Starting phenix.real_space_refine (version: dev) on Mon Feb 20 19:50:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/02_2023/8hc5_34652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/02_2023/8hc5_34652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/02_2023/8hc5_34652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/02_2023/8hc5_34652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/02_2023/8hc5_34652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc5_34652/02_2023/8hc5_34652.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1488 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11400 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4948 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain breaks: 2 Chain: "H" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "D" Number of atoms: 1665 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "E" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.56, per 1000 atoms: 0.66 Number of scatterers: 11400 At special positions: 0 Unit cell: (99.552, 171.288, 161.04, 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 45 16.00 O 2231 8.00 N 1906 7.00 C 7218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 219 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 198 " 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 NAG-ASN " NAG C 701 " - " ASN C 343 " Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 34 sheets defined 4.8% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.986A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.928A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.596A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.049A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 188 through 192 removed outlier: 3.524A pdb=" N SER H 191 " --> pdb=" O PRO H 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 192 " --> pdb=" O SER H 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 188 through 192' Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.612A pdb=" N LYS L 127 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.566A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.962A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.872A pdb=" N GLN E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN E 133 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.142A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 67 removed outlier: 3.509A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.504A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.504A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 312 through 313 removed outlier: 3.710A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.708A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.737A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.087A pdb=" N ARG C 466 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY D 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 468 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 102 " --> pdb=" O ILE C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.750A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 664 through 667 removed outlier: 3.670A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.189A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.129A pdb=" N ARG H 97 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 123 through 127 removed outlier: 4.202A pdb=" N GLY H 142 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 183 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP H 147 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 179 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 184 " --> pdb=" O HIS H 167 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 123 through 127 removed outlier: 4.202A pdb=" N GLY H 142 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 183 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP H 147 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 179 " --> pdb=" O ASP H 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.559A pdb=" N THR H 154 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN H 202 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS H 199 " --> pdb=" O LYS H 212 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL H 201 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL H 210 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.650A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.822A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLN L 90 " --> pdb=" O THR L 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 112 through 119 removed outlier: 7.156A pdb=" N ALA L 113 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE L 140 " --> pdb=" O ALA L 113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL L 133 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU L 180 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.792A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL L 197 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL L 206 " --> pdb=" O VAL L 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.034A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.670A pdb=" N ASN D 100 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE D 111 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 68 through 69 Processing sheet with id=AD1, first strand: chain 'D' and resid 131 through 135 removed outlier: 3.675A pdb=" N LYS D 154 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE D 133 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 152 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 150 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 149 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 163 through 165 removed outlier: 3.690A pdb=" N SER D 164 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 208 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR D 205 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS D 220 " --> pdb=" O CYS D 207 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D 209 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 218 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 216 " --> pdb=" O HIS D 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.941A pdb=" N THR E 109 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 88 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.941A pdb=" N THR E 109 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 88 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 17 through 22 removed outlier: 4.166A pdb=" N VAL E 18 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE E 77 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 20 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.586A pdb=" N SER E 181 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 141 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E 179 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP E 143 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR E 177 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 150 through 154 removed outlier: 4.277A pdb=" N THR E 150 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 201 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS E 154 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 197 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 196 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS E 198 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS E 209 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 200 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 207 " --> pdb=" O VAL E 200 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 768 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: 3.88 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3657 1.35 - 1.46: 2889 1.46 - 1.58: 5078 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 11678 Sorted by residual: bond pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CA PHE D 157 " pdb=" C PHE D 157 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.68e+00 bond pdb=" CA LYS H 213 " pdb=" C LYS H 213 " ideal model delta sigma weight residual 1.526 1.509 0.017 1.42e-02 4.96e+03 1.38e+00 bond pdb=" C GLU D 159 " pdb=" O GLU D 159 " ideal model delta sigma weight residual 1.241 1.230 0.011 9.80e-03 1.04e+04 1.28e+00 bond pdb=" C LYS H 204 " pdb=" N PRO H 205 " ideal model delta sigma weight residual 1.335 1.350 -0.014 1.36e-02 5.41e+03 1.11e+00 ... (remaining 11673 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 417 107.34 - 114.00: 6451 114.00 - 120.66: 4271 120.66 - 127.32: 4644 127.32 - 133.98: 122 Bond angle restraints: 15905 Sorted by residual: angle pdb=" CA GLU D 89 " pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU D 159 " pdb=" C GLU D 159 " pdb=" N PRO D 160 " ideal model delta sigma weight residual 120.79 117.78 3.01 9.70e-01 1.06e+00 9.65e+00 angle pdb=" CA LEU H 181 " pdb=" CB LEU H 181 " pdb=" CG LEU H 181 " ideal model delta sigma weight residual 116.30 126.58 -10.28 3.50e+00 8.16e-02 8.63e+00 angle pdb=" N LYS H 204 " pdb=" CA LYS H 204 " pdb=" C LYS H 204 " ideal model delta sigma weight residual 109.81 116.20 -6.39 2.21e+00 2.05e-01 8.35e+00 angle pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " pdb=" CD GLU D 89 " ideal model delta sigma weight residual 112.60 117.50 -4.90 1.70e+00 3.46e-01 8.31e+00 ... (remaining 15900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6082 17.58 - 35.17: 652 35.17 - 52.75: 177 52.75 - 70.33: 21 70.33 - 87.91: 14 Dihedral angle restraints: 6946 sinusoidal: 2637 harmonic: 4309 Sorted by residual: dihedral pdb=" CB CYS H 143 " pdb=" SG CYS H 143 " pdb=" SG CYS H 199 " pdb=" CB CYS H 199 " ideal model delta sinusoidal sigma weight residual 93.00 165.28 -72.28 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.44 -52.44 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 63.78 29.22 1 1.00e+01 1.00e-02 1.22e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1362 0.043 - 0.086: 277 0.086 - 0.130: 146 0.130 - 0.173: 4 0.173 - 0.216: 1 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL L 147 " pdb=" CA VAL L 147 " pdb=" CG1 VAL L 147 " pdb=" CG2 VAL L 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA VAL D 161 " pdb=" N VAL D 161 " pdb=" C VAL D 161 " pdb=" CB VAL D 161 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 1787 not shown) Planarity restraints: 2049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 112 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLY E 112 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY E 112 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN E 113 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 204 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO H 205 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO H 205 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 205 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 133 " -0.010 2.00e-02 2.50e+03 1.46e-02 3.71e+00 pdb=" CG PHE D 133 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 133 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 133 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE D 133 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 133 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 133 " 0.000 2.00e-02 2.50e+03 ... (remaining 2046 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2089 2.78 - 3.31: 9272 3.31 - 3.84: 18298 3.84 - 4.37: 19741 4.37 - 4.90: 35658 Nonbonded interactions: 85058 Sorted by model distance: nonbonded pdb=" OD1 ASN L 92 " pdb=" N SER L 93 " model vdw 2.249 2.520 nonbonded pdb=" O LEU C 455 " pdb=" OH TYR H 33 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.300 2.440 nonbonded pdb=" O CYS D 151 " pdb=" OG SER D 191 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR E 33 " pdb=" OG SER E 95 " model vdw 2.337 2.440 ... (remaining 85053 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7218 2.51 5 N 1906 2.21 5 O 2231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 2.700 Check model and map are aligned: 0.170 Process input model: 32.700 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 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 : 0.002 0.042 11678 Z= 0.138 Angle : 0.525 10.282 15905 Z= 0.275 Chirality : 0.043 0.216 1790 Planarity : 0.004 0.068 2048 Dihedral : 15.565 87.915 4141 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.79 (0.21), residues: 1479 helix: -3.27 (0.45), residues: 57 sheet: 0.50 (0.25), residues: 460 loop : -0.89 (0.19), residues: 962 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.438 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1919 time to fit residues: 23.2528 Evaluate side-chains 65 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 40.0000 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 40.0000 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 133 optimal weight: 5.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN H 72 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN E 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11678 Z= 0.254 Angle : 0.547 7.950 15905 Z= 0.285 Chirality : 0.044 0.215 1790 Planarity : 0.004 0.056 2048 Dihedral : 3.338 21.537 1613 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1479 helix: -2.51 (0.60), residues: 54 sheet: 0.45 (0.24), residues: 502 loop : -0.69 (0.20), residues: 923 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 1.214 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 93 average time/residue: 0.2192 time to fit residues: 31.4267 Evaluate side-chains 80 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1070 time to fit residues: 4.5103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 90 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 144 optimal weight: 50.0000 chunk 119 optimal weight: 0.0000 chunk 132 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN H 39 GLN L 38 GLN E 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11678 Z= 0.151 Angle : 0.473 6.748 15905 Z= 0.241 Chirality : 0.043 0.153 1790 Planarity : 0.004 0.048 2048 Dihedral : 3.185 20.720 1613 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.22), residues: 1479 helix: -1.88 (0.71), residues: 48 sheet: 0.28 (0.23), residues: 546 loop : -0.52 (0.21), residues: 885 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 1.219 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 84 average time/residue: 0.2203 time to fit residues: 29.1707 Evaluate side-chains 69 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1147 time to fit residues: 3.0537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 40.0000 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN H 203 HIS E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 11678 Z= 0.447 Angle : 0.655 8.473 15905 Z= 0.340 Chirality : 0.047 0.162 1790 Planarity : 0.005 0.048 2048 Dihedral : 4.214 27.030 1613 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1479 helix: -2.08 (0.68), residues: 48 sheet: 0.20 (0.23), residues: 523 loop : -0.77 (0.20), residues: 908 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 72 time to evaluate : 1.212 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 102 average time/residue: 0.2201 time to fit residues: 34.5731 Evaluate side-chains 78 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1070 time to fit residues: 5.7582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 20.0000 chunk 80 optimal weight: 0.0980 chunk 2 optimal weight: 0.0010 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 30.0000 chunk 121 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN L 27 GLN L 79 GLN L 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11678 Z= 0.177 Angle : 0.497 6.813 15905 Z= 0.255 Chirality : 0.043 0.172 1790 Planarity : 0.004 0.054 2048 Dihedral : 3.723 23.939 1613 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.58 (0.22), residues: 1479 helix: -1.74 (0.72), residues: 48 sheet: 0.21 (0.23), residues: 559 loop : -0.68 (0.21), residues: 872 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.262 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 80 average time/residue: 0.2259 time to fit residues: 27.5327 Evaluate side-chains 66 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1101 time to fit residues: 3.1036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 0.1980 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 0.0170 overall best weight: 1.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN L 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11678 Z= 0.232 Angle : 0.526 6.988 15905 Z= 0.271 Chirality : 0.044 0.151 1790 Planarity : 0.004 0.045 2048 Dihedral : 3.798 23.444 1613 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.51 (0.22), residues: 1479 helix: -1.66 (0.74), residues: 48 sheet: 0.25 (0.23), residues: 540 loop : -0.61 (0.21), residues: 891 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 1.184 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 83 average time/residue: 0.2117 time to fit residues: 27.4516 Evaluate side-chains 70 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1070 time to fit residues: 3.5584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 40.0000 chunk 81 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 141 optimal weight: 30.0000 chunk 88 optimal weight: 0.0670 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11678 Z= 0.209 Angle : 0.513 7.739 15905 Z= 0.263 Chirality : 0.044 0.152 1790 Planarity : 0.004 0.045 2048 Dihedral : 3.774 23.228 1613 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.51 (0.22), residues: 1479 helix: -1.49 (0.76), residues: 48 sheet: 0.27 (0.23), residues: 546 loop : -0.64 (0.21), residues: 885 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 1.142 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.2409 time to fit residues: 26.2258 Evaluate side-chains 64 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1181 time to fit residues: 2.5980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 30.0000 chunk 84 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11678 Z= 0.184 Angle : 0.504 7.478 15905 Z= 0.258 Chirality : 0.043 0.176 1790 Planarity : 0.004 0.051 2048 Dihedral : 3.703 22.601 1613 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.47 (0.22), residues: 1479 helix: -1.39 (0.77), residues: 48 sheet: 0.24 (0.23), residues: 549 loop : -0.57 (0.21), residues: 882 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.292 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 72 average time/residue: 0.2189 time to fit residues: 24.6346 Evaluate side-chains 65 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1089 time to fit residues: 2.0584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 131 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 11678 Z= 0.326 Angle : 0.591 8.770 15905 Z= 0.305 Chirality : 0.046 0.183 1790 Planarity : 0.004 0.048 2048 Dihedral : 4.119 24.669 1613 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.64 (0.22), residues: 1479 helix: -1.53 (0.75), residues: 48 sheet: 0.22 (0.23), residues: 552 loop : -0.77 (0.20), residues: 879 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 1.242 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.2271 time to fit residues: 23.8559 Evaluate side-chains 63 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1078 time to fit residues: 2.0602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 50.0000 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 40.0000 chunk 134 optimal weight: 0.7980 chunk 116 optimal weight: 0.0370 chunk 12 optimal weight: 40.0000 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 11678 Z= 0.161 Angle : 0.496 7.590 15905 Z= 0.254 Chirality : 0.043 0.160 1790 Planarity : 0.004 0.048 2048 Dihedral : 3.730 22.062 1613 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.53 (0.22), residues: 1479 helix: -1.35 (0.77), residues: 48 sheet: 0.28 (0.23), residues: 547 loop : -0.68 (0.21), residues: 884 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.304 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.2329 time to fit residues: 23.4679 Evaluate side-chains 64 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.450 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 40.0000 chunk 21 optimal weight: 0.0060 chunk 102 optimal weight: 0.6980 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 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 = 0.4727 r_free = 0.4727 target = 0.246902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.206855 restraints weight = 16366.824| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 4.73 r_work: 0.4083 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4727 r_free = 0.4727 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4727 r_free = 0.4727 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11678 Z= 0.220 Angle : 0.525 7.574 15905 Z= 0.269 Chirality : 0.044 0.164 1790 Planarity : 0.004 0.044 2048 Dihedral : 3.826 22.795 1613 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.49 (0.22), residues: 1479 helix: -1.30 (0.84), residues: 42 sheet: 0.27 (0.23), residues: 549 loop : -0.65 (0.21), residues: 888 =============================================================================== Job complete usr+sys time: 2132.16 seconds wall clock time: 39 minutes 44.23 seconds (2384.23 seconds total)