Starting phenix.real_space_refine on Tue Apr 9 10:59:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfs_34726/04_2024/8hfs_34726.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfs_34726/04_2024/8hfs_34726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfs_34726/04_2024/8hfs_34726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfs_34726/04_2024/8hfs_34726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfs_34726/04_2024/8hfs_34726.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfs_34726/04_2024/8hfs_34726.pdb" } resolution = 2.98 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10627 2.51 5 N 2674 2.21 5 O 2843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y ASP 73": "OD1" <-> "OD2" Residue "Y GLU 134": "OE1" <-> "OE2" Residue "Z GLU 53": "OE1" <-> "OE2" Residue "Z GLU 54": "OE1" <-> "OE2" Residue "Z GLU 57": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "Z TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 259": "OD1" <-> "OD2" Residue "Z PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "A ASP 12": "OD1" <-> "OD2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F ASP 173": "OD1" <-> "OD2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 238": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16216 Number of models: 1 Model: "" Number of chains: 11 Chain: "Y" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1799 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain: "Z" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2341 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "A" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 409 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "E" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1795 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Chain: "F" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2332 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain: "C" Number of atoms: 3092 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1795 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 248, 1795 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} bond proxies already assigned to first conformer: 508 Chain: "D" Number of atoms: 3669 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 302, 2332 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Conformer: "B" Number of residues, atoms: 302, 2332 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} bond proxies already assigned to first conformer: 1014 Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 352 residue: pdb=" N AMET C 1 " occ=0.48 ... (14 atoms not shown) pdb=" CE BMET C 1 " occ=0.52 residue: pdb=" N AGLU C 2 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 2 " occ=0.52 residue: pdb=" N ATYR C 3 " occ=0.48 ... (22 atoms not shown) pdb=" OH BTYR C 3 " occ=0.52 residue: pdb=" N AGLY C 4 " occ=0.48 ... (6 atoms not shown) pdb=" O BGLY C 4 " occ=0.52 residue: pdb=" N AVAL C 5 " occ=0.48 ... (12 atoms not shown) pdb=" CG2BVAL C 5 " occ=0.52 residue: pdb=" N ALEU C 6 " occ=0.48 ... (14 atoms not shown) pdb=" CD2BLEU C 6 " occ=0.52 residue: pdb=" N ASER C 7 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER C 7 " occ=0.52 residue: pdb=" N AVAL C 8 " occ=0.48 ... (12 atoms not shown) pdb=" CG2BVAL C 8 " occ=0.52 residue: pdb=" N AILE C 9 " occ=0.48 ... (14 atoms not shown) pdb=" CD1BILE C 9 " occ=0.52 residue: pdb=" N ALEU C 10 " occ=0.48 ... (14 atoms not shown) pdb=" CD2BLEU C 10 " occ=0.52 residue: pdb=" N AVAL C 11 " occ=0.48 ... (12 atoms not shown) pdb=" CG2BVAL C 11 " occ=0.52 residue: pdb=" N AILE C 12 " occ=0.48 ... (14 atoms not shown) pdb=" CD1BILE C 12 " occ=0.52 ... (remaining 340 not shown) Time building chain proxies: 9.23, per 1000 atoms: 0.57 Number of scatterers: 16216 At special positions: 0 Unit cell: (131.052, 127.83, 111.717, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2843 8.00 N 2674 7.00 C 10627 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: 6.78 Conformation dependent library (CDL) restraints added in 3.6 seconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3854 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 4 sheets defined 75.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.511A pdb=" N VAL Y 8 " --> pdb=" O GLY Y 4 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 43 removed outlier: 4.042A pdb=" N SER Y 37 " --> pdb=" O ILE Y 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR Y 43 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 removed outlier: 3.844A pdb=" N GLY Y 49 " --> pdb=" O HIS Y 45 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE Y 59 " --> pdb=" O SER Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 88 removed outlier: 3.731A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 93 through 135 removed outlier: 4.198A pdb=" N MET Y 97 " --> pdb=" O LEU Y 93 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL Y 101 " --> pdb=" O MET Y 97 " (cutoff:3.500A) Proline residue: Y 102 - end of helix removed outlier: 4.046A pdb=" N VAL Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Y 124 " --> pdb=" O MET Y 120 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU Y 125 " --> pdb=" O LEU Y 121 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN Y 135 " --> pdb=" O ARG Y 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 137 through 166 removed outlier: 3.618A pdb=" N VAL Y 141 " --> pdb=" O SER Y 137 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE Y 156 " --> pdb=" O GLN Y 152 " (cutoff:3.500A) Proline residue: Y 159 - end of helix Processing helix chain 'Y' and resid 167 through 178 removed outlier: 4.059A pdb=" N ILE Y 171 " --> pdb=" O SER Y 167 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN Y 172 " --> pdb=" O PRO Y 168 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE Y 178 " --> pdb=" O ALA Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 204 removed outlier: 3.836A pdb=" N MET Y 192 " --> pdb=" O VAL Y 188 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL Y 194 " --> pdb=" O GLY Y 190 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA Y 195 " --> pdb=" O GLY Y 191 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL Y 196 " --> pdb=" O MET Y 192 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY Y 197 " --> pdb=" O VAL Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 210 through 221 Processing helix chain 'Y' and resid 227 through 249 Processing helix chain 'Z' and resid 9 through 20 Processing helix chain 'Z' and resid 21 through 23 No H-bonds generated for 'chain 'Z' and resid 21 through 23' Processing helix chain 'Z' and resid 34 through 49 Proline residue: Z 43 - end of helix Processing helix chain 'Z' and resid 52 through 63 Processing helix chain 'Z' and resid 73 through 89 removed outlier: 3.626A pdb=" N GLU Z 86 " --> pdb=" O ALA Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 118 removed outlier: 3.773A pdb=" N MET Z 105 " --> pdb=" O VAL Z 101 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY Z 107 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) Proline residue: Z 108 - end of helix Proline residue: Z 115 - end of helix Processing helix chain 'Z' and resid 120 through 132 removed outlier: 3.698A pdb=" N ILE Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Z 132 " --> pdb=" O ILE Z 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 138 through 167 removed outlier: 3.597A pdb=" N LEU Z 142 " --> pdb=" O ILE Z 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 170 through 175 Processing helix chain 'Z' and resid 178 through 202 removed outlier: 3.717A pdb=" N VAL Z 182 " --> pdb=" O LEU Z 178 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL Z 202 " --> pdb=" O ILE Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 246 removed outlier: 3.635A pdb=" N LYS Z 246 " --> pdb=" O GLN Z 242 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 265 Processing helix chain 'Z' and resid 267 through 283 Processing helix chain 'Z' and resid 286 through 304 removed outlier: 3.542A pdb=" N ILE Z 290 " --> pdb=" O SER Z 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.962A pdb=" N GLU B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 41 removed outlier: 3.879A pdb=" N ASN B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.803A pdb=" N TYR B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'A' and resid 29 through 48 removed outlier: 3.643A pdb=" N GLY A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 25 removed outlier: 4.242A pdb=" N ILE E 9 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 43 removed outlier: 4.164A pdb=" N SER E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.846A pdb=" N GLY E 49 " --> pdb=" O HIS E 45 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 removed outlier: 3.741A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.766A pdb=" N ILE E 100 " --> pdb=" O ILE E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 134 removed outlier: 3.848A pdb=" N VAL E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 166 removed outlier: 4.216A pdb=" N VAL E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 148 " --> pdb=" O TRP E 144 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG E 155 " --> pdb=" O CYS E 151 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Proline residue: E 159 - end of helix removed outlier: 3.554A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL E 165 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.778A pdb=" N ILE E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 193 Processing helix chain 'E' and resid 193 through 205 removed outlier: 4.437A pdb=" N GLY E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 220 Processing helix chain 'E' and resid 227 through 247 Processing helix chain 'F' and resid 9 through 21 Processing helix chain 'F' and resid 34 through 49 Proline residue: F 43 - end of helix Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 73 through 90 Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.843A pdb=" N MET F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 119 Proline residue: F 115 - end of helix Processing helix chain 'F' and resid 120 through 132 removed outlier: 3.839A pdb=" N ILE F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 167 removed outlier: 4.050A pdb=" N LEU F 142 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 177 through 201 removed outlier: 3.582A pdb=" N THR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 246 removed outlier: 4.008A pdb=" N HIS F 237 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 246 " --> pdb=" O GLN F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 265 Processing helix chain 'F' and resid 267 through 283 removed outlier: 3.507A pdb=" N LEU F 271 " --> pdb=" O GLY F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 304 removed outlier: 3.501A pdb=" N ILE F 290 " --> pdb=" O SER F 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.533A pdb=" N AVAL C 13 " --> pdb=" O AILE C 9 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N AILE C 23 " --> pdb=" O AGLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 4.107A pdb=" N ASER C 37 " --> pdb=" O AILE C 33 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N BVAL C 42 " --> pdb=" O BLEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 61 removed outlier: 3.734A pdb=" N AILE C 51 " --> pdb=" O ASER C 47 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALEU C 52 " --> pdb=" O AALA C 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N AGLY C 53 " --> pdb=" O AGLY C 49 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N BLEU C 58 " --> pdb=" O BGLY C 54 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N AILE C 59 " --> pdb=" O ASER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 removed outlier: 4.443A pdb=" N AALA C 77 " --> pdb=" O AASP C 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N AILE C 79 " --> pdb=" O AALA C 75 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALEU C 84 " --> pdb=" O AALA C 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N AMET C 85 " --> pdb=" O ASER C 81 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N AVAL C 86 " --> pdb=" O ASER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 100 through 134 removed outlier: 3.536A pdb=" N AALA C 104 " --> pdb=" O AILE C 100 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N AILE C 105 " --> pdb=" O AVAL C 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALEU C 106 " --> pdb=" O APRO C 102 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N AVAL C 113 " --> pdb=" O ATHR C 109 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N BSER C 122 " --> pdb=" O BVAL C 118 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N AVAL C 123 " --> pdb=" O AARG C 119 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N AVAL C 124 " --> pdb=" O AMET C 120 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALEU C 125 " --> pdb=" O ALEU C 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N AGLU C 134 " --> pdb=" O AASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 removed outlier: 3.996A pdb=" N BARG C 155 " --> pdb=" O BCYS C 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N AILE C 156 " --> pdb=" O AGLN C 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N BALA C 157 " --> pdb=" O BGLY C 153 " (cutoff:3.500A) Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.940A pdb=" N AILE C 171 " --> pdb=" O ASER C 167 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N BILE C 178 " --> pdb=" O BALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 193 through 205 removed outlier: 4.228A pdb=" N GLY C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 227 through 247 Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 34 through 49 removed outlier: 3.678A pdb=" N AALA D 38 " --> pdb=" O AASN D 34 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N BLEU D 41 " --> pdb=" O BTRP D 37 " (cutoff:3.500A) Proline residue: D 43 - end of helix removed outlier: 3.743A pdb=" N BLYS D 46 " --> pdb=" O BILE D 42 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N BLYS D 47 " --> pdb=" O BPRO D 43 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N BLEU D 48 " --> pdb=" O BALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 removed outlier: 4.318A pdb=" N BLYS D 56 " --> pdb=" O BGLY D 52 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N BGLU D 57 " --> pdb=" O BGLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.736A pdb=" N AASN D 89 " --> pdb=" O AGLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.600A pdb=" N BLYS D 102 " --> pdb=" O BILE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.801A pdb=" N BASP D 114 " --> pdb=" O BALA D 110 " (cutoff:3.500A) Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 121 through 132 removed outlier: 3.606A pdb=" N BSER D 131 " --> pdb=" O BALA D 127 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALEU D 132 " --> pdb=" O AILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 167 removed outlier: 3.714A pdb=" N BPHE D 144 " --> pdb=" O BALA D 140 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N AALA D 150 " --> pdb=" O AILE D 146 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N AILE D 151 " --> pdb=" O AVAL D 147 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N AARG D 152 " --> pdb=" O ATRP D 148 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N AILE D 153 " --> pdb=" O AASN D 149 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ATRP D 157 " --> pdb=" O AILE D 153 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ATYR D 158 " --> pdb=" O AALA D 154 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N AGLN D 160 " --> pdb=" O ALEU D 156 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N BGLU D 161 " --> pdb=" O BTRP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 201 removed outlier: 3.533A pdb=" N THR D 181 " --> pdb=" O AGLY D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 246 removed outlier: 3.588A pdb=" N LYS D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 265 Processing helix chain 'D' and resid 267 through 283 Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.578A pdb=" N ILE D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 212 through 214 Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 7 removed outlier: 5.944A pdb=" N PHE A 4 " --> pdb=" O TYR A 15 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A 15 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 212 through 217 Processing sheet with id=AA4, first strand: chain 'D' and resid 212 through 217 removed outlier: 3.586A pdb=" N SER D 214 " --> pdb=" O THR D 255 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5081 1.34 - 1.46: 3036 1.46 - 1.58: 8317 1.58 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 16567 Sorted by residual: bond pdb=" C THR B 57 " pdb=" N PRO B 58 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" CA MET C 205 " pdb=" CB MET C 205 " ideal model delta sigma weight residual 1.528 1.560 -0.032 1.51e-02 4.39e+03 4.45e+00 bond pdb=" C ILE F 42 " pdb=" N PRO F 43 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.16e+00 bond pdb=" C5 MAN Z 401 " pdb=" O5 MAN Z 401 " ideal model delta sigma weight residual 1.418 1.447 -0.029 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 MAN Z 401 " pdb=" C2 MAN Z 401 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 16562 not shown) Histogram of bond angle deviations from ideal: 96.32 - 104.77: 280 104.77 - 113.21: 9449 113.21 - 121.66: 9507 121.66 - 130.11: 3194 130.11 - 138.56: 135 Bond angle restraints: 22565 Sorted by residual: angle pdb=" C THR B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta sigma weight residual 118.85 113.11 5.74 1.09e+00 8.42e-01 2.78e+01 angle pdb=" CG1 ILE D 204 " pdb=" CB ILE D 204 " pdb=" CG2 ILE D 204 " ideal model delta sigma weight residual 110.70 96.32 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N AVAL D 116 " pdb=" CA AVAL D 116 " pdb=" C AVAL D 116 " ideal model delta sigma weight residual 113.53 109.22 4.31 9.80e-01 1.04e+00 1.94e+01 angle pdb=" N ILE Y 156 " pdb=" CA ILE Y 156 " pdb=" C ILE Y 156 " ideal model delta sigma weight residual 112.96 109.02 3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA GLU F 57 " pdb=" CB GLU F 57 " pdb=" CG GLU F 57 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 ... (remaining 22560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 8442 18.14 - 36.28: 949 36.28 - 54.42: 253 54.42 - 72.56: 32 72.56 - 90.70: 27 Dihedral angle restraints: 9703 sinusoidal: 3658 harmonic: 6045 Sorted by residual: dihedral pdb=" CA ARG B 63 " pdb=" C ARG B 63 " pdb=" N THR B 64 " pdb=" CA THR B 64 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA MET C 192 " pdb=" C MET C 192 " pdb=" N VAL C 193 " pdb=" CA VAL C 193 " ideal model delta harmonic sigma weight residual 180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA MET F 32 " pdb=" C MET F 32 " pdb=" N GLN F 33 " pdb=" CA GLN F 33 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 9700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2244 0.054 - 0.107: 415 0.107 - 0.161: 47 0.161 - 0.214: 0 0.214 - 0.268: 1 Chirality restraints: 2707 Sorted by residual: chirality pdb=" CB ILE D 204 " pdb=" CA ILE D 204 " pdb=" CG1 ILE D 204 " pdb=" CG2 ILE D 204 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA LEU C 186 " pdb=" N LEU C 186 " pdb=" C LEU C 186 " pdb=" CB LEU C 186 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA PRO Y 72 " pdb=" N PRO Y 72 " pdb=" C PRO Y 72 " pdb=" CB PRO Y 72 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2704 not shown) Planarity restraints: 2790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 208 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO D 209 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 209 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 209 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 49 " 0.051 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO F 50 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO F 50 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 50 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 71 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO Y 72 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO Y 72 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO Y 72 " 0.036 5.00e-02 4.00e+02 ... (remaining 2787 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 465 2.71 - 3.26: 17449 3.26 - 3.81: 27732 3.81 - 4.35: 33593 4.35 - 4.90: 56210 Nonbonded interactions: 135449 Sorted by model distance: nonbonded pdb=" O APRO D 115 " pdb=" OG1ATHR D 120 " model vdw 2.164 2.440 nonbonded pdb=" OD2 ASP F 114 " pdb=" O6 MAN F 401 " model vdw 2.173 2.440 nonbonded pdb=" OG SER B 25 " pdb=" OE1 GLU B 28 " model vdw 2.177 2.440 nonbonded pdb=" OD2 ASP Y 130 " pdb=" NH2 ARG Z 31 " model vdw 2.181 2.520 nonbonded pdb=" OG SER Y 122 " pdb=" O TRP Z 27 " model vdw 2.188 2.440 ... (remaining 135444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and resid 180 through 248) selection = (chain 'E' and resid 180 through 248) selection = (chain 'Y' and resid 180 through 248) } ncs_group { reference = (chain 'D' and resid 178 through 307) selection = (chain 'F' and resid 178 through 307) selection = (chain 'Z' and resid 178 through 307) } 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=0.46 max=1.00 mean=0.84 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.360 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 45.620 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.003 0.042 16567 Z= 0.211 Angle : 0.648 14.381 22565 Z= 0.339 Chirality : 0.040 0.268 2707 Planarity : 0.005 0.082 2790 Dihedral : 16.845 90.700 5849 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.28 % Allowed : 24.39 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 2133 helix: 0.93 (0.14), residues: 1514 sheet: -0.67 (1.17), residues: 26 loop : -1.95 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 201 HIS 0.007 0.001 HIS D 237 PHE 0.009 0.001 PHE C 213 TYR 0.022 0.001 TYR Z 49 ARG 0.008 0.001 ARG Y 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.459 Fit side-chains REVERT: Z 230 SER cc_start: 0.7763 (t) cc_final: 0.7530 (p) REVERT: E 121 LEU cc_start: 0.8422 (tm) cc_final: 0.8177 (tt) REVERT: F 84 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7423 (mm-30) REVERT: F 86 GLU cc_start: 0.6844 (tt0) cc_final: 0.6593 (tt0) outliers start: 32 outliers final: 26 residues processed: 166 average time/residue: 1.1567 time to fit residues: 216.6752 Evaluate side-chains 158 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 165 VAL Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 234 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 0.0270 chunk 89 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16567 Z= 0.157 Angle : 0.563 12.091 22565 Z= 0.283 Chirality : 0.039 0.244 2707 Planarity : 0.004 0.070 2790 Dihedral : 5.708 52.087 2380 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.19 % Allowed : 22.42 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 2133 helix: 1.15 (0.14), residues: 1518 sheet: -0.34 (1.42), residues: 18 loop : -2.15 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 201 HIS 0.003 0.001 HIS D 237 PHE 0.010 0.001 PHE E 16 TYR 0.006 0.001 TYR Z 256 ARG 0.003 0.000 ARG Y 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 156 time to evaluate : 1.280 Fit side-chains REVERT: Y 147 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8151 (mp) REVERT: Z 49 TYR cc_start: 0.6923 (p90) cc_final: 0.6124 (p90) REVERT: E 120 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5245 (mtt) REVERT: E 121 LEU cc_start: 0.8374 (tm) cc_final: 0.8155 (tt) REVERT: E 142 GLU cc_start: 0.4269 (OUTLIER) cc_final: 0.3367 (mp0) outliers start: 58 outliers final: 23 residues processed: 193 average time/residue: 1.0884 time to fit residues: 238.8377 Evaluate side-chains 163 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 92 ASP Chi-restraints excluded: chain Y residue 137 SER Chi-restraints excluded: chain Y residue 147 ILE Chi-restraints excluded: chain Y residue 231 THR Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 265 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 0.2980 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16567 Z= 0.199 Angle : 0.584 10.635 22565 Z= 0.293 Chirality : 0.040 0.265 2707 Planarity : 0.005 0.066 2790 Dihedral : 4.938 55.026 2351 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.96 % Allowed : 23.14 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 2133 helix: 1.05 (0.14), residues: 1540 sheet: -0.55 (1.39), residues: 18 loop : -2.12 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 201 HIS 0.005 0.001 HIS Y 145 PHE 0.011 0.001 PHE Y 215 TYR 0.010 0.001 TYR Z 71 ARG 0.002 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 141 time to evaluate : 1.280 Fit side-chains REVERT: Z 49 TYR cc_start: 0.6987 (p90) cc_final: 0.6052 (p90) REVERT: E 120 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5256 (mtt) REVERT: E 142 GLU cc_start: 0.4384 (OUTLIER) cc_final: 0.3372 (mp0) REVERT: E 205 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7180 (ptp) outliers start: 61 outliers final: 30 residues processed: 188 average time/residue: 1.0824 time to fit residues: 231.1719 Evaluate side-chains 166 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 165 VAL Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN ** Z 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN C 89 ASN A ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16567 Z= 0.192 Angle : 0.577 9.567 22565 Z= 0.290 Chirality : 0.040 0.297 2707 Planarity : 0.005 0.066 2790 Dihedral : 4.890 59.833 2348 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 6.74 % Allowed : 23.91 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 2133 helix: 1.10 (0.14), residues: 1538 sheet: -0.56 (1.40), residues: 18 loop : -2.18 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 201 HIS 0.004 0.001 HIS Y 145 PHE 0.009 0.001 PHE Y 215 TYR 0.009 0.001 TYR Z 71 ARG 0.008 0.000 ARG Y 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 142 time to evaluate : 1.401 Fit side-chains REVERT: Z 49 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6084 (p90) REVERT: E 120 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5247 (mtt) REVERT: E 142 GLU cc_start: 0.4386 (OUTLIER) cc_final: 0.3390 (mp0) REVERT: E 205 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7207 (ptp) outliers start: 69 outliers final: 33 residues processed: 193 average time/residue: 1.0632 time to fit residues: 233.3082 Evaluate side-chains 169 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 0.0060 chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN ** Z 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16567 Z= 0.214 Angle : 0.593 10.225 22565 Z= 0.299 Chirality : 0.041 0.301 2707 Planarity : 0.005 0.066 2790 Dihedral : 4.938 52.421 2348 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 7.45 % Allowed : 23.43 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.19), residues: 2133 helix: 1.11 (0.14), residues: 1527 sheet: -0.67 (1.39), residues: 18 loop : -2.19 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 201 HIS 0.006 0.001 HIS Y 145 PHE 0.012 0.001 PHE Z 66 TYR 0.012 0.001 TYR Z 71 ARG 0.002 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 140 time to evaluate : 1.575 Fit side-chains REVERT: Z 49 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6040 (p90) REVERT: E 120 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5246 (mtt) REVERT: E 142 GLU cc_start: 0.4438 (OUTLIER) cc_final: 0.3389 (mp0) REVERT: E 205 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7182 (ptp) REVERT: F 49 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.5785 (p90) outliers start: 73 outliers final: 43 residues processed: 196 average time/residue: 1.0829 time to fit residues: 241.3760 Evaluate side-chains 181 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 133 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 165 VAL Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 306 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN Z 242 GLN Z 263 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16567 Z= 0.226 Angle : 0.605 10.689 22565 Z= 0.304 Chirality : 0.041 0.313 2707 Planarity : 0.005 0.068 2790 Dihedral : 4.984 44.623 2348 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 7.33 % Allowed : 24.21 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2133 helix: 1.07 (0.14), residues: 1536 sheet: -0.72 (1.37), residues: 18 loop : -2.22 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 201 HIS 0.005 0.001 HIS Y 145 PHE 0.012 0.001 PHE Z 66 TYR 0.013 0.001 TYR Z 71 ARG 0.010 0.001 ARG Y 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 141 time to evaluate : 1.488 Fit side-chains REVERT: Z 49 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6008 (p90) REVERT: B 13 ARG cc_start: 0.6995 (mtt-85) cc_final: 0.6741 (mtt-85) REVERT: B 43 GLU cc_start: 0.6017 (tt0) cc_final: 0.5672 (tp30) REVERT: E 120 MET cc_start: 0.5891 (OUTLIER) cc_final: 0.5280 (mtt) REVERT: E 142 GLU cc_start: 0.4280 (OUTLIER) cc_final: 0.3313 (mp0) REVERT: E 175 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6674 (mt) REVERT: E 205 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7114 (ptp) REVERT: F 49 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.5800 (p90) outliers start: 71 outliers final: 44 residues processed: 195 average time/residue: 1.0865 time to fit residues: 240.4758 Evaluate side-chains 187 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 137 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 170 ILE Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN Z 263 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN F 207 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16567 Z= 0.194 Angle : 0.591 11.596 22565 Z= 0.297 Chirality : 0.041 0.341 2707 Planarity : 0.005 0.067 2790 Dihedral : 4.896 46.533 2348 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 7.51 % Allowed : 24.57 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.19), residues: 2133 helix: 1.16 (0.14), residues: 1532 sheet: -0.75 (1.37), residues: 18 loop : -2.18 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 201 HIS 0.004 0.001 HIS Y 145 PHE 0.008 0.001 PHE Z 66 TYR 0.011 0.001 TYR B 44 ARG 0.010 0.000 ARG Y 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 142 time to evaluate : 1.478 Fit side-chains REVERT: Z 49 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.5952 (p90) REVERT: E 120 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5397 (mtt) REVERT: E 142 GLU cc_start: 0.4304 (OUTLIER) cc_final: 0.3350 (mp0) REVERT: E 175 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6647 (mt) REVERT: E 205 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7109 (ptp) REVERT: F 49 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.5687 (p90) REVERT: F 84 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7111 (mm-30) REVERT: C 225 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7907 (mt-10) outliers start: 73 outliers final: 46 residues processed: 201 average time/residue: 1.0571 time to fit residues: 241.9164 Evaluate side-chains 186 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 306 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 0.0000 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN ** Z 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16567 Z= 0.178 Angle : 0.594 12.771 22565 Z= 0.295 Chirality : 0.040 0.337 2707 Planarity : 0.005 0.068 2790 Dihedral : 4.813 47.144 2348 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 7.04 % Allowed : 24.93 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2133 helix: 1.17 (0.14), residues: 1544 sheet: -0.74 (1.37), residues: 18 loop : -2.20 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 201 HIS 0.003 0.001 HIS Z 62 PHE 0.008 0.001 PHE F 143 TYR 0.015 0.001 TYR B 44 ARG 0.010 0.000 ARG Y 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 144 time to evaluate : 1.393 Fit side-chains REVERT: Y 147 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8168 (mt) REVERT: Z 49 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5970 (p90) REVERT: E 120 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5376 (mtt) REVERT: E 142 GLU cc_start: 0.4250 (OUTLIER) cc_final: 0.3336 (mp0) REVERT: E 175 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6626 (mt) REVERT: E 205 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7117 (ptp) REVERT: F 49 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.5897 (p90) REVERT: F 139 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6908 (pp) outliers start: 64 outliers final: 38 residues processed: 193 average time/residue: 1.0976 time to fit residues: 242.1561 Evaluate side-chains 177 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 147 ILE Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 27 TRP Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 255 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN Y 203 ASN Z 263 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16567 Z= 0.193 Angle : 0.608 12.871 22565 Z= 0.302 Chirality : 0.041 0.342 2707 Planarity : 0.005 0.066 2790 Dihedral : 4.853 48.769 2348 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.56 % Allowed : 25.76 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 2133 helix: 1.17 (0.14), residues: 1542 sheet: -0.44 (1.50), residues: 13 loop : -2.16 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 201 HIS 0.004 0.001 HIS Y 145 PHE 0.009 0.001 PHE F 226 TYR 0.016 0.001 TYR B 44 ARG 0.011 0.000 ARG Y 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 135 time to evaluate : 1.293 Fit side-chains REVERT: Y 147 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8178 (mt) REVERT: Z 49 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.5986 (p90) REVERT: E 120 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.5391 (mtt) REVERT: E 142 GLU cc_start: 0.4278 (OUTLIER) cc_final: 0.3344 (mp0) REVERT: E 175 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6632 (mt) REVERT: E 205 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7108 (ptp) REVERT: F 49 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.5911 (p90) outliers start: 55 outliers final: 41 residues processed: 175 average time/residue: 1.1287 time to fit residues: 224.3471 Evaluate side-chains 179 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 131 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 147 ILE Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 255 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16567 Z= 0.222 Angle : 0.629 12.897 22565 Z= 0.312 Chirality : 0.042 0.344 2707 Planarity : 0.005 0.067 2790 Dihedral : 4.976 50.907 2348 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.50 % Allowed : 25.88 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 2133 helix: 1.10 (0.14), residues: 1543 sheet: -0.49 (1.49), residues: 13 loop : -2.21 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP F 201 HIS 0.005 0.001 HIS Y 145 PHE 0.011 0.001 PHE Z 66 TYR 0.017 0.001 TYR B 44 ARG 0.011 0.001 ARG Y 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 133 time to evaluate : 1.251 Fit side-chains REVERT: Z 49 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.5923 (p90) REVERT: E 120 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5463 (mtt) REVERT: E 142 GLU cc_start: 0.4313 (OUTLIER) cc_final: 0.3358 (mp0) REVERT: E 175 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6670 (mt) REVERT: E 205 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7120 (ptp) REVERT: F 24 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.6792 (mp10) REVERT: F 49 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.5947 (p90) outliers start: 54 outliers final: 38 residues processed: 175 average time/residue: 1.1057 time to fit residues: 219.5958 Evaluate side-chains 175 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 130 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 255 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.165951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138193 restraints weight = 29631.557| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.81 r_work: 0.3597 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16567 Z= 0.217 Angle : 0.626 12.829 22565 Z= 0.312 Chirality : 0.042 0.344 2707 Planarity : 0.005 0.067 2790 Dihedral : 4.991 53.537 2348 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 6.38 % Allowed : 26.06 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 2133 helix: 1.10 (0.14), residues: 1543 sheet: -0.81 (1.35), residues: 18 loop : -2.23 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP F 201 HIS 0.005 0.001 HIS Y 145 PHE 0.011 0.001 PHE Z 66 TYR 0.015 0.001 TYR B 44 ARG 0.011 0.001 ARG Y 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5202.29 seconds wall clock time: 94 minutes 48.85 seconds (5688.85 seconds total)