Starting phenix.real_space_refine on Thu Mar 14 15:24:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/03_2024/7nzm_12665_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/03_2024/7nzm_12665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/03_2024/7nzm_12665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/03_2024/7nzm_12665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/03_2024/7nzm_12665_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nzm_12665/03_2024/7nzm_12665_updated.pdb" } resolution = 3.96 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= 0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 4 5.49 5 S 53 5.16 5 C 5776 2.51 5 N 1538 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 14": "OE1" <-> "OE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 93": "OD1" <-> "OD2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 595": "NH1" <-> "NH2" Residue "C ARG 612": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9109 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1392 Classifications: {'peptide': 178} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 173} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2312 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 279} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2884 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2024 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 437 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.12, per 1000 atoms: 0.56 Number of scatterers: 9109 At special positions: 0 Unit cell: (95.192, 110.84, 112.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 53 16.00 P 4 15.00 O 1737 8.00 N 1538 7.00 C 5776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN D 18 " Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 12 sheets defined 39.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.510A pdb=" N GLY E 65 " --> pdb=" O ILE E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 91 through 118 removed outlier: 3.824A pdb=" N LYS E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 117 " --> pdb=" O HIS E 113 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 134 through 141 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.178A pdb=" N VAL E 156 " --> pdb=" O PHE E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 169 through 180 removed outlier: 3.529A pdb=" N VAL E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.094A pdb=" N LEU B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.788A pdb=" N GLU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.545A pdb=" N THR B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 200 through 206 removed outlier: 3.595A pdb=" N LEU B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 238 removed outlier: 3.525A pdb=" N LYS B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.645A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.568A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 203 through 206 No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.661A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.645A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.928A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.533A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.880A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.518A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 19 through 31 removed outlier: 3.645A pdb=" N ARG D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 137 through 158 removed outlier: 3.636A pdb=" N ALA D 140 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL D 141 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 144 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D 151 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP D 158 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.881A pdb=" N SER D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 188 No H-bonds generated for 'chain 'D' and resid 185 through 188' Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 235 through 238 No H-bonds generated for 'chain 'D' and resid 235 through 238' Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'C' and resid 583 through 606 removed outlier: 3.564A pdb=" N ARG C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 588 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 602 " --> pdb=" O GLN C 598 " (cutoff:3.500A) Proline residue: C 605 - end of helix Processing helix chain 'C' and resid 609 through 617 removed outlier: 3.743A pdb=" N ARG C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TRP C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 617 " --> pdb=" O ALA C 613 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 18 through 20 removed outlier: 6.783A pdb=" N ASP E 83 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL E 75 " --> pdb=" O TYR E 81 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR E 81 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.922A pdb=" N ALA E 31 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 30 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER E 25 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER E 34 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL E 23 " --> pdb=" O SER E 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.777A pdb=" N TYR B 87 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS B 60 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 59 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 285 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 162 through 165 Processing sheet with id= E, first strand: chain 'B' and resid 216 through 218 Processing sheet with id= F, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.508A pdb=" N VAL B 264 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 265 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU B 256 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.921A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.745A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.236A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 162 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.501A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 240 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 248 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 4 through 7 Processing sheet with id= L, first strand: chain 'D' and resid 213 through 217 removed outlier: 3.801A pdb=" N ARG D 213 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET D 164 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA D 129 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET D 166 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL D 131 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP D 168 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU D 133 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE D 128 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 118 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 114 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 115 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 95 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP D 93 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 119 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL D 91 " --> pdb=" O SER D 119 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 702 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: 2.34 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2587 1.33 - 1.45: 1632 1.45 - 1.57: 4997 1.57 - 1.70: 9 1.70 - 1.82: 80 Bond restraints: 9305 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C5 ATP A 401 " pdb=" C6 ATP A 401 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.61e+01 bond pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.53e+01 bond pdb=" C5 ATP A 401 " pdb=" N7 ATP A 401 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" C8 ATP A 401 " pdb=" N7 ATP A 401 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.80e+01 ... (remaining 9300 not shown) Histogram of bond angle deviations from ideal: 97.67 - 105.24: 184 105.24 - 112.81: 4781 112.81 - 120.38: 3928 120.38 - 127.95: 3672 127.95 - 135.53: 70 Bond angle restraints: 12635 Sorted by residual: angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 115.35 21.48 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 118.69 21.18 1.00e+00 1.00e+00 4.49e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" N3 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 127.04 134.93 -7.89 1.15e+00 7.59e-01 4.72e+01 angle pdb=" C ARG B 96 " pdb=" N GLY B 97 " pdb=" CA GLY B 97 " ideal model delta sigma weight residual 121.67 114.60 7.07 1.43e+00 4.89e-01 2.45e+01 ... (remaining 12630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5118 18.00 - 36.00: 402 36.00 - 54.00: 79 54.00 - 72.00: 19 72.00 - 90.00: 11 Dihedral angle restraints: 5629 sinusoidal: 2247 harmonic: 3382 Sorted by residual: dihedral pdb=" CA LEU D 133 " pdb=" C LEU D 133 " pdb=" N HIS D 134 " pdb=" CA HIS D 134 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CB CYS E 69 " pdb=" SG CYS E 69 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual 93.00 55.62 37.38 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA VAL A 43 " pdb=" C VAL A 43 " pdb=" N MET A 44 " pdb=" CA MET A 44 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1078 0.065 - 0.129: 295 0.129 - 0.194: 36 0.194 - 0.259: 4 0.259 - 0.323: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA ARG B 96 " pdb=" N ARG B 96 " pdb=" C ARG B 96 " pdb=" CB ARG B 96 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA CYS A 257 " pdb=" N CYS A 257 " pdb=" C CYS A 257 " pdb=" CB CYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU E 16 " pdb=" N GLU E 16 " pdb=" C GLU E 16 " pdb=" CB GLU E 16 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1412 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 90 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO E 91 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO E 91 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 91 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 111 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO A 112 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 76 " 0.024 2.00e-02 2.50e+03 1.86e-02 6.91e+00 pdb=" CG TYR D 76 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 76 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 76 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 76 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 76 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 76 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 22 2.40 - 3.02: 5395 3.02 - 3.65: 12971 3.65 - 4.27: 19483 4.27 - 4.90: 32258 Nonbonded interactions: 70129 Sorted by model distance: nonbonded pdb=" OD2 ASP B 92 " pdb="MN MN B 401 " model vdw 1.774 2.320 nonbonded pdb=" ND1 HIS B 248 " pdb="MN MN B 401 " model vdw 1.926 2.400 nonbonded pdb=" NE2 HIS B 173 " pdb="MN MN B 401 " model vdw 1.993 2.400 nonbonded pdb=" CE1 HIS B 248 " pdb="MN MN B 401 " model vdw 1.999 2.540 nonbonded pdb=" O LEU B 38 " pdb=" OG SER B 42 " model vdw 2.110 2.440 ... (remaining 70124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.880 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 26.860 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 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 : 0.007 0.071 9305 Z= 0.435 Angle : 1.122 21.476 12635 Z= 0.685 Chirality : 0.058 0.323 1415 Planarity : 0.006 0.114 1627 Dihedral : 14.316 89.997 3445 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.22), residues: 1144 helix: -1.35 (0.21), residues: 406 sheet: -0.40 (0.37), residues: 166 loop : -0.87 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 616 HIS 0.008 0.002 HIS B 248 PHE 0.023 0.003 PHE D 109 TYR 0.045 0.004 TYR D 76 ARG 0.015 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 603 LEU cc_start: 0.6489 (tp) cc_final: 0.6282 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2596 time to fit residues: 39.7074 Evaluate side-chains 67 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN E 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9305 Z= 0.184 Angle : 0.668 10.653 12635 Z= 0.346 Chirality : 0.045 0.209 1415 Planarity : 0.004 0.075 1627 Dihedral : 7.158 87.841 1345 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.56 % Allowed : 6.86 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.26 (0.24), residues: 1144 helix: 0.01 (0.24), residues: 430 sheet: -0.29 (0.37), residues: 157 loop : -0.12 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.006 0.001 HIS B 173 PHE 0.017 0.001 PHE B 225 TYR 0.016 0.001 TYR B 137 ARG 0.006 0.001 ARG C 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.6255 (p0) cc_final: 0.6036 (p0) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 0.2328 time to fit residues: 26.3941 Evaluate side-chains 64 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain C residue 561 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 0.0170 chunk 28 optimal weight: 20.0000 chunk 102 optimal weight: 0.0050 chunk 111 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.0870 chunk 35 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 overall best weight: 0.9812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9305 Z= 0.151 Angle : 0.601 9.990 12635 Z= 0.305 Chirality : 0.043 0.149 1415 Planarity : 0.004 0.065 1627 Dihedral : 6.550 89.383 1345 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.77 % Allowed : 8.42 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.16 (0.24), residues: 1144 helix: 0.10 (0.24), residues: 444 sheet: 0.22 (0.40), residues: 146 loop : -0.22 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 356 HIS 0.005 0.001 HIS B 173 PHE 0.013 0.001 PHE B 225 TYR 0.011 0.001 TYR E 81 ARG 0.003 0.000 ARG C 612 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.6028 (mpp) cc_final: 0.5676 (ptp) outliers start: 17 outliers final: 8 residues processed: 74 average time/residue: 0.2213 time to fit residues: 23.1937 Evaluate side-chains 62 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain C residue 561 LYS Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 49 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 0.0020 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN C 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9305 Z= 0.162 Angle : 0.570 8.545 12635 Z= 0.287 Chirality : 0.042 0.148 1415 Planarity : 0.004 0.062 1627 Dihedral : 6.239 87.281 1345 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.14 % Allowed : 10.08 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.01 (0.24), residues: 1144 helix: 0.26 (0.25), residues: 444 sheet: 0.10 (0.40), residues: 152 loop : -0.08 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 340 HIS 0.005 0.001 HIS A 161 PHE 0.013 0.001 PHE B 225 TYR 0.016 0.001 TYR E 81 ARG 0.008 0.000 ARG E 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.2200 time to fit residues: 21.5616 Evaluate side-chains 60 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain C residue 561 LYS Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 598 GLN Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN A 296 ASN C 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9305 Z= 0.239 Angle : 0.604 7.978 12635 Z= 0.311 Chirality : 0.041 0.149 1415 Planarity : 0.005 0.095 1627 Dihedral : 6.358 83.362 1345 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.94 % Allowed : 12.16 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.16 (0.24), residues: 1144 helix: 0.31 (0.24), residues: 445 sheet: 0.00 (0.41), residues: 157 loop : 0.14 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 206 HIS 0.005 0.001 HIS B 248 PHE 0.015 0.002 PHE B 225 TYR 0.013 0.002 TYR D 32 ARG 0.011 0.001 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7034 (tpp) cc_final: 0.5870 (tpp) outliers start: 9 outliers final: 3 residues processed: 57 average time/residue: 0.2294 time to fit residues: 18.9744 Evaluate side-chains 53 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9305 Z= 0.299 Angle : 0.678 8.802 12635 Z= 0.354 Chirality : 0.043 0.178 1415 Planarity : 0.005 0.059 1627 Dihedral : 6.768 89.436 1345 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.87 % Allowed : 12.06 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.13 (0.25), residues: 1144 helix: 0.28 (0.24), residues: 430 sheet: -0.45 (0.39), residues: 173 loop : 0.32 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 79 HIS 0.007 0.002 HIS A 161 PHE 0.017 0.002 PHE B 225 TYR 0.021 0.002 TYR D 32 ARG 0.005 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 0.856 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 63 average time/residue: 0.1793 time to fit residues: 16.9842 Evaluate side-chains 50 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain C residue 598 GLN Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN A 111 ASN A 225 ASN D 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9305 Z= 0.243 Angle : 0.624 9.802 12635 Z= 0.319 Chirality : 0.042 0.158 1415 Planarity : 0.004 0.059 1627 Dihedral : 6.634 86.418 1345 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.14 % Allowed : 13.72 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.24 (0.25), residues: 1144 helix: 0.37 (0.25), residues: 435 sheet: -0.36 (0.40), residues: 167 loop : 0.36 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 582 HIS 0.007 0.001 HIS B 173 PHE 0.015 0.002 PHE B 225 TYR 0.017 0.001 TYR D 175 ARG 0.007 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.6790 (ppp) cc_final: 0.5881 (ppp) outliers start: 11 outliers final: 4 residues processed: 58 average time/residue: 0.1903 time to fit residues: 16.7638 Evaluate side-chains 50 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9305 Z= 0.263 Angle : 0.679 14.940 12635 Z= 0.343 Chirality : 0.042 0.165 1415 Planarity : 0.004 0.063 1627 Dihedral : 6.640 84.461 1345 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.14 % Allowed : 14.55 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.19 (0.25), residues: 1144 helix: 0.21 (0.25), residues: 431 sheet: -0.26 (0.41), residues: 160 loop : 0.40 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.007 0.002 HIS B 173 PHE 0.025 0.002 PHE E 130 TYR 0.019 0.002 TYR D 32 ARG 0.005 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: D 16 MET cc_start: 0.6726 (ppp) cc_final: 0.5887 (ppp) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1715 time to fit residues: 14.6434 Evaluate side-chains 54 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0970 chunk 104 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 0.0050 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9305 Z= 0.144 Angle : 0.623 9.699 12635 Z= 0.302 Chirality : 0.043 0.175 1415 Planarity : 0.003 0.057 1627 Dihedral : 6.302 81.079 1345 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.52 % Allowed : 15.38 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.52 (0.26), residues: 1144 helix: 0.69 (0.26), residues: 436 sheet: -0.06 (0.41), residues: 167 loop : 0.39 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 582 HIS 0.006 0.001 HIS B 173 PHE 0.034 0.001 PHE E 130 TYR 0.011 0.001 TYR E 141 ARG 0.003 0.000 ARG E 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: D 16 MET cc_start: 0.6541 (ppp) cc_final: 0.5739 (ppp) REVERT: D 245 MET cc_start: 0.8329 (pmm) cc_final: 0.7892 (pmm) outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 0.1764 time to fit residues: 15.2661 Evaluate side-chains 43 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9305 Z= 0.262 Angle : 0.693 9.785 12635 Z= 0.342 Chirality : 0.042 0.176 1415 Planarity : 0.004 0.058 1627 Dihedral : 6.406 81.781 1345 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.62 % Allowed : 15.70 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1144 helix: 0.59 (0.25), residues: 435 sheet: -0.38 (0.40), residues: 167 loop : 0.34 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 181 HIS 0.006 0.001 HIS B 173 PHE 0.030 0.002 PHE E 130 TYR 0.018 0.002 TYR E 81 ARG 0.011 0.001 ARG C 591 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 1.076 Fit side-chains REVERT: D 16 MET cc_start: 0.6729 (ppp) cc_final: 0.5934 (ppp) REVERT: D 245 MET cc_start: 0.8399 (pmm) cc_final: 0.7926 (pmm) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.1747 time to fit residues: 13.2947 Evaluate side-chains 49 residues out of total 1003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain C residue 598 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 5 optimal weight: 0.0060 chunk 64 optimal weight: 5.9990 overall best weight: 2.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.022826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.016353 restraints weight = 120394.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.017044 restraints weight = 71242.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.017566 restraints weight = 49597.282| |-----------------------------------------------------------------------------| r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 9305 Z= 0.330 Angle : 0.972 59.200 12635 Z= 0.543 Chirality : 0.041 0.172 1415 Planarity : 0.004 0.057 1627 Dihedral : 6.435 81.777 1345 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.62 % Allowed : 15.28 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: 0.39 (0.25), residues: 1144 helix: 0.63 (0.25), residues: 429 sheet: -0.38 (0.40), residues: 167 loop : 0.36 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 582 HIS 0.006 0.001 HIS B 173 PHE 0.029 0.002 PHE E 130 TYR 0.019 0.002 TYR E 81 ARG 0.009 0.001 ARG C 591 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.12 seconds wall clock time: 31 minutes 18.24 seconds (1878.24 seconds total)