Starting phenix.real_space_refine on Thu Aug 8 12:56:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/08_2024/7xct_33127.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/08_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_33127/08_2024/7xct_33127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/08_2024/7xct_33127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/08_2024/7xct_33127.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xct_33127/08_2024/7xct_33127.cif" } 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-5409/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: 10.38, per 1000 atoms: 0.56 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: 9.02 Conformation dependent library (CDL) restraints added in 2.3 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... Secondary structure from input PDB file: 71 helices and 14 sheets defined 51.5% alpha, 6.9% beta 125 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 8.30 Creating SS restraints... Processing helix chain 'L' and resid 22 through 34 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 56 through 60 removed outlier: 3.803A pdb=" N ASN L 60 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 36 through 41 removed outlier: 3.726A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.588A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.517A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.553A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 36 through 45 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 50 through 55 Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 75 through 80 Processing helix chain 'K' and resid 82 through 87 Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 105 through 119 removed outlier: 3.599A pdb=" N HIS K 109 " --> pdb=" O GLY K 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 167 through 175 removed outlier: 3.577A pdb=" N LEU K 171 " --> pdb=" O GLY K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 209 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) removed outlier: 3.756A pdb=" N TYR K 209 " --> pdb=" O TRP K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 234 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 246 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 256 through 260 removed outlier: 3.817A pdb=" N ASN K 259 " --> pdb=" O ARG K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 289 Processing helix chain 'K' and resid 320 through 325 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 79 removed outlier: 3.614A pdb=" N NLE E 79 " --> pdb=" O GLN E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 79' Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.576A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.626A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.525A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 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) removed outlier: 3.569A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.655A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 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 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.612A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.601A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 45 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 50 through 55 Processing helix chain 'M' and resid 68 through 73 Processing helix chain 'M' and resid 75 through 80 Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'M' and resid 105 through 119 removed outlier: 3.599A pdb=" N HIS M 109 " --> pdb=" O GLY M 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN M 116 " --> pdb=" O GLN M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 127 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 167 through 175 removed outlier: 3.577A pdb=" N LEU M 171 " --> pdb=" O GLY M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 209 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) removed outlier: 3.756A pdb=" N TYR M 209 " --> pdb=" O TRP M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 234 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 246 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 256 through 260 removed outlier: 3.817A pdb=" N ASN M 259 " --> pdb=" O ARG M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 289 Processing helix chain 'M' and resid 320 through 325 Processing helix chain 'N' and resid 22 through 34 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 56 through 60 removed outlier: 3.802A pdb=" N ASN N 60 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing sheet with id=AA1, 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: 6.410A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU L 71 " --> pdb=" O LYS L 6 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS L 68 " --> pdb=" O ILE L 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.167A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.417A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.147A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'K' and resid 7 through 8 removed outlier: 3.558A pdb=" N LEU K 7 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 215 through 220 removed outlier: 6.418A pdb=" N HIS K 182 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU K 219 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE K 159 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL K 185 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP K 161 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.199A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AB3, first strand: chain 'M' and resid 7 through 8 removed outlier: 3.559A pdb=" N LEU M 7 " --> pdb=" O TYR M 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 215 through 220 removed outlier: 6.417A pdb=" N HIS M 182 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU M 219 " --> pdb=" O HIS M 182 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY M 184 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE M 159 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL M 185 " --> pdb=" O PHE M 159 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP M 161 " --> pdb=" O VAL M 185 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE M 238 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AB5, 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: 6.410A pdb=" N PHE N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU N 69 " --> pdb=" O PHE N 4 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS N 68 " --> pdb=" O ILE N 44 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1518 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: 6.63 Time building geometry restraints manager: 9.77 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: 2964 2.76 - 3.29: 15464 3.29 - 3.83: 33115 3.83 - 4.36: 42587 4.36 - 4.90: 63026 Nonbonded interactions: 157156 Sorted by model distance: nonbonded pdb=" OG1 THR F 82 " pdb=" O MET F 84 " model vdw 2.220 3.040 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 3.040 nonbonded pdb=" OE2 GLU K 186 " pdb=" O2' SAM K 500 " model vdw 2.302 3.040 nonbonded pdb=" OE2 GLU M 186 " pdb=" O2' SAM M 500 " model vdw 2.303 3.040 ... (remaining 157151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.230 Process input model: 57.400 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.590 ------------------------------------------------------------------------------- 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= 0.731 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 : 1.686 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: 1.9634 time to fit residues: 579.5253 Evaluate side-chains 181 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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: 0.8980 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 139 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19592 Z= 0.209 Angle : 0.697 15.285 27729 Z= 0.397 Chirality : 0.042 0.232 3117 Planarity : 0.006 0.072 2519 Dihedral : 27.783 173.119 4980 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 3.53 % Allowed : 10.46 % Favored : 86.01 % 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: -2.36 (0.20), residues: 1545 helix: -1.43 (0.16), residues: 797 sheet: -0.68 (0.49), residues: 140 loop : -1.77 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 22 HIS 0.004 0.001 HIS G 82 PHE 0.019 0.002 PHE K 223 TYR 0.013 0.001 TYR K 312 ARG 0.008 0.001 ARG G 99 *********************** 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 257 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 209 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7541 (tptt) REVERT: H 35 GLU cc_start: 0.7378 (pt0) cc_final: 0.7153 (pt0) REVERT: K 71 MET cc_start: 0.5051 (OUTLIER) cc_final: 0.4361 (mpp) REVERT: K 104 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7958 (t) REVERT: K 129 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: A 122 LYS cc_start: 0.8769 (pttt) cc_final: 0.8552 (pttp) REVERT: C 41 GLU cc_start: 0.8006 (tt0) cc_final: 0.7690 (tt0) REVERT: C 95 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8478 (mmmt) REVERT: M 71 MET cc_start: 0.4359 (mmt) cc_final: 0.3900 (tpp) REVERT: M 248 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7099 (mm-30) outliers start: 48 outliers final: 13 residues processed: 234 average time/residue: 1.7945 time to fit residues: 456.9874 Evaluate side-chains 197 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 71 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 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 87 SER Chi-restraints excluded: chain A residue 73 GLU 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: 7.9990 chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** 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 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 19592 Z= 0.472 Angle : 0.780 14.679 27729 Z= 0.434 Chirality : 0.050 0.243 3117 Planarity : 0.006 0.077 2519 Dihedral : 28.041 172.994 4978 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.30 % Rotamer: Outliers : 4.42 % Allowed : 12.67 % Favored : 82.92 % 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: -1.49 (0.21), residues: 1545 helix: -0.49 (0.18), residues: 805 sheet: -0.51 (0.48), residues: 141 loop : -1.67 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 228 HIS 0.011 0.001 HIS F 18 PHE 0.028 0.002 PHE K 223 TYR 0.025 0.002 TYR K 312 ARG 0.008 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 243 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 183 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: G 13 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.6590 (mttt) REVERT: G 91 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: G 92 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: K 104 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8153 (t) REVERT: K 276 ASN cc_start: 0.7104 (p0) cc_final: 0.6899 (p0) REVERT: E 49 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8286 (ttm170) REVERT: E 53 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7917 (ttt180) REVERT: D 108 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8390 (mtpt) REVERT: B 67 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8132 (ttm110) REVERT: M 22 TRP cc_start: 0.2897 (OUTLIER) cc_final: 0.2531 (t-100) REVERT: M 55 MET cc_start: 0.1696 (mtm) cc_final: 0.1433 (mtt) REVERT: M 71 MET cc_start: 0.4334 (mmt) cc_final: 0.3873 (tpp) outliers start: 60 outliers final: 27 residues processed: 219 average time/residue: 1.7204 time to fit residues: 410.8250 Evaluate side-chains 209 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 71 THR 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 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 96 THR Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 104 THR 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 49 ARG Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 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 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 200 ARG 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: 20.0000 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 172 optimal weight: 30.0000 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 143 optimal weight: 0.8980 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN 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 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19592 Z= 0.220 Angle : 0.668 15.077 27729 Z= 0.377 Chirality : 0.042 0.252 3117 Planarity : 0.005 0.078 2519 Dihedral : 27.955 172.405 4978 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 3.46 % Allowed : 14.06 % Favored : 82.47 % 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: -0.79 (0.22), residues: 1545 helix: 0.18 (0.19), residues: 801 sheet: -0.26 (0.49), residues: 140 loop : -1.47 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 22 HIS 0.005 0.001 HIS F 18 PHE 0.018 0.001 PHE K 223 TYR 0.015 0.001 TYR M 209 ARG 0.008 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 228 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 92 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: K 55 MET cc_start: 0.2557 (mtm) cc_final: 0.1084 (mmt) REVERT: K 104 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8121 (t) REVERT: K 129 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: K 170 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8772 (t) REVERT: A 59 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: A 120 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8006 (mmm) REVERT: D 57 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8549 (mtpt) REVERT: C 59 THR cc_start: 0.8889 (t) cc_final: 0.8656 (p) REVERT: B 67 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8119 (ttm110) REVERT: M 22 TRP cc_start: 0.3149 (OUTLIER) cc_final: 0.2831 (t-100) REVERT: M 55 MET cc_start: 0.1833 (mtm) cc_final: 0.1606 (mtt) REVERT: M 71 MET cc_start: 0.4253 (mmt) cc_final: 0.3857 (tpp) outliers start: 47 outliers final: 20 residues processed: 211 average time/residue: 1.7256 time to fit residues: 397.0439 Evaluate side-chains 204 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 38 ASN Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 106 LEU 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 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 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 106 LEU Chi-restraints excluded: chain M residue 120 THR 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: 4.9990 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 87 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN K 113 GLN E 85 GLN A 68 GLN D 84 ASN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19592 Z= 0.360 Angle : 0.707 14.289 27729 Z= 0.395 Chirality : 0.045 0.247 3117 Planarity : 0.006 0.081 2519 Dihedral : 27.923 169.377 4978 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 3.98 % Allowed : 14.51 % Favored : 81.52 % 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: -0.71 (0.22), residues: 1545 helix: 0.23 (0.19), residues: 808 sheet: -0.16 (0.49), residues: 140 loop : -1.44 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 22 HIS 0.010 0.001 HIS F 18 PHE 0.022 0.002 PHE K 223 TYR 0.014 0.002 TYR K 312 ARG 0.008 0.001 ARG A 131 *********************** 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 237 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 183 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: G 92 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: K 55 MET cc_start: 0.2025 (mtm) cc_final: 0.0759 (mmt) REVERT: K 104 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8166 (t) REVERT: K 129 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: A 59 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: A 120 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8112 (mmm) REVERT: D 57 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8617 (mtpt) REVERT: D 108 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8380 (mtpt) REVERT: M 22 TRP cc_start: 0.3206 (OUTLIER) cc_final: 0.2868 (t-100) REVERT: M 55 MET cc_start: 0.1782 (mtm) cc_final: 0.1543 (mtt) outliers start: 54 outliers final: 26 residues processed: 218 average time/residue: 1.7230 time to fit residues: 410.0196 Evaluate side-chains 209 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 38 ASN 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 K residue 22 TRP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 135 VAL 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 87 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET 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 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 201 GLU Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 300 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.0030 chunk 34 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 172 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 113 GLN E 85 GLN B 25 ASN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19592 Z= 0.248 Angle : 0.669 14.272 27729 Z= 0.377 Chirality : 0.042 0.242 3117 Planarity : 0.005 0.081 2519 Dihedral : 27.895 169.070 4978 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.83 % Favored : 93.98 % Rotamer: Outliers : 3.98 % Allowed : 15.54 % Favored : 80.49 % 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: -0.50 (0.22), residues: 1545 helix: 0.43 (0.19), residues: 808 sheet: -0.13 (0.49), residues: 140 loop : -1.37 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 22 HIS 0.007 0.001 HIS F 18 PHE 0.018 0.001 PHE K 223 TYR 0.010 0.001 TYR B 51 ARG 0.006 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 234 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: K 55 MET cc_start: 0.1859 (mtm) cc_final: 0.0636 (mmt) REVERT: K 104 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8156 (t) REVERT: K 129 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: A 59 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: A 120 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8071 (mmm) REVERT: D 57 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8592 (mtpt) REVERT: D 108 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8338 (mtpt) REVERT: M 22 TRP cc_start: 0.3231 (OUTLIER) cc_final: 0.2812 (t-100) REVERT: M 55 MET cc_start: 0.1770 (mtm) cc_final: 0.1525 (mtt) outliers start: 54 outliers final: 33 residues processed: 215 average time/residue: 1.5940 time to fit residues: 375.7443 Evaluate side-chains 216 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 96 LEU 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 K residue 22 TRP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 104 THR 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 255 GLU Chi-restraints excluded: chain K residue 286 ASP 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 73 GLU Chi-restraints excluded: chain A residue 120 MET 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 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 201 GLU Chi-restraints excluded: chain M residue 226 GLU Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 300 LYS 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: 0.7980 chunk 125 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** M 113 GLN M 182 HIS M 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19592 Z= 0.224 Angle : 0.638 14.153 27729 Z= 0.359 Chirality : 0.041 0.243 3117 Planarity : 0.005 0.082 2519 Dihedral : 27.681 165.954 4978 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.63 % Favored : 94.17 % Rotamer: Outliers : 3.98 % Allowed : 15.91 % Favored : 80.12 % 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: -0.26 (0.22), residues: 1545 helix: 0.65 (0.19), residues: 809 sheet: 0.05 (0.49), residues: 140 loop : -1.32 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 22 HIS 0.005 0.001 HIS F 18 PHE 0.016 0.001 PHE K 223 TYR 0.011 0.001 TYR H 37 ARG 0.007 0.000 ARG G 71 *********************** 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 230 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 176 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 91 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: K 55 MET cc_start: 0.2060 (mtm) cc_final: 0.0846 (mmt) REVERT: K 104 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8304 (t) REVERT: K 129 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: K 170 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8803 (t) REVERT: E 73 GLU cc_start: 0.8244 (tt0) cc_final: 0.8021 (tt0) REVERT: A 120 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8044 (mmm) REVERT: A 129 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6987 (tpt-90) REVERT: D 108 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8332 (mtpt) REVERT: C 59 THR cc_start: 0.8898 (t) cc_final: 0.8658 (p) REVERT: M 22 TRP cc_start: 0.3258 (OUTLIER) cc_final: 0.2790 (t-100) REVERT: M 71 MET cc_start: 0.4183 (mmt) cc_final: 0.3787 (tpp) REVERT: M 278 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7441 (ptp90) outliers start: 54 outliers final: 26 residues processed: 211 average time/residue: 1.5877 time to fit residues: 367.7836 Evaluate side-chains 206 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 104 THR 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 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG 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 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 44 VAL Chi-restraints excluded: chain M residue 106 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 GLN M 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 19592 Z= 0.416 Angle : 0.721 14.089 27729 Z= 0.402 Chirality : 0.047 0.242 3117 Planarity : 0.006 0.088 2519 Dihedral : 27.898 162.440 4978 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.92 % Rotamer: Outliers : 3.39 % Allowed : 17.01 % Favored : 79.60 % 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: -0.50 (0.22), residues: 1545 helix: 0.42 (0.19), residues: 814 sheet: 0.07 (0.49), residues: 140 loop : -1.43 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 89 HIS 0.010 0.001 HIS F 18 PHE 0.023 0.002 PHE K 223 TYR 0.016 0.002 TYR H 37 ARG 0.006 0.001 ARG A 131 *********************** 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 218 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.626 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: K 55 MET cc_start: 0.2150 (mtm) cc_final: 0.0821 (mmt) REVERT: K 104 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8254 (t) REVERT: K 129 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 120 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: A 129 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7013 (tpt-90) REVERT: D 108 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8365 (mtpt) REVERT: C 11 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.5561 (ptt-90) REVERT: M 22 TRP cc_start: 0.3280 (OUTLIER) cc_final: 0.2757 (t-100) REVERT: M 55 MET cc_start: 0.1141 (mtt) cc_final: 0.0161 (mmt) REVERT: M 71 MET cc_start: 0.4169 (mmt) cc_final: 0.3691 (tpp) REVERT: M 212 LYS cc_start: 0.6551 (pttt) cc_final: 0.6312 (pptt) REVERT: M 248 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: M 278 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7461 (ptp90) outliers start: 46 outliers final: 28 residues processed: 207 average time/residue: 1.7032 time to fit residues: 386.7056 Evaluate side-chains 209 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 38 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 135 VAL 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 K residue 286 ASP Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG 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 11 ARG 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 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 226 GLU 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: 8.9990 chunk 159 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 A 76 GLN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3187 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= 0.224 Angle : 0.671 14.928 27729 Z= 0.377 Chirality : 0.042 0.267 3117 Planarity : 0.005 0.088 2519 Dihedral : 27.918 162.364 4978 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.92 % Rotamer: Outliers : 3.02 % Allowed : 17.53 % Favored : 79.46 % 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: -0.25 (0.22), residues: 1545 helix: 0.64 (0.19), residues: 807 sheet: 0.11 (0.49), residues: 140 loop : -1.30 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 22 HIS 0.007 0.001 HIS F 18 PHE 0.019 0.001 PHE K 223 TYR 0.018 0.001 TYR H 37 ARG 0.007 0.001 ARG G 71 *********************** 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 214 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: K 55 MET cc_start: 0.2206 (mtm) cc_final: 0.0909 (mmt) REVERT: K 104 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8223 (t) REVERT: K 129 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 120 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8091 (mmm) REVERT: A 129 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6979 (tpt-90) REVERT: D 108 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8354 (mtpt) REVERT: M 22 TRP cc_start: 0.3267 (OUTLIER) cc_final: 0.2736 (t-100) REVERT: M 55 MET cc_start: 0.1074 (mtt) cc_final: 0.0095 (mmt) REVERT: M 71 MET cc_start: 0.4131 (mmt) cc_final: 0.3647 (tpp) REVERT: M 212 LYS cc_start: 0.6526 (pttt) cc_final: 0.6319 (pptt) REVERT: M 278 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7401 (ptp90) outliers start: 41 outliers final: 27 residues processed: 200 average time/residue: 1.7475 time to fit residues: 381.9843 Evaluate side-chains 207 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 38 ASN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 22 TRP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 104 THR 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 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 39 VAL 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 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: 5.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 113 GLN A 39 HIS A 68 GLN M 113 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 19592 Z= 0.447 Angle : 0.738 14.387 27729 Z= 0.411 Chirality : 0.048 0.295 3117 Planarity : 0.006 0.088 2519 Dihedral : 27.994 158.695 4978 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.15 % Favored : 93.66 % Rotamer: Outliers : 3.17 % Allowed : 17.53 % Favored : 79.31 % 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: -0.55 (0.22), residues: 1545 helix: 0.39 (0.19), residues: 815 sheet: -0.03 (0.48), residues: 140 loop : -1.45 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 89 HIS 0.011 0.001 HIS F 18 PHE 0.024 0.002 PHE K 223 TYR 0.018 0.002 TYR H 37 ARG 0.009 0.001 ARG A 131 ********************** 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 215 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 172 time to evaluate : 1.867 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: K 55 MET cc_start: 0.2907 (mtm) cc_final: 0.1424 (mmt) REVERT: K 104 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8273 (t) REVERT: K 129 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: A 120 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8085 (mmm) REVERT: A 129 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7011 (tpt-90) REVERT: D 108 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8361 (mtpt) REVERT: M 55 MET cc_start: 0.1191 (mtt) cc_final: 0.0970 (mtp) REVERT: M 71 MET cc_start: 0.4097 (mmt) cc_final: 0.3607 (tpp) REVERT: M 260 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8442 (mtm) REVERT: M 278 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7428 (ptp90) outliers start: 43 outliers final: 28 residues processed: 201 average time/residue: 1.7996 time to fit residues: 404.1937 Evaluate side-chains 204 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 1.792 ------------------------------------------------------------------------------- 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 38 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 104 THR 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 255 GLU Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG 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 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 106 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6919 > 50: distance: 18 - 23: 33.316 distance: 23 - 24: 57.777 distance: 24 - 27: 40.473 distance: 25 - 26: 38.768 distance: 25 - 32: 55.546 distance: 27 - 28: 47.755 distance: 28 - 29: 40.827 distance: 29 - 30: 44.013 distance: 29 - 31: 56.905 distance: 32 - 33: 57.042 distance: 33 - 34: 39.194 distance: 33 - 36: 40.628 distance: 34 - 35: 55.758 distance: 34 - 39: 40.185 distance: 36 - 37: 40.569 distance: 37 - 38: 55.371 distance: 39 - 40: 7.429 distance: 40 - 41: 69.473 distance: 40 - 43: 40.036 distance: 41 - 42: 55.883 distance: 41 - 47: 40.856 distance: 43 - 44: 40.267 distance: 44 - 45: 29.744 distance: 45 - 46: 49.784 distance: 47 - 48: 52.133 distance: 48 - 49: 52.323 distance: 48 - 51: 51.593 distance: 49 - 50: 40.892 distance: 49 - 56: 68.895 distance: 51 - 52: 56.298 distance: 52 - 53: 41.288 distance: 53 - 54: 56.811 distance: 54 - 55: 52.615 distance: 57 - 58: 38.611 distance: 57 - 60: 9.106 distance: 58 - 59: 40.467 distance: 58 - 64: 41.215 distance: 60 - 61: 57.352 distance: 61 - 62: 70.030 distance: 61 - 63: 59.021 distance: 64 - 65: 50.846 distance: 65 - 66: 40.216 distance: 65 - 68: 40.390 distance: 66 - 67: 3.338 distance: 66 - 72: 39.107 distance: 68 - 69: 33.753 distance: 69 - 70: 23.333 distance: 69 - 71: 27.420 distance: 72 - 73: 40.399 distance: 73 - 74: 53.013 distance: 73 - 76: 66.431 distance: 74 - 79: 56.620 distance: 76 - 77: 57.237 distance: 76 - 78: 40.418 distance: 79 - 80: 39.896 distance: 80 - 81: 39.181 distance: 80 - 83: 56.110 distance: 81 - 82: 56.860 distance: 83 - 84: 17.939 distance: 84 - 85: 22.234 distance: 86 - 87: 33.364 distance: 87 - 88: 38.650 distance: 87 - 89: 13.577 distance: 90 - 96: 39.814 distance: 91 - 92: 55.689 distance: 91 - 94: 69.116 distance: 92 - 93: 24.313 distance: 92 - 97: 52.613 distance: 94 - 95: 38.468 distance: 95 - 96: 38.766 distance: 97 - 98: 52.514 distance: 99 - 100: 57.348 distance: 99 - 103: 34.721