Starting phenix.real_space_refine on Sat Mar 16 22:51:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/03_2024/8evj_28631.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/03_2024/8evj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/03_2024/8evj_28631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/03_2024/8evj_28631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/03_2024/8evj_28631.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evj_28631/03_2024/8evj_28631.pdb" } 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 Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "M TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 214": "OD1" <-> "OD2" Residue "M PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.26, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 7.46 Conformation dependent library (CDL) restraints added in 1.8 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: 6.69 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: 6.34 Time building geometry restraints manager: 7.91 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: 97.48 - 104.86: 1210 104.86 - 112.24: 8873 112.24 - 119.62: 5847 119.62 - 127.00: 7214 127.00 - 134.38: 743 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 2.440 nonbonded pdb=" OE2 GLU D 102 " pdb=" OH TYR N 54 " model vdw 2.287 2.440 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.300 2.440 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 2.440 ... (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 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 48.000 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.360 ------------------------------------------------------------------------------- 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 16818 Z= 0.280 Angle : 0.935 16.093 23887 Z= 0.510 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 1.355 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: 0.3125 time to fit residues: 118.9587 Evaluate side-chains 200 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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: 7.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** F 27 GLN ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16818 Z= 0.182 Angle : 0.577 9.065 23887 Z= 0.338 Chirality : 0.035 0.146 2680 Planarity : 0.004 0.067 2052 Dihedral : 29.331 143.908 4500 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: -0.28 (0.23), residues: 1275 helix: 0.54 (0.21), residues: 571 sheet: 0.05 (0.35), residues: 244 loop : -1.13 (0.26), residues: 460 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 0.010 0.001 PHE H 62 TYR 0.030 0.001 TYR F 88 ARG 0.003 0.000 ARG H 76 *********************** 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 234 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9378 (pttm) cc_final: 0.9148 (pttm) REVERT: A 64 LYS cc_start: 0.9723 (mptt) cc_final: 0.9505 (mmtm) REVERT: A 106 ASP cc_start: 0.9133 (m-30) cc_final: 0.8913 (m-30) REVERT: D 54 LYS cc_start: 0.9551 (mmmm) cc_final: 0.9245 (mtpt) REVERT: D 65 ASP cc_start: 0.9340 (t70) cc_final: 0.8981 (t0) REVERT: D 66 ILE cc_start: 0.9576 (mm) cc_final: 0.9293 (mm) REVERT: E 50 GLU cc_start: 0.9130 (pm20) cc_final: 0.8918 (pm20) REVERT: E 65 LEU cc_start: 0.9645 (tp) cc_final: 0.9064 (tp) REVERT: E 79 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8784 (tmmt) REVERT: E 89 VAL cc_start: 0.9613 (t) cc_final: 0.9167 (p) REVERT: E 90 MET cc_start: 0.9197 (mmp) cc_final: 0.8922 (mmm) REVERT: E 103 LEU cc_start: 0.9691 (tt) cc_final: 0.9471 (tp) REVERT: E 105 GLU cc_start: 0.8931 (pp20) cc_final: 0.8510 (pp20) REVERT: E 106 ASP cc_start: 0.9299 (m-30) cc_final: 0.8869 (m-30) REVERT: E 109 LEU cc_start: 0.9825 (mm) cc_final: 0.9535 (mm) REVERT: E 125 GLN cc_start: 0.9556 (mt0) cc_final: 0.9257 (mt0) REVERT: F 70 VAL cc_start: 0.9398 (p) cc_final: 0.8948 (p) REVERT: F 84 MET cc_start: 0.8808 (tpt) cc_final: 0.8225 (tpp) REVERT: F 93 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8060 (tm-30) REVERT: G 36 LYS cc_start: 0.9223 (mmtm) cc_final: 0.8831 (mmtm) REVERT: G 56 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8750 (mm-30) REVERT: G 64 GLU cc_start: 0.8763 (tp30) cc_final: 0.8219 (tp30) REVERT: G 95 LYS cc_start: 0.9585 (tptt) cc_final: 0.9358 (ttmm) REVERT: H 56 MET cc_start: 0.9250 (tpp) cc_final: 0.9038 (tpp) REVERT: H 65 ASP cc_start: 0.8880 (t0) cc_final: 0.8307 (t0) REVERT: H 99 LEU cc_start: 0.9170 (mm) cc_final: 0.8957 (mm) REVERT: H 102 GLU cc_start: 0.8519 (pp20) cc_final: 0.8010 (pp20) REVERT: M 103 MET cc_start: 0.9292 (tpt) cc_final: 0.8948 (tpt) REVERT: M 235 ASN cc_start: 0.9519 (t0) cc_final: 0.9174 (t0) REVERT: N 220 PHE cc_start: 0.9330 (m-80) cc_final: 0.9062 (m-80) REVERT: N 256 PHE cc_start: 0.8907 (m-80) cc_final: 0.8593 (m-80) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3141 time to fit residues: 104.2913 Evaluate side-chains 186 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 136 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN M 249 HIS N 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16818 Z= 0.155 Angle : 0.569 10.091 23887 Z= 0.329 Chirality : 0.035 0.146 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.044 143.947 4500 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.27 % Allowed : 3.52 % Favored : 96.21 % 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: 0.22 (0.23), residues: 1275 helix: 1.09 (0.22), residues: 571 sheet: 0.15 (0.35), residues: 252 loop : -1.01 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 193 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE H 62 TYR 0.033 0.001 TYR H 80 ARG 0.004 0.000 ARG D 76 *********************** 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 245 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 242 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9398 (pttm) cc_final: 0.9164 (pttm) REVERT: A 64 LYS cc_start: 0.9696 (mptt) cc_final: 0.9492 (mmtm) REVERT: A 94 GLU cc_start: 0.8841 (tt0) cc_final: 0.8528 (tt0) REVERT: A 96 CYS cc_start: 0.9074 (p) cc_final: 0.8836 (p) REVERT: A 97 GLU cc_start: 0.8703 (mp0) cc_final: 0.8366 (mp0) REVERT: A 106 ASP cc_start: 0.9105 (m-30) cc_final: 0.8837 (m-30) REVERT: B 49 LEU cc_start: 0.9291 (mp) cc_final: 0.8758 (tp) REVERT: B 52 GLU cc_start: 0.9080 (mp0) cc_final: 0.8766 (mp0) REVERT: B 63 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8918 (pp20) REVERT: B 98 TYR cc_start: 0.9317 (m-80) cc_final: 0.9019 (m-80) REVERT: C 57 TYR cc_start: 0.9090 (t80) cc_final: 0.8889 (t80) REVERT: C 73 ASN cc_start: 0.9508 (OUTLIER) cc_final: 0.9217 (t0) REVERT: C 75 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9120 (mmmm) REVERT: D 42 LEU cc_start: 0.9550 (tt) cc_final: 0.9328 (pp) REVERT: D 54 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9231 (mtpt) REVERT: D 65 ASP cc_start: 0.9349 (t70) cc_final: 0.9018 (t0) REVERT: D 66 ILE cc_start: 0.9635 (mm) cc_final: 0.9372 (mm) REVERT: E 50 GLU cc_start: 0.9084 (pm20) cc_final: 0.8874 (pm20) REVERT: E 65 LEU cc_start: 0.9664 (tp) cc_final: 0.9053 (tp) REVERT: E 79 LYS cc_start: 0.9200 (ttpt) cc_final: 0.8976 (ttpp) REVERT: E 93 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7718 (tm-30) REVERT: E 105 GLU cc_start: 0.8931 (pp20) cc_final: 0.8431 (pp20) REVERT: E 106 ASP cc_start: 0.9332 (m-30) cc_final: 0.8826 (m-30) REVERT: E 109 LEU cc_start: 0.9819 (mm) cc_final: 0.9525 (mm) REVERT: F 59 LYS cc_start: 0.9638 (tmtt) cc_final: 0.9116 (tmtt) REVERT: F 84 MET cc_start: 0.8694 (tpt) cc_final: 0.7933 (tpp) REVERT: F 93 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8060 (tm-30) REVERT: G 36 LYS cc_start: 0.9322 (mmtm) cc_final: 0.8945 (mmtm) REVERT: G 64 GLU cc_start: 0.8703 (tp30) cc_final: 0.8217 (tp30) REVERT: G 95 LYS cc_start: 0.9578 (tptt) cc_final: 0.9371 (ttmm) REVERT: H 58 ILE cc_start: 0.9871 (mm) cc_final: 0.9659 (mt) REVERT: H 65 ASP cc_start: 0.9041 (t0) cc_final: 0.8671 (t0) REVERT: H 99 LEU cc_start: 0.9046 (mm) cc_final: 0.8786 (mm) REVERT: H 102 GLU cc_start: 0.8419 (pp20) cc_final: 0.7878 (pp20) REVERT: M 235 ASN cc_start: 0.9514 (t0) cc_final: 0.9146 (t0) REVERT: N 103 MET cc_start: 0.9233 (tpt) cc_final: 0.8912 (tpt) REVERT: N 220 PHE cc_start: 0.9309 (m-80) cc_final: 0.9090 (m-80) REVERT: N 256 PHE cc_start: 0.8744 (m-80) cc_final: 0.8423 (m-80) outliers start: 3 outliers final: 0 residues processed: 243 average time/residue: 0.3178 time to fit residues: 110.2354 Evaluate side-chains 200 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 50.0000 chunk 71 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- 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 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16818 Z= 0.210 Angle : 0.582 11.103 23887 Z= 0.337 Chirality : 0.036 0.149 2680 Planarity : 0.004 0.060 2052 Dihedral : 29.062 145.518 4500 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: 1.40 (0.22), residues: 577 sheet: 0.21 (0.36), residues: 254 loop : -0.85 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 193 HIS 0.008 0.001 HIS F 75 PHE 0.008 0.001 PHE H 62 TYR 0.025 0.001 TYR D 37 ARG 0.004 0.000 ARG D 76 *********************** 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 236 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.574 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: 0.9417 (pttm) cc_final: 0.9207 (pttm) REVERT: A 92 LEU cc_start: 0.9804 (mp) cc_final: 0.9544 (mp) REVERT: A 106 ASP cc_start: 0.9134 (m-30) cc_final: 0.8851 (m-30) REVERT: B 49 LEU cc_start: 0.9343 (mp) cc_final: 0.8886 (tp) REVERT: B 52 GLU cc_start: 0.9190 (mp0) cc_final: 0.8825 (mp0) REVERT: B 59 LYS cc_start: 0.9029 (tptm) cc_final: 0.8783 (tptp) REVERT: B 63 GLU cc_start: 0.8957 (pm20) cc_final: 0.8728 (pm20) REVERT: B 98 TYR cc_start: 0.9231 (m-80) cc_final: 0.8946 (m-80) REVERT: C 73 ASN cc_start: 0.9530 (t0) cc_final: 0.9289 (t0) REVERT: C 75 LYS cc_start: 0.9479 (mmmm) cc_final: 0.9175 (mmmm) REVERT: D 65 ASP cc_start: 0.9394 (t70) cc_final: 0.9138 (t0) REVERT: D 66 ILE cc_start: 0.9702 (mm) cc_final: 0.9448 (mm) REVERT: D 105 LYS cc_start: 0.9238 (ptmm) cc_final: 0.9010 (ptmm) REVERT: E 65 LEU cc_start: 0.9704 (tp) cc_final: 0.9059 (tp) REVERT: E 93 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7762 (tm-30) REVERT: E 105 GLU cc_start: 0.8932 (pp20) cc_final: 0.8468 (pp20) REVERT: E 106 ASP cc_start: 0.9314 (m-30) cc_final: 0.8810 (m-30) REVERT: E 109 LEU cc_start: 0.9832 (mm) cc_final: 0.9524 (mm) REVERT: F 59 LYS cc_start: 0.9566 (tmtt) cc_final: 0.8505 (tmtt) REVERT: F 63 GLU cc_start: 0.9195 (pt0) cc_final: 0.8494 (pt0) REVERT: F 84 MET cc_start: 0.9024 (tpt) cc_final: 0.8401 (tpp) REVERT: F 93 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8193 (tm-30) REVERT: G 36 LYS cc_start: 0.9374 (mmtm) cc_final: 0.9036 (mmtm) REVERT: G 56 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8675 (mm-30) REVERT: G 61 GLU cc_start: 0.8898 (tp30) cc_final: 0.8625 (tp30) REVERT: G 64 GLU cc_start: 0.8613 (tp30) cc_final: 0.8131 (tp30) REVERT: G 95 LYS cc_start: 0.9599 (tptt) cc_final: 0.9350 (ttmm) REVERT: H 30 ARG cc_start: 0.7667 (mpp-170) cc_final: 0.7398 (mtm-85) REVERT: H 65 ASP cc_start: 0.9133 (t0) cc_final: 0.8688 (t0) REVERT: H 99 LEU cc_start: 0.9195 (mm) cc_final: 0.8925 (mm) REVERT: M 76 TYR cc_start: 0.8564 (t80) cc_final: 0.8297 (t80) REVERT: M 162 MET cc_start: 0.8108 (ppp) cc_final: 0.7625 (ppp) REVERT: M 235 ASN cc_start: 0.9544 (t0) cc_final: 0.9179 (t0) REVERT: M 262 LEU cc_start: 0.9278 (tp) cc_final: 0.9030 (tt) REVERT: N 103 MET cc_start: 0.9170 (tpt) cc_final: 0.8793 (tpt) REVERT: N 220 PHE cc_start: 0.9366 (m-80) cc_final: 0.9143 (m-80) REVERT: N 256 PHE cc_start: 0.8805 (m-80) cc_final: 0.8483 (m-80) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3136 time to fit residues: 105.2583 Evaluate side-chains 191 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 0 optimal weight: 70.0000 chunk 74 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16818 Z= 0.163 Angle : 0.572 9.915 23887 Z= 0.328 Chirality : 0.035 0.156 2680 Planarity : 0.004 0.058 2052 Dihedral : 28.915 143.910 4500 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.24), residues: 1275 helix: 1.48 (0.22), residues: 577 sheet: 0.33 (0.36), residues: 252 loop : -0.82 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 193 HIS 0.011 0.001 HIS H 106 PHE 0.009 0.001 PHE A 67 TYR 0.021 0.001 TYR D 37 ARG 0.009 0.000 ARG H 76 *********************** 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 247 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9409 (pttm) cc_final: 0.9191 (pttm) REVERT: A 106 ASP cc_start: 0.9111 (m-30) cc_final: 0.8820 (m-30) REVERT: B 49 LEU cc_start: 0.9259 (mp) cc_final: 0.8830 (tp) REVERT: B 98 TYR cc_start: 0.9216 (m-10) cc_final: 0.8934 (m-80) REVERT: C 51 MET cc_start: 0.9395 (mmm) cc_final: 0.8972 (mmm) REVERT: C 55 LEU cc_start: 0.9723 (mt) cc_final: 0.9422 (mt) REVERT: C 73 ASN cc_start: 0.9524 (t0) cc_final: 0.9254 (t0) REVERT: C 75 LYS cc_start: 0.9467 (mmmm) cc_final: 0.9202 (mmmm) REVERT: D 42 LEU cc_start: 0.9554 (tt) cc_final: 0.9326 (pp) REVERT: D 65 ASP cc_start: 0.9398 (t70) cc_final: 0.9156 (t0) REVERT: D 66 ILE cc_start: 0.9670 (mm) cc_final: 0.9411 (mm) REVERT: E 60 LEU cc_start: 0.9290 (mp) cc_final: 0.8993 (mt) REVERT: E 65 LEU cc_start: 0.9686 (tp) cc_final: 0.9064 (tp) REVERT: E 105 GLU cc_start: 0.8958 (pp20) cc_final: 0.8477 (pp20) REVERT: E 106 ASP cc_start: 0.9299 (m-30) cc_final: 0.8857 (m-30) REVERT: E 109 LEU cc_start: 0.9819 (mm) cc_final: 0.9505 (mm) REVERT: F 59 LYS cc_start: 0.9588 (tmtt) cc_final: 0.8456 (tmtt) REVERT: F 63 GLU cc_start: 0.9210 (pt0) cc_final: 0.8432 (pt0) REVERT: F 84 MET cc_start: 0.8862 (tpt) cc_final: 0.8134 (tpp) REVERT: F 93 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8188 (tm-30) REVERT: G 61 GLU cc_start: 0.8796 (tp30) cc_final: 0.8470 (tp30) REVERT: G 64 GLU cc_start: 0.8611 (tp30) cc_final: 0.8138 (tp30) REVERT: G 95 LYS cc_start: 0.9614 (tptt) cc_final: 0.9359 (ttmm) REVERT: H 30 ARG cc_start: 0.7650 (mpp-170) cc_final: 0.7396 (mtm-85) REVERT: H 65 ASP cc_start: 0.9047 (t0) cc_final: 0.8711 (t0) REVERT: H 99 LEU cc_start: 0.9226 (mm) cc_final: 0.8937 (mm) REVERT: M 76 TYR cc_start: 0.8525 (t80) cc_final: 0.8175 (t80) REVERT: M 235 ASN cc_start: 0.9519 (t0) cc_final: 0.9138 (t0) REVERT: N 103 MET cc_start: 0.9147 (tpt) cc_final: 0.8830 (tpt) REVERT: N 220 PHE cc_start: 0.9367 (m-80) cc_final: 0.9149 (m-80) REVERT: N 256 PHE cc_start: 0.8781 (m-80) cc_final: 0.8434 (m-80) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.3304 time to fit residues: 113.5489 Evaluate side-chains 192 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 40.0000 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16818 Z= 0.203 Angle : 0.594 10.512 23887 Z= 0.340 Chirality : 0.036 0.189 2680 Planarity : 0.004 0.058 2052 Dihedral : 28.947 145.073 4500 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 0.68 (0.24), residues: 1275 helix: 1.49 (0.22), residues: 576 sheet: 0.26 (0.35), residues: 254 loop : -0.75 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 193 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.045 0.001 TYR H 80 ARG 0.005 0.000 ARG H 96 *********************** 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 237 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.463 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 56 LYS cc_start: 0.9402 (pttm) cc_final: 0.9177 (pttm) REVERT: A 92 LEU cc_start: 0.9767 (mp) cc_final: 0.9486 (mp) REVERT: A 94 GLU cc_start: 0.8888 (tt0) cc_final: 0.8610 (tt0) REVERT: A 97 GLU cc_start: 0.8737 (mp0) cc_final: 0.8436 (mp0) REVERT: A 106 ASP cc_start: 0.9119 (m-30) cc_final: 0.8829 (m-30) REVERT: B 49 LEU cc_start: 0.9277 (mp) cc_final: 0.8918 (tp) REVERT: B 98 TYR cc_start: 0.9183 (m-10) cc_final: 0.8936 (m-80) REVERT: C 51 MET cc_start: 0.9393 (mmm) cc_final: 0.8977 (mmm) REVERT: C 55 LEU cc_start: 0.9741 (mt) cc_final: 0.9452 (mt) REVERT: C 73 ASN cc_start: 0.9579 (t0) cc_final: 0.9203 (t0) REVERT: D 42 LEU cc_start: 0.9569 (tt) cc_final: 0.9363 (pp) REVERT: D 65 ASP cc_start: 0.9386 (t70) cc_final: 0.9185 (t0) REVERT: D 66 ILE cc_start: 0.9685 (mm) cc_final: 0.9447 (mm) REVERT: D 99 LEU cc_start: 0.9320 (mt) cc_final: 0.9056 (mp) REVERT: E 60 LEU cc_start: 0.9288 (mp) cc_final: 0.8883 (mt) REVERT: E 65 LEU cc_start: 0.9683 (tp) cc_final: 0.9084 (tp) REVERT: E 97 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7455 (mt-10) REVERT: E 105 GLU cc_start: 0.8958 (pp20) cc_final: 0.8533 (pp20) REVERT: E 106 ASP cc_start: 0.9287 (m-30) cc_final: 0.8829 (m-30) REVERT: E 109 LEU cc_start: 0.9787 (mm) cc_final: 0.9461 (mm) REVERT: F 59 LYS cc_start: 0.9616 (tmtt) cc_final: 0.8518 (tmtt) REVERT: F 63 GLU cc_start: 0.9212 (pt0) cc_final: 0.8454 (pt0) REVERT: F 70 VAL cc_start: 0.9172 (p) cc_final: 0.8513 (p) REVERT: F 74 GLU cc_start: 0.8986 (mp0) cc_final: 0.8616 (mp0) REVERT: F 84 MET cc_start: 0.8769 (tpt) cc_final: 0.8078 (tpp) REVERT: F 93 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8208 (tm-30) REVERT: G 56 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8935 (mm-30) REVERT: G 61 GLU cc_start: 0.8833 (tp30) cc_final: 0.8538 (tp30) REVERT: G 64 GLU cc_start: 0.8632 (tp30) cc_final: 0.8163 (tp30) REVERT: G 94 ASN cc_start: 0.9217 (m-40) cc_final: 0.8987 (m-40) REVERT: G 95 LYS cc_start: 0.9611 (tptt) cc_final: 0.9367 (ttmm) REVERT: H 30 ARG cc_start: 0.7690 (mpp-170) cc_final: 0.7435 (mtm-85) REVERT: H 65 ASP cc_start: 0.9085 (t0) cc_final: 0.8659 (t0) REVERT: H 99 LEU cc_start: 0.9350 (mm) cc_final: 0.9111 (mm) REVERT: H 102 GLU cc_start: 0.8179 (pp20) cc_final: 0.7834 (pp20) REVERT: H 108 VAL cc_start: 0.9613 (m) cc_final: 0.9405 (m) REVERT: M 76 TYR cc_start: 0.8634 (t80) cc_final: 0.8323 (t80) REVERT: M 262 LEU cc_start: 0.9286 (tp) cc_final: 0.9037 (tt) REVERT: N 103 MET cc_start: 0.9154 (tpt) cc_final: 0.8855 (tpt) REVERT: N 220 PHE cc_start: 0.9375 (m-80) cc_final: 0.9117 (m-80) REVERT: N 256 PHE cc_start: 0.8789 (m-80) cc_final: 0.8426 (m-80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3139 time to fit residues: 104.9055 Evaluate side-chains 189 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 0.0010 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.5792 ------------------------------------------------------------------------------- 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16818 Z= 0.181 Angle : 0.589 11.136 23887 Z= 0.336 Chirality : 0.036 0.230 2680 Planarity : 0.004 0.057 2052 Dihedral : 28.910 144.113 4500 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: 0.70 (0.24), residues: 1275 helix: 1.51 (0.22), residues: 577 sheet: 0.29 (0.35), residues: 252 loop : -0.76 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.006 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.019 0.001 TYR D 37 ARG 0.005 0.000 ARG H 96 *********************** 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 237 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9386 (pttm) cc_final: 0.9150 (ptpp) REVERT: A 106 ASP cc_start: 0.9110 (m-30) cc_final: 0.8852 (m-30) REVERT: B 49 LEU cc_start: 0.9286 (mp) cc_final: 0.8942 (tp) REVERT: B 98 TYR cc_start: 0.9127 (m-10) cc_final: 0.8927 (m-80) REVERT: C 51 MET cc_start: 0.9383 (mmm) cc_final: 0.8929 (mmm) REVERT: C 55 LEU cc_start: 0.9737 (mt) cc_final: 0.9409 (mt) REVERT: C 73 ASN cc_start: 0.9556 (t0) cc_final: 0.9185 (t0) REVERT: D 65 ASP cc_start: 0.9384 (t70) cc_final: 0.9128 (t0) REVERT: D 66 ILE cc_start: 0.9658 (mm) cc_final: 0.9418 (mm) REVERT: D 68 GLU cc_start: 0.8643 (mp0) cc_final: 0.8314 (mp0) REVERT: E 50 GLU cc_start: 0.9284 (mp0) cc_final: 0.9025 (pm20) REVERT: E 65 LEU cc_start: 0.9671 (tp) cc_final: 0.9065 (tp) REVERT: E 93 GLN cc_start: 0.8237 (tm-30) cc_final: 0.6877 (tm-30) REVERT: E 97 GLU cc_start: 0.8157 (mt-10) cc_final: 0.6901 (mt-10) REVERT: E 105 GLU cc_start: 0.8953 (pp20) cc_final: 0.8526 (pp20) REVERT: E 106 ASP cc_start: 0.9288 (m-30) cc_final: 0.8850 (m-30) REVERT: E 109 LEU cc_start: 0.9791 (mm) cc_final: 0.9440 (mm) REVERT: F 59 LYS cc_start: 0.9629 (tmtt) cc_final: 0.8537 (tmtt) REVERT: F 63 GLU cc_start: 0.9230 (pt0) cc_final: 0.8428 (pt0) REVERT: F 84 MET cc_start: 0.8936 (tpt) cc_final: 0.8697 (tpp) REVERT: F 88 TYR cc_start: 0.9020 (m-10) cc_final: 0.8406 (m-10) REVERT: F 93 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8229 (tm-30) REVERT: G 64 GLU cc_start: 0.8599 (tp30) cc_final: 0.8146 (tp30) REVERT: G 94 ASN cc_start: 0.9196 (m-40) cc_final: 0.8968 (m-40) REVERT: G 95 LYS cc_start: 0.9608 (tptt) cc_final: 0.9361 (ttmm) REVERT: H 30 ARG cc_start: 0.7714 (mpp-170) cc_final: 0.7473 (mtm-85) REVERT: H 65 ASP cc_start: 0.9087 (t0) cc_final: 0.8661 (t0) REVERT: H 99 LEU cc_start: 0.9331 (mm) cc_final: 0.9065 (mm) REVERT: H 102 GLU cc_start: 0.8131 (pp20) cc_final: 0.7663 (pp20) REVERT: M 162 MET cc_start: 0.8217 (ppp) cc_final: 0.7717 (ppp) REVERT: M 256 PHE cc_start: 0.9053 (m-80) cc_final: 0.8515 (m-80) REVERT: M 262 LEU cc_start: 0.9285 (tp) cc_final: 0.9033 (tt) REVERT: N 103 MET cc_start: 0.9126 (tpt) cc_final: 0.8813 (tpt) REVERT: N 220 PHE cc_start: 0.9375 (m-80) cc_final: 0.9106 (m-80) REVERT: N 256 PHE cc_start: 0.8778 (m-80) cc_final: 0.8414 (m-80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3125 time to fit residues: 104.3297 Evaluate side-chains 195 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 HIS N 195 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16818 Z= 0.273 Angle : 0.635 11.563 23887 Z= 0.359 Chirality : 0.037 0.162 2680 Planarity : 0.004 0.056 2052 Dihedral : 29.155 145.822 4500 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 0.56 (0.24), residues: 1275 helix: 1.41 (0.22), residues: 577 sheet: 0.18 (0.35), residues: 250 loop : -0.82 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 193 HIS 0.006 0.001 HIS F 75 PHE 0.020 0.002 PHE H 62 TYR 0.024 0.002 TYR D 37 ARG 0.005 0.001 ARG A 63 *********************** 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 226 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.316 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 94 GLU cc_start: 0.8922 (tt0) cc_final: 0.8642 (tt0) REVERT: A 96 CYS cc_start: 0.9156 (p) cc_final: 0.8898 (p) REVERT: A 97 GLU cc_start: 0.8756 (mp0) cc_final: 0.8381 (mp0) REVERT: A 106 ASP cc_start: 0.9160 (m-30) cc_final: 0.8905 (m-30) REVERT: B 31 LYS cc_start: 0.9691 (ptmm) cc_final: 0.9347 (ptmm) REVERT: C 64 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8781 (mm-30) REVERT: C 73 ASN cc_start: 0.9631 (t0) cc_final: 0.9262 (t0) REVERT: C 104 GLN cc_start: 0.8561 (mp10) cc_final: 0.8150 (mp10) REVERT: D 65 ASP cc_start: 0.9363 (t70) cc_final: 0.9109 (t0) REVERT: D 66 ILE cc_start: 0.9690 (mm) cc_final: 0.9449 (mm) REVERT: D 68 GLU cc_start: 0.8642 (mp0) cc_final: 0.8347 (mp0) REVERT: D 99 LEU cc_start: 0.9367 (mt) cc_final: 0.9137 (mp) REVERT: E 64 LYS cc_start: 0.9660 (mppt) cc_final: 0.9406 (mmtm) REVERT: E 65 LEU cc_start: 0.9668 (tp) cc_final: 0.9075 (tp) REVERT: E 90 MET cc_start: 0.9296 (mmp) cc_final: 0.9072 (mmp) REVERT: E 93 GLN cc_start: 0.8255 (tm-30) cc_final: 0.6798 (tm-30) REVERT: E 97 GLU cc_start: 0.8094 (mt-10) cc_final: 0.6634 (mt-10) REVERT: E 105 GLU cc_start: 0.9052 (pp20) cc_final: 0.8601 (pp20) REVERT: E 106 ASP cc_start: 0.9322 (m-30) cc_final: 0.8833 (m-30) REVERT: E 109 LEU cc_start: 0.9797 (mm) cc_final: 0.9412 (mm) REVERT: F 63 GLU cc_start: 0.9235 (pt0) cc_final: 0.9007 (pt0) REVERT: F 74 GLU cc_start: 0.9016 (mp0) cc_final: 0.8486 (mp0) REVERT: F 84 MET cc_start: 0.9078 (tpt) cc_final: 0.8784 (tpp) REVERT: F 88 TYR cc_start: 0.9000 (m-10) cc_final: 0.8291 (m-10) REVERT: F 93 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8287 (tm-30) REVERT: G 64 GLU cc_start: 0.8664 (tp30) cc_final: 0.8228 (tp30) REVERT: G 82 HIS cc_start: 0.9245 (m90) cc_final: 0.8994 (m90) REVERT: G 89 ASN cc_start: 0.9434 (m-40) cc_final: 0.9210 (m-40) REVERT: G 95 LYS cc_start: 0.9580 (tptt) cc_final: 0.9377 (ttmm) REVERT: H 65 ASP cc_start: 0.9136 (t0) cc_final: 0.8521 (t0) REVERT: H 73 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9176 (mm-30) REVERT: H 99 LEU cc_start: 0.9462 (mm) cc_final: 0.9208 (mm) REVERT: H 102 GLU cc_start: 0.7732 (pp20) cc_final: 0.7490 (pp20) REVERT: M 262 LEU cc_start: 0.9337 (tp) cc_final: 0.9062 (tt) REVERT: N 103 MET cc_start: 0.9181 (tpt) cc_final: 0.8879 (tpt) REVERT: N 193 TRP cc_start: 0.8764 (m100) cc_final: 0.8555 (m100) REVERT: N 220 PHE cc_start: 0.9422 (m-80) cc_final: 0.9074 (m-80) REVERT: N 256 PHE cc_start: 0.8881 (m-80) cc_final: 0.8487 (m-80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3146 time to fit residues: 101.0988 Evaluate side-chains 186 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 0.0060 chunk 86 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16818 Z= 0.173 Angle : 0.609 11.368 23887 Z= 0.342 Chirality : 0.037 0.181 2680 Planarity : 0.004 0.056 2052 Dihedral : 28.947 142.776 4500 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.63 (0.24), residues: 1275 helix: 1.50 (0.22), residues: 575 sheet: 0.18 (0.35), residues: 254 loop : -0.80 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP O 215 HIS 0.006 0.001 HIS F 75 PHE 0.012 0.001 PHE H 62 TYR 0.023 0.001 TYR F 98 ARG 0.006 0.000 ARG H 96 *********************** 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 243 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.539 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 92 LEU cc_start: 0.9763 (mp) cc_final: 0.9514 (mp) REVERT: A 94 GLU cc_start: 0.8906 (tt0) cc_final: 0.8624 (tt0) REVERT: A 106 ASP cc_start: 0.9113 (m-30) cc_final: 0.8833 (m-30) REVERT: B 31 LYS cc_start: 0.9719 (ptmm) cc_final: 0.9383 (ptmm) REVERT: C 64 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8368 (mm-30) REVERT: C 73 ASN cc_start: 0.9584 (t0) cc_final: 0.9197 (t0) REVERT: C 104 GLN cc_start: 0.8451 (mp10) cc_final: 0.7566 (mp10) REVERT: D 54 LYS cc_start: 0.9691 (mmmm) cc_final: 0.9235 (mtpp) REVERT: D 64 ASN cc_start: 0.9332 (m-40) cc_final: 0.8999 (m-40) REVERT: D 65 ASP cc_start: 0.9391 (t70) cc_final: 0.9123 (t0) REVERT: D 66 ILE cc_start: 0.9720 (mm) cc_final: 0.9498 (mm) REVERT: D 68 GLU cc_start: 0.8618 (mp0) cc_final: 0.8398 (mp0) REVERT: D 91 ILE cc_start: 0.9408 (tt) cc_final: 0.9202 (tt) REVERT: E 50 GLU cc_start: 0.9338 (mp0) cc_final: 0.8979 (mp0) REVERT: E 60 LEU cc_start: 0.9341 (mt) cc_final: 0.9136 (mt) REVERT: E 64 LYS cc_start: 0.9642 (mppt) cc_final: 0.9411 (mmtm) REVERT: E 65 LEU cc_start: 0.9643 (tp) cc_final: 0.9083 (tp) REVERT: E 93 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7036 (tm-30) REVERT: E 97 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7032 (mt-10) REVERT: E 105 GLU cc_start: 0.8980 (pp20) cc_final: 0.8623 (pp20) REVERT: E 106 ASP cc_start: 0.9259 (m-30) cc_final: 0.8797 (m-30) REVERT: E 109 LEU cc_start: 0.9787 (mm) cc_final: 0.9582 (mm) REVERT: E 120 MET cc_start: 0.8794 (mpp) cc_final: 0.8587 (mpp) REVERT: F 59 LYS cc_start: 0.9631 (tmtt) cc_final: 0.8501 (tmtt) REVERT: F 63 GLU cc_start: 0.9247 (pt0) cc_final: 0.8434 (pt0) REVERT: F 74 GLU cc_start: 0.8977 (mp0) cc_final: 0.8448 (mp0) REVERT: F 84 MET cc_start: 0.8810 (tpt) cc_final: 0.8485 (tpp) REVERT: F 88 TYR cc_start: 0.9014 (m-10) cc_final: 0.8319 (m-10) REVERT: F 93 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8201 (tm-30) REVERT: G 56 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8630 (mm-30) REVERT: G 61 GLU cc_start: 0.8797 (tp30) cc_final: 0.8489 (tp30) REVERT: G 64 GLU cc_start: 0.8550 (tp30) cc_final: 0.8098 (tp30) REVERT: G 95 LYS cc_start: 0.9570 (tptt) cc_final: 0.9359 (ttmm) REVERT: H 65 ASP cc_start: 0.8966 (t0) cc_final: 0.8389 (t0) REVERT: H 99 LEU cc_start: 0.9356 (mm) cc_final: 0.9075 (mm) REVERT: H 102 GLU cc_start: 0.7975 (pp20) cc_final: 0.7468 (pp20) REVERT: M 256 PHE cc_start: 0.9084 (m-80) cc_final: 0.8535 (m-80) REVERT: N 42 MET cc_start: 0.9362 (pmm) cc_final: 0.9162 (pmm) REVERT: N 103 MET cc_start: 0.9134 (tpt) cc_final: 0.8806 (tpt) REVERT: N 220 PHE cc_start: 0.9412 (m-80) cc_final: 0.9080 (m-80) REVERT: N 256 PHE cc_start: 0.8765 (m-80) cc_final: 0.8381 (m-80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3430 time to fit residues: 118.0564 Evaluate side-chains 189 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16818 Z= 0.180 Angle : 0.616 11.304 23887 Z= 0.346 Chirality : 0.037 0.256 2680 Planarity : 0.004 0.056 2052 Dihedral : 28.887 143.762 4500 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1275 helix: 1.45 (0.22), residues: 573 sheet: 0.20 (0.35), residues: 254 loop : -0.82 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP N 193 HIS 0.009 0.001 HIS B 75 PHE 0.014 0.001 PHE H 62 TYR 0.020 0.001 TYR D 37 ARG 0.006 0.000 ARG H 96 ********************** 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 239 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.404 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 56 LYS cc_start: 0.9364 (pttm) cc_final: 0.9146 (pttm) REVERT: A 106 ASP cc_start: 0.9004 (m-30) cc_final: 0.8742 (m-30) REVERT: B 31 LYS cc_start: 0.9718 (ptmm) cc_final: 0.9390 (ptmm) REVERT: C 55 LEU cc_start: 0.9729 (mt) cc_final: 0.9401 (mt) REVERT: C 64 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8414 (mm-30) REVERT: C 73 ASN cc_start: 0.9543 (t0) cc_final: 0.9169 (t0) REVERT: D 54 LYS cc_start: 0.9689 (mmmm) cc_final: 0.9482 (mtpt) REVERT: D 65 ASP cc_start: 0.9381 (t70) cc_final: 0.9130 (t0) REVERT: D 66 ILE cc_start: 0.9706 (mm) cc_final: 0.9489 (mm) REVERT: E 50 GLU cc_start: 0.9332 (mp0) cc_final: 0.8974 (mp0) REVERT: E 64 LYS cc_start: 0.9637 (mppt) cc_final: 0.9401 (mmtm) REVERT: E 65 LEU cc_start: 0.9634 (tp) cc_final: 0.9061 (tp) REVERT: E 93 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7022 (tm-30) REVERT: E 97 GLU cc_start: 0.8097 (mt-10) cc_final: 0.6827 (mt-10) REVERT: E 105 GLU cc_start: 0.9014 (pp20) cc_final: 0.8661 (pp20) REVERT: E 106 ASP cc_start: 0.9279 (m-30) cc_final: 0.8767 (m-30) REVERT: E 120 MET cc_start: 0.8764 (mpp) cc_final: 0.8555 (mpp) REVERT: F 59 LYS cc_start: 0.9621 (tmtt) cc_final: 0.8527 (tmtt) REVERT: F 63 GLU cc_start: 0.9261 (pt0) cc_final: 0.8436 (pt0) REVERT: F 74 GLU cc_start: 0.8969 (mp0) cc_final: 0.8446 (mp0) REVERT: F 84 MET cc_start: 0.8845 (tpt) cc_final: 0.8479 (tpp) REVERT: F 88 TYR cc_start: 0.8928 (m-10) cc_final: 0.8075 (m-10) REVERT: F 93 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8185 (tm-30) REVERT: G 56 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8612 (mm-30) REVERT: G 61 GLU cc_start: 0.8760 (tp30) cc_final: 0.8496 (tp30) REVERT: G 64 GLU cc_start: 0.8584 (tp30) cc_final: 0.8141 (tp30) REVERT: G 95 LYS cc_start: 0.9588 (tptt) cc_final: 0.9358 (ttmm) REVERT: H 40 LYS cc_start: 0.9714 (ttpt) cc_final: 0.9379 (ttpp) REVERT: H 65 ASP cc_start: 0.8960 (t0) cc_final: 0.8403 (t0) REVERT: H 99 LEU cc_start: 0.9400 (mm) cc_final: 0.9126 (mm) REVERT: H 102 GLU cc_start: 0.8009 (pp20) cc_final: 0.7641 (pp20) REVERT: M 256 PHE cc_start: 0.9036 (m-80) cc_final: 0.8441 (m-80) REVERT: N 42 MET cc_start: 0.9369 (pmm) cc_final: 0.9169 (pmm) REVERT: N 103 MET cc_start: 0.9142 (tpt) cc_final: 0.8810 (tpt) REVERT: N 220 PHE cc_start: 0.9399 (m-80) cc_final: 0.9076 (m-80) REVERT: N 256 PHE cc_start: 0.8730 (m-80) cc_final: 0.8329 (m-80) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3087 time to fit residues: 104.6699 Evaluate side-chains 195 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 195 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 = 0.051700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.031872 restraints weight = 119780.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.032153 restraints weight = 60422.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.032642 restraints weight = 39209.155| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 16818 Z= 0.480 Angle : 0.775 15.398 23887 Z= 0.431 Chirality : 0.042 0.267 2680 Planarity : 0.005 0.057 2052 Dihedral : 29.595 147.890 4500 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 0.12 (0.23), residues: 1275 helix: 1.04 (0.21), residues: 579 sheet: -0.20 (0.35), residues: 254 loop : -0.94 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 193 HIS 0.010 0.002 HIS F 75 PHE 0.021 0.002 PHE N 86 TYR 0.037 0.003 TYR M 76 ARG 0.007 0.001 ARG C 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3018.80 seconds wall clock time: 55 minutes 32.30 seconds (3332.30 seconds total)