0.9174 (mp) REVERT: E 60 LEU cc_start: 0.9622 (mm) cc_final: 0.9047 (mm) REVERT: E 64 LYS cc_start: 0.9611 (mppt) cc_final: 0.9297 (mmtm) REVERT: E 65 LEU cc_start: 0.9680 (tp) cc_final: 0.9181 (tp) REVERT: E 97 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8733 (mt-10) REVERT: E 105 GLU cc_start: 0.8972 (pp20) cc_final: 0.8725 (pp20) REVERT: E 106 ASP cc_start: 0.9243 (m-30) cc_final: 0.8887 (m-30) REVERT: F 59 LYS cc_start: 0.9537 (tmtt) cc_final: 0.8818 (tmtt) REVERT: F 63 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8848 (mt-10) REVERT: F 84 MET cc_start: 0.8874 (tpt) cc_final: 0.8147 (tpp) REVERT: F 93 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8370 (tm-30) REVERT: G 64 GLU cc_start: 0.8696 (tp30) cc_final: 0.8178 (tp30) REVERT: H 64 ASN cc_start: 0.9530 (m-40) cc_final: 0.9163 (m110) REVERT: H 65 ASP cc_start: 0.9016 (t0) cc_final: 0.8532 (t0) REVERT: H 73 GLU cc_start: 0.9264 (tp30) cc_final: 0.8868 (tp30) REVERT: H 76 ARG cc_start: 0.9433 (ttm-80) cc_final: 0.9177 (ttm110) REVERT: H 90 GLU cc_start: 0.9258 (mp0) cc_final: 0.8973 (mp0) REVERT: M 262 LEU cc_start: 0.9271 (tp) cc_final: 0.9026 (tt) REVERT: N 42 MET cc_start: 0.9377 (pmm) cc_final: 0.9154 (pmm) REVERT: N 220 PHE cc_start: 0.9362 (m-80) cc_final: 0.9158 (m-80) REVERT: N 256 PHE cc_start: 0.8821 (m-80) cc_final: 0.8360 (m-80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3257 time to fit residues: 101.9950 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 : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.054924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.035275 restraints weight = 115713.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035428 restraints weight = 62423.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.035891 restraints weight = 41999.469| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16823 Z= 0.193 Angle : 0.667 10.797 23897 Z= 0.376 Chirality : 0.039 0.186 2680 Planarity : 0.004 0.059 2052 Dihedral : 29.510 144.447 4500 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1275 helix: 1.19 (0.22), residues: 576 sheet: -0.24 (0.34), residues: 258 loop : -0.52 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP N 193 HIS 0.011 0.002 HIS G 82 PHE 0.011 0.001 PHE A 67 TYR 0.041 0.002 TYR H 80 ARG 0.005 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 859) hydrogen bonds : angle 4.13335 ( 2167) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.94635 ( 10) covalent geometry : bond 0.00420 (16818) covalent geometry : angle 0.66615 (23887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5845.64 seconds wall clock time: 105 minutes 9.77 seconds (6309.77 seconds total)