Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 23:16:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/04_2023/6vyg_21459.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/04_2023/6vyg_21459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/04_2023/6vyg_21459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/04_2023/6vyg_21459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/04_2023/6vyg_21459.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/04_2023/6vyg_21459.pdb" } resolution = 3.5 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= 0.000 sd= 0.004 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 92 5.16 5 C 8632 2.51 5 N 2320 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 434": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 299": "OD1" <-> "OD2" Residue "C TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 381": "OD1" <-> "OD2" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ASP 434": "OD1" <-> "OD2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 299": "OD1" <-> "OD2" Residue "D TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 381": "OD1" <-> "OD2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D ASP 389": "OD1" <-> "OD2" Residue "D ASP 434": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3404 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 14, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3404 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 14, 'TRANS': 418} Chain breaks: 3 Chain: "C" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3404 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 14, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3404 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 14, 'TRANS': 418} Chain breaks: 3 Time building chain proxies: 7.33, per 1000 atoms: 0.54 Number of scatterers: 13616 At special positions: 0 Unit cell: (117.791, 96.071, 116.121, 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 92 16.00 O 2572 8.00 N 2320 7.00 C 8632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 236 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 236 " - pdb=" SG CYS D 237 " distance=2.04 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: 5.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 51.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.595A pdb=" N HIS A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 68 removed outlier: 3.876A pdb=" N GLU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.809A pdb=" N GLY A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.530A pdb=" N LEU A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 223 " --> pdb=" O CYS A 219 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.831A pdb=" N ALA A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.334A pdb=" N LYS A 280 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.658A pdb=" N PHE A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.850A pdb=" N ILE A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.581A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.588A pdb=" N TRP A 351 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.644A pdb=" N GLY A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.597A pdb=" N LYS A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 422 removed outlier: 3.666A pdb=" N ARG A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.568A pdb=" N CYS A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 447 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.016A pdb=" N GLY A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.676A pdb=" N VAL A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.595A pdb=" N HIS B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 68 removed outlier: 3.877A pdb=" N GLU B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 removed outlier: 3.808A pdb=" N GLY B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.529A pdb=" N LEU B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 223 " --> pdb=" O CYS B 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 removed outlier: 3.832A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.335A pdb=" N LYS B 280 " --> pdb=" O PRO B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.658A pdb=" N PHE B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.850A pdb=" N ILE B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.581A pdb=" N LEU B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.588A pdb=" N TRP B 351 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.643A pdb=" N GLY B 361 " --> pdb=" O ASN B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 384 removed outlier: 3.596A pdb=" N LYS B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 422 removed outlier: 3.665A pdb=" N ARG B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 441 through 456 removed outlier: 3.568A pdb=" N CYS B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 447 " --> pdb=" O TRP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 471 through 479 removed outlier: 4.016A pdb=" N GLY B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.675A pdb=" N VAL B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.595A pdb=" N HIS C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 68 removed outlier: 3.877A pdb=" N GLU C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 165 removed outlier: 3.808A pdb=" N GLY C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.528A pdb=" N LEU C 221 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 223 " --> pdb=" O CYS C 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.831A pdb=" N ALA C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 4.335A pdb=" N LYS C 280 " --> pdb=" O PRO C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.659A pdb=" N PHE C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.851A pdb=" N ILE C 325 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 3.581A pdb=" N LEU C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.589A pdb=" N TRP C 351 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.643A pdb=" N GLY C 361 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 384 removed outlier: 3.596A pdb=" N LYS C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 422 removed outlier: 3.665A pdb=" N ARG C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 441 through 456 removed outlier: 3.568A pdb=" N CYS C 445 " --> pdb=" O ASN C 441 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 447 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 471 through 479 removed outlier: 4.017A pdb=" N GLY C 475 " --> pdb=" O GLY C 471 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 477 " --> pdb=" O GLY C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.676A pdb=" N VAL C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 removed outlier: 3.596A pdb=" N HIS D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 68 removed outlier: 3.877A pdb=" N GLU D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.808A pdb=" N GLY D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.528A pdb=" N LEU D 221 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 252 removed outlier: 3.831A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 removed outlier: 4.335A pdb=" N LYS D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.659A pdb=" N PHE D 296 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.851A pdb=" N ILE D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 341 removed outlier: 3.582A pdb=" N LEU D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 352 removed outlier: 3.588A pdb=" N TRP D 351 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.643A pdb=" N GLY D 361 " --> pdb=" O ASN D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 384 removed outlier: 3.595A pdb=" N LYS D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 422 removed outlier: 3.666A pdb=" N ARG D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 441 through 456 removed outlier: 3.567A pdb=" N CYS D 445 " --> pdb=" O ASN D 441 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 447 " --> pdb=" O TRP D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.016A pdb=" N GLY D 475 " --> pdb=" O GLY D 471 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D 477 " --> pdb=" O GLY D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 removed outlier: 3.676A pdb=" N VAL D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.657A pdb=" N SER A 84 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE A 288 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 272 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR A 261 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER A 430 " --> pdb=" O CYS A 260 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 262 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE A 429 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE A 466 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS A 431 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 removed outlier: 9.105A pdb=" N GLY A 179 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A 99 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR A 181 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 101 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 180 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.657A pdb=" N SER B 84 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 288 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 272 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR B 261 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER B 430 " --> pdb=" O CYS B 260 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 262 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE B 429 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE B 466 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 431 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 123 removed outlier: 9.105A pdb=" N GLY B 179 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR B 99 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR B 181 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 101 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 180 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.658A pdb=" N SER C 84 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE C 288 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 272 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR C 261 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER C 430 " --> pdb=" O CYS C 260 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 262 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE C 429 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE C 466 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS C 431 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123 removed outlier: 9.105A pdb=" N GLY C 179 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C 99 " --> pdb=" O GLY C 179 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR C 181 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 101 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 180 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.657A pdb=" N SER D 84 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE D 288 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 272 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR D 261 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER D 430 " --> pdb=" O CYS D 260 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 262 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE D 429 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE D 466 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS D 431 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 121 through 123 removed outlier: 9.105A pdb=" N GLY D 179 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR D 99 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR D 181 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 101 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE D 180 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 187 560 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 5.85 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: 4479 1.35 - 1.48: 3365 1.48 - 1.61: 5920 1.61 - 1.74: 0 1.74 - 1.87: 128 Bond restraints: 13892 Sorted by residual: bond pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.06e+00 bond pdb=" CB CYS C 237 " pdb=" SG CYS C 237 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.05e+00 bond pdb=" CB CYS D 237 " pdb=" SG CYS D 237 " ideal model delta sigma weight residual 1.808 1.865 -0.057 3.30e-02 9.18e+02 3.01e+00 bond pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " ideal model delta sigma weight residual 1.808 1.865 -0.057 3.30e-02 9.18e+02 3.01e+00 bond pdb=" CA ASN B 315 " pdb=" C ASN B 315 " ideal model delta sigma weight residual 1.531 1.517 0.014 1.12e-02 7.97e+03 1.53e+00 ... (remaining 13887 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.12: 337 107.12 - 113.85: 7809 113.85 - 120.59: 5466 120.59 - 127.32: 4998 127.32 - 134.05: 138 Bond angle restraints: 18748 Sorted by residual: angle pdb=" N CYS B 236 " pdb=" CA CYS B 236 " pdb=" C CYS B 236 " ideal model delta sigma weight residual 111.00 123.63 -12.63 2.80e+00 1.28e-01 2.03e+01 angle pdb=" N CYS A 236 " pdb=" CA CYS A 236 " pdb=" C CYS A 236 " ideal model delta sigma weight residual 111.00 123.62 -12.62 2.80e+00 1.28e-01 2.03e+01 angle pdb=" N CYS D 236 " pdb=" CA CYS D 236 " pdb=" C CYS D 236 " ideal model delta sigma weight residual 111.00 123.62 -12.62 2.80e+00 1.28e-01 2.03e+01 angle pdb=" N CYS C 236 " pdb=" CA CYS C 236 " pdb=" C CYS C 236 " ideal model delta sigma weight residual 111.00 123.58 -12.58 2.80e+00 1.28e-01 2.02e+01 angle pdb=" C CYS B 236 " pdb=" CA CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sigma weight residual 110.10 102.91 7.19 1.90e+00 2.77e-01 1.43e+01 ... (remaining 18743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 7302 16.03 - 32.07: 850 32.07 - 48.10: 152 48.10 - 64.14: 28 64.14 - 80.17: 20 Dihedral angle restraints: 8352 sinusoidal: 3332 harmonic: 5020 Sorted by residual: dihedral pdb=" CA CYS C 236 " pdb=" C CYS C 236 " pdb=" N CYS C 237 " pdb=" CA CYS C 237 " ideal model delta harmonic sigma weight residual 180.00 123.07 56.93 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA CYS D 236 " pdb=" C CYS D 236 " pdb=" N CYS D 237 " pdb=" CA CYS D 237 " ideal model delta harmonic sigma weight residual 180.00 123.08 56.92 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA CYS A 236 " pdb=" C CYS A 236 " pdb=" N CYS A 237 " pdb=" CA CYS A 237 " ideal model delta harmonic sigma weight residual 180.00 123.09 56.91 0 5.00e+00 4.00e-02 1.30e+02 ... (remaining 8349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1819 0.064 - 0.127: 218 0.127 - 0.191: 15 0.191 - 0.254: 0 0.254 - 0.318: 4 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA CYS D 236 " pdb=" N CYS D 236 " pdb=" C CYS D 236 " pdb=" CB CYS D 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA CYS A 236 " pdb=" N CYS A 236 " pdb=" C CYS A 236 " pdb=" CB CYS A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA CYS B 236 " pdb=" N CYS B 236 " pdb=" C CYS B 236 " pdb=" CB CYS B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2053 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 68 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO A 69 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 68 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 69 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 68 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO C 69 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " -0.022 5.00e-02 4.00e+02 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 152 2.66 - 3.22: 13210 3.22 - 3.78: 18997 3.78 - 4.34: 26786 4.34 - 4.90: 44694 Nonbonded interactions: 103839 Sorted by model distance: nonbonded pdb=" O CYS A 445 " pdb=" NE2 GLN A 449 " model vdw 2.094 2.520 nonbonded pdb=" O CYS B 445 " pdb=" NE2 GLN B 449 " model vdw 2.094 2.520 nonbonded pdb=" O CYS D 445 " pdb=" NE2 GLN D 449 " model vdw 2.095 2.520 nonbonded pdb=" O CYS C 445 " pdb=" NE2 GLN C 449 " model vdw 2.095 2.520 nonbonded pdb=" O GLU B 359 " pdb=" OG SER B 362 " model vdw 2.269 2.440 ... (remaining 103834 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.020 Extract box with map and model: 4.890 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 36.360 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 0.058 13892 Z= 0.242 Angle : 0.691 12.631 18748 Z= 0.405 Chirality : 0.044 0.318 2056 Planarity : 0.003 0.041 2404 Dihedral : 14.054 80.169 5100 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.60 (0.17), residues: 1700 helix: -1.44 (0.18), residues: 688 sheet: -1.95 (0.34), residues: 212 loop : -3.44 (0.17), residues: 800 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 227 average time/residue: 0.3202 time to fit residues: 99.4290 Evaluate side-chains 137 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1169 time to fit residues: 3.1783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN A 426 HIS B 391 GLN B 426 HIS ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 GLN C 426 HIS ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 GLN D 426 HIS ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 13892 Z= 0.182 Angle : 0.588 10.519 18748 Z= 0.308 Chirality : 0.044 0.270 2056 Planarity : 0.003 0.037 2404 Dihedral : 5.571 53.661 1856 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.19), residues: 1700 helix: -0.04 (0.19), residues: 704 sheet: -1.68 (0.36), residues: 212 loop : -2.96 (0.18), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 200 average time/residue: 0.2537 time to fit residues: 75.1929 Evaluate side-chains 164 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1274 time to fit residues: 5.7288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS B 36 HIS B 192 ASN B 252 GLN C 36 HIS C 252 GLN D 36 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 13892 Z= 0.291 Angle : 0.641 14.435 18748 Z= 0.329 Chirality : 0.045 0.147 2056 Planarity : 0.004 0.042 2404 Dihedral : 5.530 39.226 1856 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.94 (0.20), residues: 1700 helix: 0.21 (0.20), residues: 712 sheet: -1.15 (0.39), residues: 192 loop : -2.83 (0.19), residues: 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.590 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 174 average time/residue: 0.2433 time to fit residues: 63.5442 Evaluate side-chains 160 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1279 time to fit residues: 4.7337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 449 GLN C 192 ASN C 449 GLN D 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 13892 Z= 0.311 Angle : 0.634 12.583 18748 Z= 0.328 Chirality : 0.045 0.140 2056 Planarity : 0.004 0.044 2404 Dihedral : 5.487 31.547 1856 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.88 (0.20), residues: 1700 helix: 0.23 (0.20), residues: 712 sheet: -1.19 (0.39), residues: 192 loop : -2.74 (0.19), residues: 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.741 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 179 average time/residue: 0.2621 time to fit residues: 69.5659 Evaluate side-chains 173 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1227 time to fit residues: 6.9760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13892 Z= 0.204 Angle : 0.572 11.484 18748 Z= 0.296 Chirality : 0.043 0.130 2056 Planarity : 0.003 0.041 2404 Dihedral : 5.225 29.023 1856 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.20), residues: 1700 helix: 0.50 (0.20), residues: 712 sheet: -1.16 (0.40), residues: 192 loop : -2.61 (0.19), residues: 796 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.752 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 174 average time/residue: 0.2688 time to fit residues: 68.9685 Evaluate side-chains 168 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1345 time to fit residues: 4.2941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 20.0000 chunk 149 optimal weight: 0.0070 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 160 optimal weight: 0.0470 overall best weight: 2.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13892 Z= 0.199 Angle : 0.566 10.427 18748 Z= 0.294 Chirality : 0.042 0.130 2056 Planarity : 0.003 0.039 2404 Dihedral : 5.117 28.134 1856 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1700 helix: 0.62 (0.20), residues: 712 sheet: -1.13 (0.40), residues: 192 loop : -2.53 (0.19), residues: 796 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 180 average time/residue: 0.2635 time to fit residues: 69.4206 Evaluate side-chains 172 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1300 time to fit residues: 5.5652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 165 optimal weight: 0.3980 chunk 103 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13892 Z= 0.212 Angle : 0.572 9.899 18748 Z= 0.296 Chirality : 0.043 0.131 2056 Planarity : 0.003 0.039 2404 Dihedral : 5.097 28.964 1856 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.20), residues: 1700 helix: 0.66 (0.20), residues: 712 sheet: -1.13 (0.40), residues: 192 loop : -2.50 (0.19), residues: 796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.853 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 169 average time/residue: 0.2554 time to fit residues: 64.1699 Evaluate side-chains 161 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1282 time to fit residues: 4.5411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 70 ASN C 70 ASN D 70 ASN D 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 13892 Z= 0.394 Angle : 0.670 9.669 18748 Z= 0.350 Chirality : 0.047 0.161 2056 Planarity : 0.004 0.043 2404 Dihedral : 5.551 30.769 1856 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.78 (0.20), residues: 1700 helix: 0.29 (0.20), residues: 712 sheet: -1.17 (0.39), residues: 192 loop : -2.66 (0.19), residues: 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.743 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 162 average time/residue: 0.2723 time to fit residues: 65.1251 Evaluate side-chains 161 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1200 time to fit residues: 5.9060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 13892 Z= 0.170 Angle : 0.565 9.944 18748 Z= 0.290 Chirality : 0.042 0.125 2056 Planarity : 0.003 0.040 2404 Dihedral : 5.109 28.157 1856 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1700 helix: 0.67 (0.20), residues: 712 sheet: -1.06 (0.40), residues: 192 loop : -2.42 (0.20), residues: 796 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.715 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.2807 time to fit residues: 63.4387 Evaluate side-chains 145 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 0.0040 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 108 optimal weight: 0.0470 chunk 145 optimal weight: 10.0000 overall best weight: 1.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13892 Z= 0.144 Angle : 0.548 9.634 18748 Z= 0.279 Chirality : 0.042 0.154 2056 Planarity : 0.003 0.038 2404 Dihedral : 4.784 26.584 1856 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1700 helix: 0.95 (0.20), residues: 716 sheet: -1.06 (0.40), residues: 192 loop : -2.28 (0.20), residues: 792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2868 time to fit residues: 71.2473 Evaluate side-chains 156 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0270 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120969 restraints weight = 21744.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123307 restraints weight = 13587.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124804 restraints weight = 10193.646| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13892 Z= 0.123 Angle : 0.521 9.063 18748 Z= 0.265 Chirality : 0.041 0.135 2056 Planarity : 0.003 0.035 2404 Dihedral : 4.492 25.481 1856 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1700 helix: 1.24 (0.21), residues: 696 sheet: -1.08 (0.39), residues: 192 loop : -2.03 (0.21), residues: 812 =============================================================================== Job complete usr+sys time: 2353.98 seconds wall clock time: 44 minutes 3.68 seconds (2643.68 seconds total)