Starting phenix.real_space_refine on Thu Feb 15 22:45:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/02_2024/6vyg_21459.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/02_2024/6vyg_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_21459/02_2024/6vyg_21459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/02_2024/6vyg_21459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/02_2024/6vyg_21459.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyg_21459/02_2024/6vyg_21459.pdb" } resolution = 3.5 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= 0.004 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.32, 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: 5.77 Conformation dependent library (CDL) restraints added in 2.4 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: 1.68 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: 4.42 Time building geometry restraints manager: 6.12 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.460 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 38.960 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.810 ------------------------------------------------------------------------------- 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 % Allowed : 5.96 % Favored : 93.50 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 199 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE B 54 TYR 0.016 0.001 TYR B 284 ARG 0.002 0.000 ARG D 216 *********************** 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 : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5303 (mtp) cc_final: 0.4797 (mmm) REVERT: A 299 ASP cc_start: 0.7097 (p0) cc_final: 0.6838 (p0) REVERT: B 164 MET cc_start: 0.5353 (mtp) cc_final: 0.4793 (mmm) REVERT: B 299 ASP cc_start: 0.7147 (p0) cc_final: 0.6926 (p0) REVERT: C 112 ARG cc_start: 0.6056 (mtp180) cc_final: 0.5078 (mtp180) REVERT: C 164 MET cc_start: 0.5376 (mtp) cc_final: 0.4942 (mmm) REVERT: C 203 PHE cc_start: 0.6420 (m-80) cc_final: 0.6183 (m-80) REVERT: C 299 ASP cc_start: 0.7131 (p0) cc_final: 0.6865 (p0) REVERT: D 164 MET cc_start: 0.5106 (mtp) cc_final: 0.4621 (mmm) REVERT: D 299 ASP cc_start: 0.7038 (p0) cc_final: 0.6809 (p0) outliers start: 8 outliers final: 4 residues processed: 227 average time/residue: 0.3426 time to fit residues: 106.8464 Evaluate side-chains 142 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain D residue 236 CYS 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 ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8247 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13892 Z= 0.193 Angle : 0.561 7.765 18748 Z= 0.298 Chirality : 0.043 0.135 2056 Planarity : 0.003 0.038 2404 Dihedral : 5.285 36.795 1860 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 1.96 % Allowed : 11.59 % Favored : 86.45 % 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: -2.24 (0.19), residues: 1700 helix: 0.04 (0.19), residues: 700 sheet: -1.69 (0.35), residues: 212 loop : -2.94 (0.18), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 383 HIS 0.005 0.001 HIS A 75 PHE 0.016 0.002 PHE A 153 TYR 0.014 0.001 TYR D 284 ARG 0.004 0.000 ARG B 216 *********************** 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 216 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5283 (mtp) cc_final: 0.4705 (mmm) REVERT: A 299 ASP cc_start: 0.7195 (p0) cc_final: 0.6905 (p0) REVERT: B 164 MET cc_start: 0.5185 (mtp) cc_final: 0.4551 (mmm) REVERT: B 221 LEU cc_start: 0.7109 (tt) cc_final: 0.6726 (tt) REVERT: B 246 LEU cc_start: 0.8706 (tp) cc_final: 0.8248 (tt) REVERT: B 299 ASP cc_start: 0.7165 (p0) cc_final: 0.6887 (p0) REVERT: C 112 ARG cc_start: 0.6096 (mtp180) cc_final: 0.5129 (mtp180) REVERT: C 164 MET cc_start: 0.5367 (mtp) cc_final: 0.4795 (mmm) REVERT: C 299 ASP cc_start: 0.7158 (p0) cc_final: 0.6871 (p0) REVERT: D 153 PHE cc_start: 0.4705 (m-10) cc_final: 0.4462 (m-10) REVERT: D 164 MET cc_start: 0.4709 (mtp) cc_final: 0.4388 (mmm) REVERT: D 221 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6730 (tt) REVERT: D 299 ASP cc_start: 0.7155 (p0) cc_final: 0.6852 (p0) outliers start: 29 outliers final: 15 residues processed: 206 average time/residue: 0.2508 time to fit residues: 76.3209 Evaluate side-chains 171 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 221 LEU 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: 10.0000 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 C 36 HIS C 252 GLN D 36 HIS ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13892 Z= 0.339 Angle : 0.693 16.899 18748 Z= 0.352 Chirality : 0.049 0.458 2056 Planarity : 0.004 0.042 2404 Dihedral : 6.011 63.382 1856 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 2.71 % Allowed : 14.43 % Favored : 82.86 % 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: -2.03 (0.19), residues: 1700 helix: 0.14 (0.19), residues: 712 sheet: -1.20 (0.39), residues: 192 loop : -2.88 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 72 HIS 0.004 0.001 HIS D 75 PHE 0.014 0.002 PHE C 108 TYR 0.019 0.002 TYR D 284 ARG 0.004 0.000 ARG C 216 *********************** 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 198 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5348 (mtp) cc_final: 0.4754 (mmm) REVERT: A 299 ASP cc_start: 0.7380 (p0) cc_final: 0.7026 (p0) REVERT: B 153 PHE cc_start: 0.4858 (m-10) cc_final: 0.4655 (m-10) REVERT: B 164 MET cc_start: 0.5311 (mtp) cc_final: 0.4673 (mmm) REVERT: B 221 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6858 (tt) REVERT: B 299 ASP cc_start: 0.7360 (p0) cc_final: 0.6999 (p0) REVERT: C 164 MET cc_start: 0.5310 (mtp) cc_final: 0.4756 (mmm) REVERT: C 299 ASP cc_start: 0.7388 (p0) cc_final: 0.7042 (p0) REVERT: D 164 MET cc_start: 0.5177 (mtp) cc_final: 0.4598 (mmm) REVERT: D 221 LEU cc_start: 0.7324 (tt) cc_final: 0.6969 (tt) REVERT: D 299 ASP cc_start: 0.7370 (p0) cc_final: 0.7023 (p0) outliers start: 40 outliers final: 29 residues processed: 182 average time/residue: 0.2386 time to fit residues: 64.9441 Evaluate side-chains 183 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 13892 Z= 0.296 Angle : 0.680 18.665 18748 Z= 0.342 Chirality : 0.049 0.512 2056 Planarity : 0.003 0.043 2404 Dihedral : 5.915 60.883 1856 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 3.52 % Allowed : 15.99 % Favored : 80.49 % 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: -1.85 (0.20), residues: 1700 helix: 0.29 (0.20), residues: 712 sheet: -1.19 (0.40), residues: 192 loop : -2.75 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 72 HIS 0.004 0.001 HIS A 75 PHE 0.016 0.002 PHE C 153 TYR 0.015 0.002 TYR D 284 ARG 0.004 0.000 ARG A 216 *********************** 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 213 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5300 (mtp) cc_final: 0.4706 (mmm) REVERT: B 153 PHE cc_start: 0.4781 (m-10) cc_final: 0.4573 (m-10) REVERT: B 164 MET cc_start: 0.5278 (mtp) cc_final: 0.4657 (mmm) REVERT: B 221 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6818 (tt) REVERT: C 164 MET cc_start: 0.5298 (mtp) cc_final: 0.4751 (mmm) REVERT: C 299 ASP cc_start: 0.7358 (p0) cc_final: 0.7001 (p0) REVERT: D 164 MET cc_start: 0.5156 (mtp) cc_final: 0.4585 (mmm) REVERT: D 221 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7026 (tt) REVERT: D 299 ASP cc_start: 0.7360 (p0) cc_final: 0.7009 (p0) outliers start: 52 outliers final: 41 residues processed: 196 average time/residue: 0.2351 time to fit residues: 69.0262 Evaluate side-chains 199 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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: 0.8285 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13892 Z= 0.223 Angle : 0.603 12.350 18748 Z= 0.310 Chirality : 0.045 0.308 2056 Planarity : 0.003 0.042 2404 Dihedral : 5.610 53.290 1856 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.39 % Allowed : 17.55 % Favored : 79.07 % 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: -1.62 (0.20), residues: 1700 helix: 0.51 (0.20), residues: 712 sheet: -1.17 (0.40), residues: 192 loop : -2.64 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 443 HIS 0.005 0.001 HIS C 75 PHE 0.014 0.001 PHE C 108 TYR 0.012 0.001 TYR D 284 ARG 0.008 0.000 ARG A 123 *********************** 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 212 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5283 (mtp) cc_final: 0.4652 (mmm) REVERT: B 153 PHE cc_start: 0.4641 (m-10) cc_final: 0.4425 (m-10) REVERT: B 164 MET cc_start: 0.5298 (mtp) cc_final: 0.4653 (mmm) REVERT: B 221 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6745 (tt) REVERT: C 164 MET cc_start: 0.5320 (mtp) cc_final: 0.4727 (mmm) REVERT: D 164 MET cc_start: 0.5096 (mtp) cc_final: 0.4525 (mmm) REVERT: D 221 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7072 (tt) REVERT: D 299 ASP cc_start: 0.7419 (p0) cc_final: 0.7106 (p0) outliers start: 50 outliers final: 39 residues processed: 194 average time/residue: 0.2491 time to fit residues: 72.1218 Evaluate side-chains 199 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 VAL 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: 0.0050 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 77 optimal weight: 0.4980 chunk 13 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 160 optimal weight: 0.3980 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 13892 Z= 0.185 Angle : 0.655 24.553 18748 Z= 0.318 Chirality : 0.050 0.709 2056 Planarity : 0.003 0.038 2404 Dihedral : 5.605 66.655 1856 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.85 % Allowed : 18.16 % Favored : 79.00 % 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: -1.28 (0.20), residues: 1700 helix: 0.84 (0.20), residues: 712 sheet: -1.09 (0.41), residues: 192 loop : -2.46 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 199 HIS 0.005 0.001 HIS C 75 PHE 0.013 0.001 PHE C 108 TYR 0.008 0.001 TYR D 284 ARG 0.006 0.000 ARG A 123 *********************** 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 222 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5074 (mtp) cc_final: 0.4596 (mmm) REVERT: A 299 ASP cc_start: 0.7242 (p0) cc_final: 0.6930 (p0) REVERT: B 153 PHE cc_start: 0.4432 (m-10) cc_final: 0.4210 (m-10) REVERT: B 164 MET cc_start: 0.5052 (mtp) cc_final: 0.4553 (mmm) REVERT: B 221 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6798 (tt) REVERT: B 299 ASP cc_start: 0.7276 (p0) cc_final: 0.6969 (p0) REVERT: C 164 MET cc_start: 0.5225 (mtp) cc_final: 0.4776 (mmm) REVERT: C 299 ASP cc_start: 0.7221 (p0) cc_final: 0.6927 (p0) REVERT: D 164 MET cc_start: 0.4931 (mtp) cc_final: 0.4502 (mmm) REVERT: D 221 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7126 (tt) REVERT: D 299 ASP cc_start: 0.7215 (p0) cc_final: 0.6927 (p0) outliers start: 42 outliers final: 29 residues processed: 206 average time/residue: 0.2720 time to fit residues: 80.4000 Evaluate side-chains 199 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 324 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 13892 Z= 0.390 Angle : 0.717 18.767 18748 Z= 0.365 Chirality : 0.050 0.508 2056 Planarity : 0.004 0.041 2404 Dihedral : 5.903 60.462 1856 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 3.79 % Allowed : 18.36 % Favored : 77.85 % 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: -1.65 (0.20), residues: 1700 helix: 0.43 (0.20), residues: 712 sheet: -1.09 (0.41), residues: 192 loop : -2.63 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 199 HIS 0.003 0.001 HIS D 75 PHE 0.015 0.002 PHE D 108 TYR 0.018 0.002 TYR D 284 ARG 0.007 0.001 ARG D 123 *********************** 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 215 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 159 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5254 (mtp) cc_final: 0.4690 (mmm) REVERT: B 164 MET cc_start: 0.5282 (mtp) cc_final: 0.4692 (mmm) REVERT: C 164 MET cc_start: 0.5331 (mtp) cc_final: 0.4809 (mmm) REVERT: D 164 MET cc_start: 0.5128 (mtp) cc_final: 0.4571 (mmm) REVERT: D 221 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7146 (tt) outliers start: 56 outliers final: 47 residues processed: 205 average time/residue: 0.2387 time to fit residues: 72.4472 Evaluate side-chains 203 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 155 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 0.0970 chunk 144 optimal weight: 0.2980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN D 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 13892 Z= 0.147 Angle : 0.580 14.810 18748 Z= 0.292 Chirality : 0.044 0.385 2056 Planarity : 0.003 0.037 2404 Dihedral : 5.474 60.766 1856 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.03 % Allowed : 20.39 % Favored : 77.57 % 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: -1.15 (0.21), residues: 1700 helix: 0.91 (0.20), residues: 712 sheet: -1.07 (0.41), residues: 192 loop : -2.34 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 383 HIS 0.005 0.001 HIS C 75 PHE 0.012 0.001 PHE D 108 TYR 0.004 0.001 TYR C 284 ARG 0.008 0.000 ARG D 123 *********************** 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 200 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5059 (mtp) cc_final: 0.4572 (mmm) REVERT: A 299 ASP cc_start: 0.7240 (p0) cc_final: 0.6935 (p0) REVERT: B 164 MET cc_start: 0.5024 (mtp) cc_final: 0.4528 (mmm) REVERT: B 221 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7115 (tt) REVERT: B 299 ASP cc_start: 0.7256 (p0) cc_final: 0.6948 (p0) REVERT: C 164 MET cc_start: 0.5277 (mtp) cc_final: 0.4802 (mmm) REVERT: C 299 ASP cc_start: 0.7209 (p0) cc_final: 0.6917 (p0) REVERT: D 164 MET cc_start: 0.4965 (mtp) cc_final: 0.4612 (mmm) REVERT: D 221 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7123 (tt) REVERT: D 299 ASP cc_start: 0.7225 (p0) cc_final: 0.6941 (p0) outliers start: 30 outliers final: 22 residues processed: 193 average time/residue: 0.2620 time to fit residues: 73.5767 Evaluate side-chains 188 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 324 MET 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: 0.0980 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 0.0050 chunk 101 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 13892 Z= 0.244 Angle : 0.659 27.471 18748 Z= 0.325 Chirality : 0.041 0.280 2056 Planarity : 0.003 0.044 2404 Dihedral : 5.242 60.782 1856 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.83 % Allowed : 20.33 % Favored : 77.85 % Cbeta Deviations : 0.19 % 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: -0.88 (0.21), residues: 1700 helix: 1.17 (0.20), residues: 716 sheet: -1.05 (0.41), residues: 192 loop : -2.20 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 199 HIS 0.004 0.001 HIS C 75 PHE 0.015 0.001 PHE C 153 TYR 0.008 0.001 TYR B 284 ARG 0.010 0.000 ARG A 123 *********************** 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 213 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.4975 (mtp) cc_final: 0.4762 (mmm) REVERT: A 299 ASP cc_start: 0.7215 (p0) cc_final: 0.6954 (p0) REVERT: B 164 MET cc_start: 0.5001 (mtp) cc_final: 0.4450 (mmt) REVERT: B 221 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7168 (tt) REVERT: B 299 ASP cc_start: 0.7208 (p0) cc_final: 0.6886 (p0) REVERT: C 164 MET cc_start: 0.5046 (mtp) cc_final: 0.4761 (mmm) REVERT: C 299 ASP cc_start: 0.7200 (p0) cc_final: 0.6893 (p0) REVERT: D 221 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7184 (tt) REVERT: D 299 ASP cc_start: 0.7213 (p0) cc_final: 0.6914 (p0) outliers start: 27 outliers final: 20 residues processed: 208 average time/residue: 0.2567 time to fit residues: 77.8217 Evaluate side-chains 188 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 368 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 113 optimal weight: 0.0020 chunk 171 optimal weight: 20.0000 chunk 157 optimal weight: 0.9990 chunk 136 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** C 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 13892 Z= 0.192 Angle : 0.624 23.784 18748 Z= 0.302 Chirality : 0.044 0.394 2056 Planarity : 0.003 0.032 2404 Dihedral : 5.349 69.548 1856 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.56 % Allowed : 20.93 % Favored : 77.51 % Cbeta Deviations : 0.19 % 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: -0.78 (0.21), residues: 1700 helix: 1.23 (0.20), residues: 720 sheet: -1.03 (0.40), residues: 192 loop : -2.14 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 199 HIS 0.007 0.001 HIS C 65 PHE 0.011 0.001 PHE C 108 TYR 0.010 0.001 TYR D 251 ARG 0.010 0.000 ARG B 123 ********************** 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 189 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8005 (ptt-90) cc_final: 0.7771 (ptt-90) REVERT: A 164 MET cc_start: 0.4891 (mtp) cc_final: 0.4412 (mmt) REVERT: A 299 ASP cc_start: 0.7073 (p0) cc_final: 0.6836 (p0) REVERT: B 123 ARG cc_start: 0.7955 (ptt-90) cc_final: 0.7754 (ptt-90) REVERT: B 153 PHE cc_start: 0.4603 (m-10) cc_final: 0.4347 (m-10) REVERT: B 164 MET cc_start: 0.4904 (mtp) cc_final: 0.4386 (mmt) REVERT: B 221 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7016 (tt) REVERT: B 299 ASP cc_start: 0.7101 (p0) cc_final: 0.6836 (p0) REVERT: C 164 MET cc_start: 0.5069 (mtp) cc_final: 0.4792 (mmm) REVERT: C 299 ASP cc_start: 0.7137 (p0) cc_final: 0.6863 (p0) REVERT: D 123 ARG cc_start: 0.8073 (ptt-90) cc_final: 0.7812 (ptt-90) REVERT: D 221 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7245 (tt) REVERT: D 299 ASP cc_start: 0.7104 (p0) cc_final: 0.6863 (p0) outliers start: 23 outliers final: 19 residues processed: 184 average time/residue: 0.2594 time to fit residues: 69.4978 Evaluate side-chains 185 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 368 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 overall best weight: 3.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113608 restraints weight = 22263.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116059 restraints weight = 13446.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117646 restraints weight = 9970.712| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 13892 Z= 0.310 Angle : 0.680 22.632 18748 Z= 0.336 Chirality : 0.047 0.388 2056 Planarity : 0.003 0.034 2404 Dihedral : 5.608 66.985 1856 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 1.96 % Allowed : 20.60 % Favored : 77.44 % Cbeta Deviations : 0.19 % 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: -1.05 (0.21), residues: 1700 helix: 1.00 (0.20), residues: 716 sheet: -1.00 (0.41), residues: 192 loop : -2.32 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 199 HIS 0.005 0.001 HIS B 65 PHE 0.014 0.002 PHE C 153 TYR 0.029 0.002 TYR D 284 ARG 0.010 0.001 ARG B 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.12 seconds wall clock time: 48 minutes 23.48 seconds (2903.48 seconds total)