Starting phenix.real_space_refine on Sun Jul 21 04:41:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0d_36761/07_2024/8k0d_36761.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0d_36761/07_2024/8k0d_36761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0d_36761/07_2024/8k0d_36761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0d_36761/07_2024/8k0d_36761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0d_36761/07_2024/8k0d_36761.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0d_36761/07_2024/8k0d_36761.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 8414 2.51 5 N 2222 2.21 5 O 2582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 31": "OD1" <-> "OD2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 100": "OD1" <-> "OD2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 542": "OD1" <-> "OD2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 527": "OD1" <-> "OD2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13282 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3179 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 377} Chain: "C" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3179 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 377} Time building chain proxies: 5.42, per 1000 atoms: 0.41 Number of scatterers: 13282 At special positions: 0 Unit cell: (125.46, 99.22, 214.84, 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 64 16.00 O 2582 8.00 N 2222 7.00 C 8414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " 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 Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 37 sheets defined 6.2% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.662A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'F' and resid 120 through 127 removed outlier: 3.547A pdb=" N GLY F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.644A pdb=" N LEU A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.709A pdb=" N GLN A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.577A pdb=" N THR C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.146A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'B' and resid 204 through 207 removed outlier: 3.561A pdb=" N LEU B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 204 through 207' Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.553A pdb=" N GLN B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.569A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.647A pdb=" N ARG E 34 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG E 39 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.968A pdb=" N VAL E 118 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR E 101 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE E 116 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR E 103 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN E 114 " --> pdb=" O TYR E 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.585A pdb=" N VAL E 200 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AA6, first strand: chain 'E' and resid 185 through 186 removed outlier: 3.535A pdb=" N VAL E 185 " --> pdb=" O SER E 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.811A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.082A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.517A pdb=" N ASN F 136 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 132 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 152 through 153 removed outlier: 3.705A pdb=" N LYS F 144 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 196 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN F 146 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F 206 " --> pdb=" O CYS F 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 202 removed outlier: 5.435A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AB4, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.045A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 256 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU A 265 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 279 through 287 removed outlier: 5.460A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER A 313 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET A 316 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 318 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 333 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.308A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.308A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.581A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.423A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.630A pdb=" N VAL C 123 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG C 34 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TRP C 35 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR C 51 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP C 37 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.630A pdb=" N VAL C 123 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS C 97 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP C 119 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG C 99 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.504A pdb=" N GLY C 155 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.504A pdb=" N GLY C 155 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 197 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS C 180 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.615A pdb=" N LYS C 225 " --> pdb=" O CYS C 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.058A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.536A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 113 through 117 removed outlier: 3.664A pdb=" N SER D 176 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR D 172 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 153 through 154 removed outlier: 4.418A pdb=" N TRP D 147 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 208 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS D 206 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 201 through 202 removed outlier: 5.382A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AD5, first strand: chain 'B' and resid 217 through 218 removed outlier: 6.488A pdb=" N TYR B 231 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 250 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS B 233 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG B 248 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 235 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 244 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 265 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 279 through 287 removed outlier: 5.589A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 313 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.357A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.357A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.522A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 511 through 515 removed outlier: 6.397A pdb=" N ILE B 520 " --> pdb=" O ILE B 514 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1254 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: 5.10 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4237 1.34 - 1.46: 3144 1.46 - 1.58: 6161 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 13624 Sorted by residual: bond pdb=" C LYS A 443 " pdb=" N ILE A 444 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.48e-02 4.57e+03 2.14e+00 bond pdb=" C LYS B 443 " pdb=" N ILE B 444 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.48e-02 4.57e+03 2.08e+00 bond pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.37e+00 bond pdb=" CA SER C 106 " pdb=" C SER C 106 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.19e+00 bond pdb=" CA SER E 106 " pdb=" C SER E 106 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.17e+00 ... (remaining 13619 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.59: 380 105.59 - 112.69: 7234 112.69 - 119.79: 4207 119.79 - 126.90: 6531 126.90 - 134.00: 208 Bond angle restraints: 18560 Sorted by residual: angle pdb=" N ARG A 402 " pdb=" CA ARG A 402 " pdb=" C ARG A 402 " ideal model delta sigma weight residual 110.40 99.73 10.67 1.43e+00 4.89e-01 5.57e+01 angle pdb=" N VAL A 484 " pdb=" CA VAL A 484 " pdb=" C VAL A 484 " ideal model delta sigma weight residual 113.71 110.17 3.54 9.50e-01 1.11e+00 1.38e+01 angle pdb=" C TYR F 185 " pdb=" N GLU F 186 " pdb=" CA GLU F 186 " ideal model delta sigma weight residual 122.38 116.69 5.69 1.81e+00 3.05e-01 9.87e+00 angle pdb=" N ILE A 401 " pdb=" CA ILE A 401 " pdb=" C ILE A 401 " ideal model delta sigma weight residual 110.42 113.24 -2.82 9.60e-01 1.09e+00 8.66e+00 angle pdb=" C PHE A 290 " pdb=" N TYR A 291 " pdb=" CA TYR A 291 " ideal model delta sigma weight residual 122.86 118.76 4.10 1.42e+00 4.96e-01 8.35e+00 ... (remaining 18555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7716 17.93 - 35.86: 364 35.86 - 53.79: 61 53.79 - 71.71: 12 71.71 - 89.64: 9 Dihedral angle restraints: 8162 sinusoidal: 3184 harmonic: 4978 Sorted by residual: dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual -86.00 -175.64 89.64 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS A 216 " pdb=" SG CYS A 216 " pdb=" SG CYS A 240 " pdb=" CB CYS A 240 " ideal model delta sinusoidal sigma weight residual 93.00 178.38 -85.38 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS B 216 " pdb=" SG CYS B 216 " pdb=" SG CYS B 240 " pdb=" CB CYS B 240 " ideal model delta sinusoidal sigma weight residual 93.00 174.35 -81.35 1 1.00e+01 1.00e-02 8.16e+01 ... (remaining 8159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1543 0.046 - 0.093: 370 0.093 - 0.139: 149 0.139 - 0.186: 0 0.186 - 0.232: 2 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CB ILE B 408 " pdb=" CA ILE B 408 " pdb=" CG1 ILE B 408 " pdb=" CG2 ILE B 408 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 408 " pdb=" CA ILE A 408 " pdb=" CG1 ILE A 408 " pdb=" CG2 ILE A 408 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE B 250 " pdb=" N ILE B 250 " pdb=" C ILE B 250 " pdb=" CB ILE B 250 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2061 not shown) Planarity restraints: 2380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 291 " -0.018 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR B 291 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 291 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 291 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 291 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 291 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 291 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 291 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 164 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO E 165 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 165 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 165 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.018 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR A 351 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " 0.001 2.00e-02 2.50e+03 ... (remaining 2377 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 200 2.63 - 3.20: 11875 3.20 - 3.77: 21302 3.77 - 4.33: 30453 4.33 - 4.90: 50325 Nonbonded interactions: 114155 Sorted by model distance: nonbonded pdb=" OG SER B 528 " pdb=" O THR B 531 " model vdw 2.065 2.440 nonbonded pdb=" NH2 ARG F 61 " pdb=" OE2 GLU F 81 " model vdw 2.153 2.520 nonbonded pdb=" O LEU A 202 " pdb=" NH2 ARG B 258 " model vdw 2.177 2.520 nonbonded pdb=" OE1 GLU D 105 " pdb=" OH TYR D 172 " model vdw 2.203 2.440 nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 22 " model vdw 2.212 2.440 ... (remaining 114150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 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: 19.780 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: 6.070 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.180 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.004 0.034 13624 Z= 0.258 Angle : 0.628 10.669 18560 Z= 0.354 Chirality : 0.046 0.232 2064 Planarity : 0.004 0.054 2380 Dihedral : 10.650 84.238 4916 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.58 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -1.60 (0.20), residues: 1702 helix: -2.82 (0.62), residues: 44 sheet: -1.34 (0.19), residues: 696 loop : -0.63 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 170 HIS 0.004 0.001 HIS F 197 PHE 0.020 0.002 PHE F 83 TYR 0.039 0.002 TYR B 291 ARG 0.008 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: E 30 SER cc_start: 0.7993 (t) cc_final: 0.7790 (t) REVERT: E 213 ASN cc_start: 0.7647 (m110) cc_final: 0.7307 (m-40) REVERT: E 215 ASN cc_start: 0.8023 (t0) cc_final: 0.7640 (t0) REVERT: E 222 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7524 (mmmm) REVERT: F 116 ILE cc_start: 0.8400 (tt) cc_final: 0.7549 (mp) REVERT: F 159 GLN cc_start: 0.8471 (mp10) cc_final: 0.8097 (mp10) REVERT: F 169 ASP cc_start: 0.8672 (p0) cc_final: 0.7843 (p0) REVERT: A 463 MET cc_start: 0.8083 (mmt) cc_final: 0.7858 (mmm) REVERT: C 160 ASP cc_start: 0.8656 (m-30) cc_final: 0.8425 (p0) REVERT: D 82 ASP cc_start: 0.7926 (m-30) cc_final: 0.7624 (m-30) REVERT: D 160 GLU cc_start: 0.8047 (tp30) cc_final: 0.7808 (tp30) REVERT: B 399 MET cc_start: 0.8870 (tpp) cc_final: 0.8584 (tpp) REVERT: B 555 ASP cc_start: 0.8418 (p0) cc_final: 0.7838 (t0) outliers start: 0 outliers final: 1 residues processed: 165 average time/residue: 1.3939 time to fit residues: 249.7024 Evaluate side-chains 104 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13624 Z= 0.316 Angle : 0.619 7.754 18560 Z= 0.326 Chirality : 0.047 0.176 2064 Planarity : 0.005 0.054 2380 Dihedral : 6.144 148.389 1857 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.23 % Favored : 94.65 % Rotamer: Outliers : 1.06 % Allowed : 7.01 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -1.48 (0.20), residues: 1702 helix: -2.49 (0.59), residues: 44 sheet: -1.18 (0.18), residues: 740 loop : -0.58 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 170 HIS 0.010 0.001 HIS A 233 PHE 0.022 0.002 PHE F 83 TYR 0.028 0.002 TYR A 351 ARG 0.006 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.497 Fit side-chains REVERT: E 222 LYS cc_start: 0.8516 (mmtt) cc_final: 0.7750 (mmmm) REVERT: F 17 ASP cc_start: 0.8359 (m-30) cc_final: 0.8034 (m-30) REVERT: F 169 ASP cc_start: 0.8629 (p0) cc_final: 0.7871 (p0) REVERT: C 99 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7831 (ttp80) REVERT: D 82 ASP cc_start: 0.7987 (m-30) cc_final: 0.7701 (m-30) outliers start: 16 outliers final: 5 residues processed: 124 average time/residue: 1.2976 time to fit residues: 176.1069 Evaluate side-chains 96 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 349 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 128 optimal weight: 40.0000 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 137 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 0.0970 chunk 124 optimal weight: 9.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN A 564 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13624 Z= 0.224 Angle : 0.571 6.903 18560 Z= 0.299 Chirality : 0.046 0.153 2064 Planarity : 0.005 0.052 2380 Dihedral : 4.919 50.226 1854 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 1.46 % Allowed : 9.06 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -1.31 (0.20), residues: 1702 helix: -2.16 (0.62), residues: 44 sheet: -1.03 (0.18), residues: 762 loop : -0.49 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 170 HIS 0.005 0.001 HIS B 281 PHE 0.024 0.002 PHE D 117 TYR 0.021 0.001 TYR A 351 ARG 0.005 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8342 (m-30) cc_final: 0.7981 (m-30) REVERT: F 116 ILE cc_start: 0.8217 (tt) cc_final: 0.7304 (pp) REVERT: F 169 ASP cc_start: 0.8624 (p0) cc_final: 0.7939 (p0) REVERT: A 393 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7932 (pp20) REVERT: C 99 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7766 (ttp80) REVERT: D 82 ASP cc_start: 0.7942 (m-30) cc_final: 0.7707 (m-30) REVERT: D 139 TYR cc_start: 0.8128 (t80) cc_final: 0.7589 (t80) outliers start: 22 outliers final: 4 residues processed: 112 average time/residue: 1.2783 time to fit residues: 158.9689 Evaluate side-chains 93 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13624 Z= 0.348 Angle : 0.605 7.854 18560 Z= 0.314 Chirality : 0.047 0.168 2064 Planarity : 0.005 0.050 2380 Dihedral : 4.949 47.937 1854 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 1.65 % Allowed : 10.05 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -1.22 (0.20), residues: 1702 helix: -1.82 (0.69), residues: 44 sheet: -0.93 (0.18), residues: 752 loop : -0.50 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 170 HIS 0.003 0.001 HIS E 216 PHE 0.020 0.002 PHE D 138 TYR 0.022 0.002 TYR B 351 ARG 0.003 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8384 (m-30) cc_final: 0.7980 (m-30) REVERT: F 116 ILE cc_start: 0.8255 (tt) cc_final: 0.7388 (pp) REVERT: F 169 ASP cc_start: 0.8655 (p0) cc_final: 0.7994 (p0) REVERT: A 393 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7838 (pp20) REVERT: A 550 GLN cc_start: 0.7592 (tt0) cc_final: 0.7388 (tt0) REVERT: C 99 ARG cc_start: 0.8144 (mtp180) cc_final: 0.7838 (ttp80) REVERT: D 82 ASP cc_start: 0.7979 (m-30) cc_final: 0.7747 (m-30) REVERT: D 139 TYR cc_start: 0.8179 (t80) cc_final: 0.7640 (t80) outliers start: 25 outliers final: 9 residues processed: 108 average time/residue: 1.2135 time to fit residues: 144.5784 Evaluate side-chains 98 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 1 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 GLN F 136 ASN A 509 ASN B 326 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13624 Z= 0.243 Angle : 0.562 8.118 18560 Z= 0.294 Chirality : 0.046 0.169 2064 Planarity : 0.004 0.050 2380 Dihedral : 4.815 45.387 1854 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 1.98 % Allowed : 11.04 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -1.13 (0.20), residues: 1702 helix: -1.69 (0.70), residues: 44 sheet: -0.87 (0.18), residues: 768 loop : -0.42 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 170 HIS 0.003 0.001 HIS A 233 PHE 0.025 0.002 PHE D 138 TYR 0.020 0.001 TYR A 291 ARG 0.006 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.508 Fit side-chains revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8364 (m-30) cc_final: 0.7932 (m-30) REVERT: F 116 ILE cc_start: 0.8174 (tt) cc_final: 0.7357 (pp) REVERT: F 169 ASP cc_start: 0.8654 (p0) cc_final: 0.8012 (p0) REVERT: A 393 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7815 (pp20) REVERT: A 455 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: A 550 GLN cc_start: 0.7489 (tt0) cc_final: 0.7247 (tt0) REVERT: C 3 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: C 99 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7797 (ttp80) REVERT: D 139 TYR cc_start: 0.8139 (t80) cc_final: 0.7644 (t80) REVERT: D 197 HIS cc_start: 0.6152 (t-90) cc_final: 0.5639 (t70) REVERT: B 555 ASP cc_start: 0.8449 (p0) cc_final: 0.7933 (t0) outliers start: 30 outliers final: 10 residues processed: 125 average time/residue: 1.1153 time to fit residues: 154.9941 Evaluate side-chains 102 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13624 Z= 0.382 Angle : 0.610 8.272 18560 Z= 0.319 Chirality : 0.047 0.174 2064 Planarity : 0.005 0.049 2380 Dihedral : 4.959 42.754 1854 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 2.31 % Allowed : 11.31 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -1.06 (0.20), residues: 1702 helix: -1.42 (0.72), residues: 44 sheet: -0.77 (0.18), residues: 760 loop : -0.46 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 48 HIS 0.003 0.001 HIS A 233 PHE 0.023 0.002 PHE D 138 TYR 0.024 0.002 TYR B 292 ARG 0.004 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: E 16 GLU cc_start: 0.8210 (mp0) cc_final: 0.7650 (mp0) REVERT: F 17 ASP cc_start: 0.8426 (m-30) cc_final: 0.8003 (m-30) REVERT: F 116 ILE cc_start: 0.8170 (tt) cc_final: 0.7369 (pp) REVERT: F 169 ASP cc_start: 0.8604 (p0) cc_final: 0.8046 (p0) REVERT: A 393 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7807 (pp20) REVERT: A 455 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: A 550 GLN cc_start: 0.7582 (tt0) cc_final: 0.7350 (tt0) REVERT: C 3 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: D 138 PHE cc_start: 0.8326 (p90) cc_final: 0.7798 (p90) REVERT: D 139 TYR cc_start: 0.8153 (t80) cc_final: 0.7729 (t80) REVERT: D 197 HIS cc_start: 0.6249 (t-90) cc_final: 0.5753 (t-90) REVERT: B 555 ASP cc_start: 0.8484 (p0) cc_final: 0.7925 (t0) outliers start: 35 outliers final: 13 residues processed: 120 average time/residue: 1.0958 time to fit residues: 146.3317 Evaluate side-chains 101 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 163 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13624 Z= 0.231 Angle : 0.562 9.600 18560 Z= 0.294 Chirality : 0.046 0.182 2064 Planarity : 0.005 0.050 2380 Dihedral : 4.814 39.761 1854 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 1.46 % Allowed : 12.04 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -1.00 (0.21), residues: 1702 helix: -1.40 (0.73), residues: 44 sheet: -0.73 (0.18), residues: 768 loop : -0.41 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 519 HIS 0.003 0.001 HIS A 233 PHE 0.023 0.002 PHE D 138 TYR 0.019 0.001 TYR D 185 ARG 0.009 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8399 (m-30) cc_final: 0.7960 (m-30) REVERT: F 116 ILE cc_start: 0.8150 (tt) cc_final: 0.7368 (pp) REVERT: F 169 ASP cc_start: 0.8595 (p0) cc_final: 0.7935 (p0) REVERT: A 393 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7770 (pp20) REVERT: A 455 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: A 550 GLN cc_start: 0.7501 (tt0) cc_final: 0.7271 (tt0) REVERT: C 3 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: D 139 TYR cc_start: 0.8144 (t80) cc_final: 0.7824 (t80) REVERT: D 197 HIS cc_start: 0.6243 (t-90) cc_final: 0.5853 (t-90) REVERT: B 555 ASP cc_start: 0.8439 (p0) cc_final: 0.7945 (t0) outliers start: 22 outliers final: 12 residues processed: 111 average time/residue: 1.1722 time to fit residues: 144.0626 Evaluate side-chains 100 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13624 Z= 0.283 Angle : 0.573 10.328 18560 Z= 0.300 Chirality : 0.046 0.175 2064 Planarity : 0.004 0.048 2380 Dihedral : 4.784 35.901 1854 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 1.92 % Allowed : 11.97 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -0.92 (0.21), residues: 1702 helix: -1.28 (0.74), residues: 44 sheet: -0.65 (0.18), residues: 768 loop : -0.39 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 170 HIS 0.004 0.001 HIS A 233 PHE 0.026 0.002 PHE D 138 TYR 0.014 0.001 TYR C 51 ARG 0.009 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8375 (m-30) cc_final: 0.7939 (m-30) REVERT: F 116 ILE cc_start: 0.8182 (tt) cc_final: 0.7376 (pp) REVERT: F 169 ASP cc_start: 0.8583 (p0) cc_final: 0.7938 (p0) REVERT: A 393 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: A 455 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: A 519 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.7118 (t60) REVERT: A 550 GLN cc_start: 0.7513 (tt0) cc_final: 0.7284 (tt0) REVERT: C 3 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: C 138 PHE cc_start: 0.7822 (m-80) cc_final: 0.7479 (m-80) REVERT: D 139 TYR cc_start: 0.8139 (t80) cc_final: 0.7817 (t80) REVERT: D 197 HIS cc_start: 0.6340 (t-90) cc_final: 0.6003 (t-90) REVERT: B 555 ASP cc_start: 0.8453 (p0) cc_final: 0.7952 (t0) outliers start: 29 outliers final: 14 residues processed: 114 average time/residue: 1.1258 time to fit residues: 142.9537 Evaluate side-chains 101 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 152 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13624 Z= 0.272 Angle : 0.592 11.834 18560 Z= 0.304 Chirality : 0.046 0.168 2064 Planarity : 0.004 0.048 2380 Dihedral : 4.748 32.442 1854 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 1.46 % Allowed : 12.63 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -0.88 (0.21), residues: 1702 helix: -1.17 (0.76), residues: 44 sheet: -0.59 (0.18), residues: 766 loop : -0.40 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 170 HIS 0.005 0.001 HIS B 281 PHE 0.026 0.002 PHE D 138 TYR 0.021 0.001 TYR D 185 ARG 0.006 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8368 (m-30) cc_final: 0.7925 (m-30) REVERT: F 116 ILE cc_start: 0.8184 (tt) cc_final: 0.7391 (pp) REVERT: F 169 ASP cc_start: 0.8554 (p0) cc_final: 0.7879 (p0) REVERT: A 393 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: A 455 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: A 519 TRP cc_start: 0.8410 (OUTLIER) cc_final: 0.7143 (t60) REVERT: A 550 GLN cc_start: 0.7518 (tt0) cc_final: 0.7276 (tt0) REVERT: C 3 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: D 138 PHE cc_start: 0.8361 (p90) cc_final: 0.7939 (p90) REVERT: D 139 TYR cc_start: 0.8032 (t80) cc_final: 0.7765 (t80) REVERT: D 197 HIS cc_start: 0.6375 (t-90) cc_final: 0.6040 (t-90) REVERT: B 555 ASP cc_start: 0.8485 (p0) cc_final: 0.7964 (t0) outliers start: 22 outliers final: 13 residues processed: 106 average time/residue: 1.1140 time to fit residues: 131.3476 Evaluate side-chains 99 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13624 Z= 0.423 Angle : 0.647 13.018 18560 Z= 0.334 Chirality : 0.047 0.167 2064 Planarity : 0.005 0.048 2380 Dihedral : 4.911 28.594 1854 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 1.52 % Allowed : 12.90 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -0.93 (0.21), residues: 1702 helix: -1.07 (0.76), residues: 44 sheet: -0.61 (0.18), residues: 760 loop : -0.47 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 119 HIS 0.006 0.001 HIS B 281 PHE 0.028 0.002 PHE D 138 TYR 0.018 0.002 TYR A 291 ARG 0.006 0.001 ARG C 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8428 (m-30) cc_final: 0.7979 (m-30) REVERT: F 116 ILE cc_start: 0.8197 (tt) cc_final: 0.7359 (pp) REVERT: F 169 ASP cc_start: 0.8567 (p0) cc_final: 0.8058 (p0) REVERT: F 191 TYR cc_start: 0.7130 (m-80) cc_final: 0.6827 (m-80) REVERT: A 393 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7850 (pp20) REVERT: A 455 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: A 519 TRP cc_start: 0.8529 (OUTLIER) cc_final: 0.7244 (t60) REVERT: A 550 GLN cc_start: 0.7605 (tt0) cc_final: 0.7356 (tt0) REVERT: C 3 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: D 138 PHE cc_start: 0.8348 (p90) cc_final: 0.7870 (p90) REVERT: D 139 TYR cc_start: 0.8069 (t80) cc_final: 0.7848 (t80) REVERT: D 197 HIS cc_start: 0.6541 (t-90) cc_final: 0.6123 (t-90) REVERT: B 351 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8202 (t80) REVERT: B 555 ASP cc_start: 0.8529 (p0) cc_final: 0.7958 (t0) outliers start: 23 outliers final: 13 residues processed: 103 average time/residue: 1.2182 time to fit residues: 139.5795 Evaluate side-chains 99 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 118 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.116807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.082633 restraints weight = 27403.692| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.55 r_work: 0.3372 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13624 Z= 0.234 Angle : 0.589 11.374 18560 Z= 0.304 Chirality : 0.046 0.164 2064 Planarity : 0.004 0.047 2380 Dihedral : 4.779 24.190 1854 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 0.99 % Allowed : 13.82 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -0.85 (0.21), residues: 1702 helix: -1.01 (0.77), residues: 44 sheet: -0.57 (0.18), residues: 766 loop : -0.40 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 115 HIS 0.004 0.001 HIS A 233 PHE 0.028 0.002 PHE D 138 TYR 0.022 0.001 TYR D 185 ARG 0.007 0.000 ARG F 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4500.89 seconds wall clock time: 81 minutes 13.51 seconds (4873.51 seconds total)