Starting phenix.real_space_refine on Mon Feb 19 10:52:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2024/7xct_33127_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2024/7xct_33127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2024/7xct_33127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2024/7xct_33127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2024/7xct_33127_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/02_2024/7xct_33127_updated.pdb" } resolution = 2.72 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= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5945 atoms to isotropic. 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 290 5.49 5 S 40 5.16 5 C 10853 2.51 5 N 3399 2.21 5 O 4051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18633 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2656 Classifications: {'peptide': 326} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 307} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 308} Chain: "N" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 residue: pdb=" N LEU N 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU N 73 " occ=0.45 residue: pdb=" N ARG N 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG N 74 " occ=0.45 residue: pdb=" N GLY N 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY N 75 " occ=0.25 residue: pdb=" N GLY N 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY N 76 " occ=0.25 Time building chain proxies: 10.25, per 1000 atoms: 0.55 Number of scatterers: 18633 At special positions: 0 Unit cell: (151.2, 123.12, 150.12, 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 40 16.00 P 290 15.00 O 4051 8.00 N 3399 7.00 C 10853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 8.74 Conformation dependent library (CDL) restraints added in 2.5 seconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 4 sheets defined 44.1% alpha, 5.3% beta 125 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 9.45 Creating SS restraints... Processing helix chain 'L' and resid 23 through 33 removed outlier: 4.357A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 59 No H-bonds generated for 'chain 'L' and resid 57 through 59' Processing helix chain 'F' and resid 31 through 34 No H-bonds generated for 'chain 'F' and resid 31 through 34' Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 50 through 56 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 93 through 99 removed outlier: 5.675A pdb=" N ARG G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.517A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 83 removed outlier: 3.553A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 105 through 123 Processing helix chain 'K' and resid 36 through 44 removed outlier: 3.689A pdb=" N ARG K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 72 No H-bonds generated for 'chain 'K' and resid 69 through 72' Processing helix chain 'K' and resid 76 through 79 No H-bonds generated for 'chain 'K' and resid 76 through 79' Processing helix chain 'K' and resid 83 through 89 removed outlier: 5.726A pdb=" N LEU K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP K 89 " --> pdb=" O ILE K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.505A pdb=" N ASN K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 168 through 174 Processing helix chain 'K' and resid 189 through 208 removed outlier: 3.540A pdb=" N GLU K 196 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 233 removed outlier: 4.366A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 255 removed outlier: 3.738A pdb=" N GLU K 255 " --> pdb=" O HIS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 259 No H-bonds generated for 'chain 'K' and resid 257 through 259' Processing helix chain 'K' and resid 287 through 289 No H-bonds generated for 'chain 'K' and resid 287 through 289' Processing helix chain 'K' and resid 321 through 324 No H-bonds generated for 'chain 'K' and resid 321 through 324' Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.692A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 112 removed outlier: 3.578A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.525A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.605A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 removed outlier: 3.551A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.612A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 93 through 99 removed outlier: 5.676A pdb=" N ARG C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.737A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.641A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 44 removed outlier: 3.690A pdb=" N ARG M 42 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TRP M 43 " --> pdb=" O GLU M 39 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 54 No H-bonds generated for 'chain 'M' and resid 51 through 54' Processing helix chain 'M' and resid 69 through 72 No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 76 through 79 No H-bonds generated for 'chain 'M' and resid 76 through 79' Processing helix chain 'M' and resid 83 through 89 removed outlier: 5.726A pdb=" N LEU M 88 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP M 89 " --> pdb=" O ILE M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 118 removed outlier: 3.505A pdb=" N ASN M 116 " --> pdb=" O GLN M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 126 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 168 through 174 Processing helix chain 'M' and resid 189 through 208 removed outlier: 3.540A pdb=" N GLU M 196 " --> pdb=" O ALA M 192 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR M 197 " --> pdb=" O LYS M 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG M 203 " --> pdb=" O ASP M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 233 removed outlier: 4.366A pdb=" N GLU M 230 " --> pdb=" O GLU M 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG M 231 " --> pdb=" O GLU M 227 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA M 233 " --> pdb=" O ARG M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 255 removed outlier: 3.737A pdb=" N GLU M 255 " --> pdb=" O HIS M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 259 No H-bonds generated for 'chain 'M' and resid 257 through 259' Processing helix chain 'M' and resid 287 through 289 No H-bonds generated for 'chain 'M' and resid 287 through 289' Processing helix chain 'M' and resid 321 through 324 No H-bonds generated for 'chain 'M' and resid 321 through 324' Processing helix chain 'N' and resid 23 through 33 removed outlier: 4.357A pdb=" N GLN N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing sheet with id= A, first strand: chain 'L' and resid 12 through 15 removed outlier: 3.566A pdb=" N VAL L 5 " --> pdb=" O ILE L 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS L 68 " --> pdb=" O ILE L 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 291 through 295 removed outlier: 4.007A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU K 215 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N GLY K 184 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR K 217 " --> pdb=" O GLY K 184 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLU K 186 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU K 219 " --> pdb=" O GLU K 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 291 through 295 removed outlier: 4.008A pdb=" N PHE M 159 " --> pdb=" O HIS M 181 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU M 215 " --> pdb=" O HIS M 182 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY M 184 " --> pdb=" O GLU M 215 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR M 217 " --> pdb=" O GLY M 184 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLU M 186 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU M 219 " --> pdb=" O GLU M 186 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 12 through 15 removed outlier: 3.566A pdb=" N VAL N 5 " --> pdb=" O ILE N 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS N 68 " --> pdb=" O ILE N 44 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 305 hydrogen bonds 590 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 6.68 Time building geometry restraints manager: 9.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2539 1.31 - 1.44: 6617 1.44 - 1.56: 9780 1.56 - 1.69: 582 1.69 - 1.81: 74 Bond restraints: 19592 Sorted by residual: bond pdb=" C1' DC J 65 " pdb=" N1 DC J 65 " ideal model delta sigma weight residual 1.490 1.595 -0.105 3.00e-02 1.11e+03 1.22e+01 bond pdb=" CB THR H 96 " pdb=" CG2 THR H 96 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.09e+00 bond pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 1.523 1.563 -0.040 1.34e-02 5.57e+03 8.89e+00 bond pdb=" CB THR B 71 " pdb=" CG2 THR B 71 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.45e+00 bond pdb=" CB THR D 96 " pdb=" CG2 THR D 96 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.62e+00 ... (remaining 19587 not shown) Histogram of bond angle deviations from ideal: 97.99 - 106.69: 2380 106.69 - 115.39: 11697 115.39 - 124.08: 12233 124.08 - 132.78: 1395 132.78 - 141.48: 24 Bond angle restraints: 27729 Sorted by residual: angle pdb=" C GLU M 47 " pdb=" N ILE M 48 " pdb=" CA ILE M 48 " ideal model delta sigma weight residual 121.70 141.48 -19.78 1.80e+00 3.09e-01 1.21e+02 angle pdb=" C GLU K 47 " pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 121.70 141.47 -19.77 1.80e+00 3.09e-01 1.21e+02 angle pdb=" C ARG F 67 " pdb=" N ASP F 68 " pdb=" CA ASP F 68 " ideal model delta sigma weight residual 121.54 135.56 -14.02 1.91e+00 2.74e-01 5.39e+01 angle pdb=" C TYR F 88 " pdb=" CA TYR F 88 " pdb=" CB TYR F 88 " ideal model delta sigma weight residual 109.83 103.87 5.96 9.90e-01 1.02e+00 3.62e+01 angle pdb=" CA GLU K 47 " pdb=" C GLU K 47 " pdb=" N ILE K 48 " ideal model delta sigma weight residual 119.01 126.49 -7.48 1.38e+00 5.25e-01 2.94e+01 ... (remaining 27724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 9745 35.58 - 71.16: 1342 71.16 - 106.74: 13 106.74 - 142.32: 1 142.32 - 177.90: 2 Dihedral angle restraints: 11103 sinusoidal: 6512 harmonic: 4591 Sorted by residual: dihedral pdb=" CA TRP K 22 " pdb=" C TRP K 22 " pdb=" N PRO K 23 " pdb=" CA PRO K 23 " ideal model delta harmonic sigma weight residual -180.00 -106.89 -73.11 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA TRP M 22 " pdb=" C TRP M 22 " pdb=" N PRO M 23 " pdb=" CA PRO M 23 " ideal model delta harmonic sigma weight residual -180.00 -106.90 -73.10 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA GLN F 27 " pdb=" C GLN F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta harmonic sigma weight residual 180.00 115.38 64.62 0 5.00e+00 4.00e-02 1.67e+02 ... (remaining 11100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2424 0.071 - 0.142: 588 0.142 - 0.213: 88 0.213 - 0.284: 13 0.284 - 0.354: 4 Chirality restraints: 3117 Sorted by residual: chirality pdb=" CB VAL F 43 " pdb=" CA VAL F 43 " pdb=" CG1 VAL F 43 " pdb=" CG2 VAL F 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE M 48 " pdb=" CA ILE M 48 " pdb=" CG1 ILE M 48 " pdb=" CG2 ILE M 48 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE K 48 " pdb=" CA ILE K 48 " pdb=" CG1 ILE K 48 " pdb=" CG2 ILE K 48 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 3114 not shown) Planarity restraints: 2519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP K 22 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO K 23 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO K 23 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 23 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.025 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE G 25 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP M 22 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO M 23 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO M 23 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 23 " 0.044 5.00e-02 4.00e+02 ... (remaining 2516 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2971 2.76 - 3.29: 15511 3.29 - 3.83: 33195 3.83 - 4.36: 42752 4.36 - 4.90: 63067 Nonbonded interactions: 157496 Sorted by model distance: nonbonded pdb=" OG1 THR F 82 " pdb=" O MET F 84 " model vdw 2.220 2.440 nonbonded pdb=" OP1 DG J 125 " pdb=" O LEU N 73 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.285 2.440 nonbonded pdb=" OE2 GLU K 186 " pdb=" O2' SAM K 500 " model vdw 2.302 2.440 nonbonded pdb=" OE2 GLU M 186 " pdb=" O2' SAM M 500 " model vdw 2.303 2.440 ... (remaining 157491 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 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'M' and (resid 5 through 330 or resid 500)) } ncs_group { reference = chain 'L' 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 4.760 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 58.300 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.012 0.111 19592 Z= 0.729 Angle : 1.114 19.779 27729 Z= 0.615 Chirality : 0.064 0.354 3117 Planarity : 0.008 0.081 2519 Dihedral : 22.813 177.902 8137 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.31 % Favored : 94.30 % Rotamer: Outliers : 0.59 % Allowed : 3.83 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.33 % 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: -5.11 (0.15), residues: 1545 helix: -4.25 (0.08), residues: 783 sheet: -1.05 (0.48), residues: 142 loop : -2.50 (0.20), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP K 22 HIS 0.018 0.003 HIS H 109 PHE 0.056 0.004 PHE G 25 TYR 0.046 0.003 TYR M 312 ARG 0.016 0.002 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 266 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.8156 (m-30) cc_final: 0.7937 (m-30) REVERT: A 122 LYS cc_start: 0.8973 (pttt) cc_final: 0.8742 (pttp) REVERT: D 59 MET cc_start: 0.8960 (tpp) cc_final: 0.8684 (tpp) REVERT: D 88 THR cc_start: 0.9058 (t) cc_final: 0.8647 (m) REVERT: M 71 MET cc_start: 0.4126 (mmt) cc_final: 0.3497 (tpp) outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 2.0795 time to fit residues: 614.8618 Evaluate side-chains 181 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.0040 chunk 72 optimal weight: 0.7980 chunk 139 optimal weight: 50.0000 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 60 ASN F 18 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 24 GLN G 73 ASN G 82 HIS H 63 ASN H 84 ASN K 31 HIS K 79 ASN K 112 GLN K 113 GLN K 315 HIS E 68 GLN E 76 GLN A 68 GLN A 113 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS C 24 GLN C 82 HIS B 25 ASN M 31 HIS M 79 ASN M 117 HIS ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 HIS M 331 ASN N 60 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19592 Z= 0.194 Angle : 0.673 15.298 27729 Z= 0.382 Chirality : 0.040 0.233 3117 Planarity : 0.006 0.075 2519 Dihedral : 27.690 172.802 4980 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.34 % Favored : 95.47 % Rotamer: Outliers : 3.02 % Allowed : 10.75 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.20 % 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: -2.68 (0.19), residues: 1545 helix: -1.78 (0.16), residues: 792 sheet: -0.68 (0.48), residues: 140 loop : -1.84 (0.22), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 22 HIS 0.003 0.001 HIS H 109 PHE 0.016 0.001 PHE K 223 TYR 0.012 0.001 TYR M 209 ARG 0.011 0.001 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7573 (tptt) REVERT: G 91 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: K 71 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4309 (mpp) REVERT: K 104 THR cc_start: 0.8256 (p) cc_final: 0.7957 (t) REVERT: E 73 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: D 59 MET cc_start: 0.8727 (tpp) cc_final: 0.8440 (tpp) REVERT: C 95 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8472 (mmmt) REVERT: M 71 MET cc_start: 0.4341 (mmt) cc_final: 0.3823 (tpp) REVERT: M 248 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7116 (mm-30) outliers start: 41 outliers final: 12 residues processed: 226 average time/residue: 1.8439 time to fit residues: 452.4658 Evaluate side-chains 197 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN A 68 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19592 Z= 0.366 Angle : 0.714 15.190 27729 Z= 0.402 Chirality : 0.046 0.251 3117 Planarity : 0.006 0.079 2519 Dihedral : 27.866 172.479 4978 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.98 % Favored : 94.76 % Rotamer: Outliers : 4.20 % Allowed : 12.00 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -1.60 (0.21), residues: 1545 helix: -0.59 (0.18), residues: 802 sheet: -0.43 (0.49), residues: 141 loop : -1.74 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 22 HIS 0.009 0.001 HIS F 18 PHE 0.025 0.002 PHE K 223 TYR 0.022 0.002 TYR K 312 ARG 0.010 0.001 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 182 time to evaluate : 1.804 Fit side-chains revert: symmetry clash REVERT: G 13 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.6513 (mttt) REVERT: G 91 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: G 92 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: K 71 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.4419 (mpp) REVERT: K 104 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8151 (t) REVERT: E 53 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7860 (ttt180) REVERT: E 73 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: A 59 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: D 59 MET cc_start: 0.8839 (tpp) cc_final: 0.8517 (tpp) REVERT: C 91 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: M 22 TRP cc_start: 0.2971 (OUTLIER) cc_final: 0.2110 (t-100) REVERT: M 55 MET cc_start: 0.1704 (mtm) cc_final: 0.1482 (mtt) REVERT: M 71 MET cc_start: 0.4382 (mmt) cc_final: 0.3908 (tpp) outliers start: 57 outliers final: 23 residues processed: 217 average time/residue: 1.8590 time to fit residues: 438.1349 Evaluate side-chains 206 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 143 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN K 113 GLN A 68 GLN A 76 GLN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19592 Z= 0.180 Angle : 0.648 14.752 27729 Z= 0.369 Chirality : 0.040 0.244 3117 Planarity : 0.005 0.089 2519 Dihedral : 27.851 172.264 4978 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.08 % Rotamer: Outliers : 3.61 % Allowed : 13.11 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -0.90 (0.22), residues: 1545 helix: 0.06 (0.19), residues: 793 sheet: -0.22 (0.50), residues: 140 loop : -1.48 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 22 HIS 0.006 0.001 HIS F 18 PHE 0.017 0.001 PHE K 223 TYR 0.015 0.001 TYR M 209 ARG 0.011 0.000 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 178 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7188 (ttm-80) cc_final: 0.6946 (tpp-160) REVERT: G 13 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.6542 (mttt) REVERT: G 91 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: H 47 GLN cc_start: 0.8414 (mt0) cc_final: 0.8183 (mt0) REVERT: K 71 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4404 (mpp) REVERT: K 104 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8121 (t) REVERT: K 129 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: E 53 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7847 (ttt180) REVERT: E 73 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: A 59 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: D 108 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8405 (mtpt) REVERT: C 59 THR cc_start: 0.8863 (t) cc_final: 0.8646 (p) REVERT: M 22 TRP cc_start: 0.3013 (OUTLIER) cc_final: 0.2755 (t-100) REVERT: M 71 MET cc_start: 0.4324 (mmt) cc_final: 0.3891 (tpp) outliers start: 49 outliers final: 23 residues processed: 207 average time/residue: 1.7912 time to fit residues: 403.9883 Evaluate side-chains 208 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 201 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 87 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 73 ASN K 113 GLN A 68 GLN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19592 Z= 0.343 Angle : 0.687 14.275 27729 Z= 0.387 Chirality : 0.044 0.240 3117 Planarity : 0.006 0.084 2519 Dihedral : 27.847 169.605 4978 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.11 % Favored : 94.69 % Rotamer: Outliers : 4.27 % Allowed : 13.03 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -0.75 (0.22), residues: 1545 helix: 0.18 (0.19), residues: 801 sheet: -0.20 (0.49), residues: 140 loop : -1.40 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 22 HIS 0.009 0.001 HIS F 18 PHE 0.023 0.002 PHE K 223 TYR 0.015 0.002 TYR K 312 ARG 0.011 0.001 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 180 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.7040 (tpp-160) REVERT: G 13 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7393 (mptt) REVERT: G 91 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: G 92 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: K 71 MET cc_start: 0.5287 (OUTLIER) cc_final: 0.4440 (mpp) REVERT: K 104 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8239 (t) REVERT: E 53 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7882 (ttt180) REVERT: E 73 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: A 59 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: D 57 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8658 (mtpp) REVERT: D 108 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8406 (mtpt) REVERT: C 91 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: M 22 TRP cc_start: 0.3320 (OUTLIER) cc_final: 0.2930 (t-100) REVERT: M 71 MET cc_start: 0.4108 (mmt) cc_final: 0.3699 (tpp) REVERT: M 153 MET cc_start: 0.6751 (ttm) cc_final: 0.6486 (ttt) REVERT: M 248 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7376 (mm-30) outliers start: 58 outliers final: 28 residues processed: 216 average time/residue: 1.7538 time to fit residues: 412.5804 Evaluate side-chains 213 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 0.0870 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN E 85 GLN B 25 ASN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19592 Z= 0.247 Angle : 0.655 14.104 27729 Z= 0.371 Chirality : 0.041 0.239 3117 Planarity : 0.005 0.089 2519 Dihedral : 27.828 169.297 4978 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 3.98 % Allowed : 14.14 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -0.58 (0.22), residues: 1545 helix: 0.34 (0.19), residues: 799 sheet: -0.16 (0.49), residues: 140 loop : -1.35 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 22 HIS 0.008 0.001 HIS F 18 PHE 0.018 0.001 PHE K 223 TYR 0.012 0.001 TYR M 209 ARG 0.009 0.000 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.7093 (tpp-160) REVERT: G 13 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7426 (mptt) REVERT: G 91 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: K 71 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.4380 (mpp) REVERT: K 104 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8264 (t) REVERT: K 129 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: E 53 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7880 (ttt180) REVERT: A 59 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: D 57 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8632 (mtpp) REVERT: D 108 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8383 (mtpt) REVERT: C 59 THR cc_start: 0.8898 (t) cc_final: 0.8659 (p) REVERT: M 22 TRP cc_start: 0.3383 (OUTLIER) cc_final: 0.3012 (t-100) REVERT: M 71 MET cc_start: 0.4032 (mmt) cc_final: 0.3634 (tpp) outliers start: 54 outliers final: 26 residues processed: 211 average time/residue: 1.7419 time to fit residues: 400.9870 Evaluate side-chains 212 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 96 optimal weight: 0.6980 chunk 171 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19592 Z= 0.246 Angle : 0.634 13.883 27729 Z= 0.359 Chirality : 0.041 0.242 3117 Planarity : 0.005 0.090 2519 Dihedral : 27.683 167.062 4978 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.37 % Favored : 94.43 % Rotamer: Outliers : 4.12 % Allowed : 14.51 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.20 % 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: -0.39 (0.22), residues: 1545 helix: 0.51 (0.19), residues: 795 sheet: -0.06 (0.50), residues: 140 loop : -1.28 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 22 HIS 0.006 0.001 HIS F 18 PHE 0.018 0.001 PHE K 223 TYR 0.011 0.001 TYR D 37 ARG 0.010 0.001 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 185 time to evaluate : 1.690 Fit side-chains REVERT: G 13 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7435 (mptt) REVERT: G 91 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: G 92 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: K 71 MET cc_start: 0.5214 (OUTLIER) cc_final: 0.4299 (mpp) REVERT: K 96 MET cc_start: 0.3761 (mtt) cc_final: 0.3377 (tpt) REVERT: K 104 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8306 (t) REVERT: K 129 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: K 170 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8784 (t) REVERT: A 59 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: D 57 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8565 (mtpt) REVERT: D 108 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8360 (mtpt) REVERT: M 22 TRP cc_start: 0.3275 (OUTLIER) cc_final: 0.2365 (t-100) REVERT: M 71 MET cc_start: 0.4284 (mmt) cc_final: 0.3826 (tpp) REVERT: M 248 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7397 (mm-30) outliers start: 56 outliers final: 29 residues processed: 217 average time/residue: 1.7024 time to fit residues: 403.7693 Evaluate side-chains 214 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 252 GLN Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN E 85 GLN M 113 GLN M 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19592 Z= 0.341 Angle : 0.676 13.691 27729 Z= 0.382 Chirality : 0.044 0.236 3117 Planarity : 0.006 0.090 2519 Dihedral : 27.788 164.220 4978 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 3.83 % Allowed : 15.32 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -0.48 (0.22), residues: 1545 helix: 0.41 (0.19), residues: 802 sheet: -0.08 (0.49), residues: 140 loop : -1.30 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 22 HIS 0.009 0.001 HIS F 18 PHE 0.021 0.002 PHE K 223 TYR 0.014 0.002 TYR D 37 ARG 0.008 0.001 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 1.660 Fit side-chains REVERT: G 13 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7518 (mmtt) REVERT: G 91 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: G 92 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: K 71 MET cc_start: 0.5326 (OUTLIER) cc_final: 0.4392 (mpp) REVERT: K 96 MET cc_start: 0.3853 (mtt) cc_final: 0.3373 (tpt) REVERT: K 104 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8244 (t) REVERT: K 129 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: A 59 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: D 57 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8617 (mtpt) REVERT: D 108 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8396 (mtpt) REVERT: M 22 TRP cc_start: 0.3203 (OUTLIER) cc_final: 0.2311 (t-100) REVERT: M 71 MET cc_start: 0.4161 (mmt) cc_final: 0.3660 (tpp) REVERT: M 248 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7395 (mm-30) outliers start: 52 outliers final: 31 residues processed: 207 average time/residue: 1.6615 time to fit residues: 377.0532 Evaluate side-chains 211 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 252 GLN Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 151 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN E 85 GLN M 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 19592 Z= 0.202 Angle : 0.638 14.026 27729 Z= 0.363 Chirality : 0.040 0.249 3117 Planarity : 0.005 0.091 2519 Dihedral : 27.805 164.159 4978 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.37 % Rotamer: Outliers : 3.46 % Allowed : 16.20 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -0.29 (0.22), residues: 1545 helix: 0.59 (0.19), residues: 798 sheet: -0.01 (0.49), residues: 140 loop : -1.23 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 22 HIS 0.006 0.001 HIS F 18 PHE 0.017 0.001 PHE K 223 TYR 0.013 0.001 TYR H 37 ARG 0.013 0.000 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 1.691 Fit side-chains REVERT: G 13 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7512 (mmtt) REVERT: G 91 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: G 92 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: K 71 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.4309 (mpp) REVERT: K 96 MET cc_start: 0.3836 (mtt) cc_final: 0.3363 (tpt) REVERT: K 129 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: A 59 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: D 57 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (mtpt) REVERT: D 108 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8391 (mtpt) REVERT: C 59 THR cc_start: 0.8894 (t) cc_final: 0.8672 (p) REVERT: B 79 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8343 (mtmt) REVERT: M 22 TRP cc_start: 0.3124 (OUTLIER) cc_final: 0.2233 (t-100) REVERT: M 71 MET cc_start: 0.4148 (mmt) cc_final: 0.3656 (tpp) outliers start: 47 outliers final: 30 residues processed: 199 average time/residue: 1.6746 time to fit residues: 364.3093 Evaluate side-chains 209 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 252 GLN Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN M 113 GLN M 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19592 Z= 0.319 Angle : 0.665 13.299 27729 Z= 0.375 Chirality : 0.043 0.242 3117 Planarity : 0.006 0.090 2519 Dihedral : 27.793 160.464 4978 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 3.09 % Allowed : 16.49 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -0.33 (0.22), residues: 1545 helix: 0.54 (0.19), residues: 796 sheet: 0.02 (0.49), residues: 140 loop : -1.22 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 89 HIS 0.009 0.001 HIS F 18 PHE 0.020 0.002 PHE K 223 TYR 0.015 0.002 TYR H 37 ARG 0.006 0.001 ARG H 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.761 Fit side-chains REVERT: G 13 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7493 (mmtt) REVERT: G 91 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: G 92 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: K 96 MET cc_start: 0.4051 (mtt) cc_final: 0.3481 (tpt) REVERT: K 129 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: E 73 GLU cc_start: 0.8253 (tt0) cc_final: 0.8026 (tt0) REVERT: A 59 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: D 108 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8392 (mtpt) REVERT: M 22 TRP cc_start: 0.2927 (OUTLIER) cc_final: 0.2067 (t-100) REVERT: M 71 MET cc_start: 0.4157 (mmt) cc_final: 0.3681 (tpp) REVERT: M 181 HIS cc_start: 0.7358 (t70) cc_final: 0.6991 (t70) REVERT: M 248 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7415 (mm-30) outliers start: 42 outliers final: 29 residues processed: 198 average time/residue: 1.7561 time to fit residues: 379.1347 Evaluate side-chains 207 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 248 GLU Chi-restraints excluded: chain K residue 252 GLN Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain M residue 22 TRP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN M 113 GLN ** M 146 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 = 0.4115 r_free = 0.4115 target = 0.172514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126804 restraints weight = 22324.724| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.26 r_work: 0.3237 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19592 Z= 0.190 Angle : 0.637 13.364 27729 Z= 0.361 Chirality : 0.040 0.231 3117 Planarity : 0.005 0.092 2519 Dihedral : 27.820 160.263 4978 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 3.24 % Allowed : 16.72 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -0.16 (0.22), residues: 1545 helix: 0.70 (0.19), residues: 796 sheet: 0.05 (0.50), residues: 140 loop : -1.18 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 22 HIS 0.006 0.001 HIS F 18 PHE 0.017 0.001 PHE K 223 TYR 0.015 0.001 TYR H 37 ARG 0.008 0.001 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7118.61 seconds wall clock time: 126 minutes 41.19 seconds (7601.19 seconds total)