Starting phenix.real_space_refine on Thu Mar 14 15:52:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shm_25130/03_2024/7shm_25130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shm_25130/03_2024/7shm_25130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shm_25130/03_2024/7shm_25130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shm_25130/03_2024/7shm_25130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shm_25130/03_2024/7shm_25130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shm_25130/03_2024/7shm_25130_updated.pdb" } resolution = 3.14 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= 0.006 sd= 0.092 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 44 5.16 5 C 5885 2.51 5 N 1623 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A ASP 649": "OD1" <-> "OD2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 638": "OD1" <-> "OD2" Residue "B GLU 640": "OE1" <-> "OE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 676": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9186 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4553 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 20, 'TRANS': 549} Chain breaks: 2 Chain: "B" Number of atoms: 4571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4571 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.56 Number of scatterers: 9186 At special positions: 0 Unit cell: (81.868, 73.428, 135.884, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 6 15.00 O 1628 8.00 N 1623 7.00 C 5885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 4 sheets defined 59.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.635A pdb=" N TRP A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 122 removed outlier: 3.546A pdb=" N VAL A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 148 removed outlier: 3.594A pdb=" N TRP A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 153 through 174 removed outlier: 3.594A pdb=" N LEU A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 193 through 196 No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 199 through 233 removed outlier: 3.553A pdb=" N ALA A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.645A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 4.181A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 288 removed outlier: 3.559A pdb=" N ALA A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 299 through 323 removed outlier: 3.504A pdb=" N LEU A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.536A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.519A pdb=" N VAL A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 378 through 403 removed outlier: 3.527A pdb=" N GLU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 removed outlier: 3.613A pdb=" N LEU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 520 removed outlier: 3.590A pdb=" N ARG A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 557 No H-bonds generated for 'chain 'A' and resid 554 through 557' Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.751A pdb=" N GLN A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.805A pdb=" N ALA A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.527A pdb=" N GLY A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 removed outlier: 4.076A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 82 removed outlier: 3.635A pdb=" N TRP B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 122 removed outlier: 3.547A pdb=" N VAL B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 148 removed outlier: 3.595A pdb=" N TRP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 153 through 174 removed outlier: 3.595A pdb=" N LEU B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 193 through 196 No H-bonds generated for 'chain 'B' and resid 193 through 196' Processing helix chain 'B' and resid 199 through 233 removed outlier: 3.553A pdb=" N ALA B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 3.646A pdb=" N ALA B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 4.181A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 288 removed outlier: 3.559A pdb=" N ALA B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 299 through 323 removed outlier: 3.504A pdb=" N LEU B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.537A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.520A pdb=" N VAL B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 377 through 403 removed outlier: 3.526A pdb=" N GLU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 430 removed outlier: 3.614A pdb=" N LEU B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 520 removed outlier: 3.659A pdb=" N ARG B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 557 No H-bonds generated for 'chain 'B' and resid 554 through 557' Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.751A pdb=" N GLN B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.805A pdb=" N ALA B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 604 No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.527A pdb=" N GLY B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 615 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 4.076A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 645 " --> pdb=" O GLY B 641 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 466 through 469 Processing sheet with id= B, first strand: chain 'A' and resid 669 through 672 removed outlier: 3.840A pdb=" N LEU A 503 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA A 626 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE A 657 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 628 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 466 through 469 Processing sheet with id= D, first strand: chain 'B' and resid 669 through 672 removed outlier: 3.840A pdb=" N LEU B 503 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA B 626 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE B 657 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 628 " --> pdb=" O ILE B 657 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2940 1.34 - 1.46: 1471 1.46 - 1.57: 4897 1.57 - 1.69: 10 1.69 - 1.81: 74 Bond restraints: 9392 Sorted by residual: bond pdb=" C ASP A 397 " pdb=" N ALA A 398 " ideal model delta sigma weight residual 1.334 1.225 0.109 1.43e-02 4.89e+03 5.82e+01 bond pdb=" C MET B 539 " pdb=" N PHE B 540 " ideal model delta sigma weight residual 1.331 1.414 -0.084 1.32e-02 5.74e+03 4.00e+01 bond pdb=" C MET A 539 " pdb=" N PHE A 540 " ideal model delta sigma weight residual 1.331 1.408 -0.077 1.32e-02 5.74e+03 3.40e+01 bond pdb=" C6 ATP A 801 " pdb=" N6 ATP A 801 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.10e-02 8.26e+03 1.60e+01 bond pdb=" C6 ATP B 801 " pdb=" N6 ATP B 801 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.10e-02 8.26e+03 1.57e+01 ... (remaining 9387 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.18: 219 106.18 - 113.39: 5123 113.39 - 120.60: 4251 120.60 - 127.80: 3042 127.80 - 135.01: 96 Bond angle restraints: 12731 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 113.71 26.16 1.00e+00 1.00e+00 6.84e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 113.94 25.93 1.00e+00 1.00e+00 6.72e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 111.65 25.18 1.00e+00 1.00e+00 6.34e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 112.25 24.58 1.00e+00 1.00e+00 6.04e+02 angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 107.40 13.87 1.00e+00 1.00e+00 1.93e+02 ... (remaining 12726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 4933 18.09 - 36.18: 575 36.18 - 54.27: 89 54.27 - 72.36: 22 72.36 - 90.46: 8 Dihedral angle restraints: 5627 sinusoidal: 2311 harmonic: 3316 Sorted by residual: dihedral pdb=" CA GLN B 630 " pdb=" C GLN B 630 " pdb=" N CYS B 631 " pdb=" CA CYS B 631 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLN A 630 " pdb=" C GLN A 630 " pdb=" N CYS A 631 " pdb=" CA CYS A 631 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA SER A 262 " pdb=" C SER A 262 " pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 5624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1262 0.084 - 0.168: 122 0.168 - 0.251: 23 0.251 - 0.335: 6 0.335 - 0.419: 3 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA ARG A 496 " pdb=" N ARG A 496 " pdb=" C ARG A 496 " pdb=" CB ARG A 496 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA ARG B 496 " pdb=" N ARG B 496 " pdb=" C ARG B 496 " pdb=" CB ARG B 496 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA TRP B 595 " pdb=" N TRP B 595 " pdb=" C TRP B 595 " pdb=" CB TRP B 595 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1413 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 349 " 0.052 5.00e-02 4.00e+02 7.85e-02 9.86e+00 pdb=" N PRO B 350 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 350 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 350 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 349 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO A 350 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 507 " 0.049 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO A 508 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " 0.041 5.00e-02 4.00e+02 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3005 2.84 - 3.35: 8298 3.35 - 3.87: 15182 3.87 - 4.38: 18673 4.38 - 4.90: 30634 Nonbonded interactions: 75792 Sorted by model distance: nonbonded pdb=" O VAL A 286 " pdb=" OG SER A 290 " model vdw 2.322 2.440 nonbonded pdb=" O VAL B 286 " pdb=" OG SER B 290 " model vdw 2.323 2.440 nonbonded pdb=" O MET A 548 " pdb=" NH2 ARG B 285 " model vdw 2.326 2.520 nonbonded pdb=" OG SER A 164 " pdb=" OH TYR B 310 " model vdw 2.328 2.440 nonbonded pdb=" O VAL B 222 " pdb=" OG SER B 226 " model vdw 2.330 2.440 ... (remaining 75787 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' and (resid 64 through 352 or resid 377 through 436 or resid 463 throu \ gh 683 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 4.660 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.360 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 0.006 0.109 9392 Z= 0.417 Angle : 1.167 26.160 12731 Z= 0.784 Chirality : 0.061 0.419 1416 Planarity : 0.008 0.079 1601 Dihedral : 15.732 90.455 3495 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.21 % Allowed : 7.80 % Favored : 92.00 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.33 (0.15), residues: 1130 helix: -4.45 (0.08), residues: 741 sheet: -2.39 (0.52), residues: 70 loop : -3.20 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 326 HIS 0.008 0.002 HIS B 283 PHE 0.019 0.002 PHE B 146 TYR 0.015 0.002 TYR A 559 ARG 0.008 0.001 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 1.023 Fit side-chains REVERT: A 477 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 565 ASP cc_start: 0.7856 (m-30) cc_final: 0.7525 (t0) REVERT: B 592 GLU cc_start: 0.6537 (tt0) cc_final: 0.6218 (pt0) REVERT: B 638 ASP cc_start: 0.7651 (p0) cc_final: 0.7381 (p0) outliers start: 2 outliers final: 2 residues processed: 185 average time/residue: 0.2756 time to fit residues: 66.2073 Evaluate side-chains 126 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 118 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 157 GLN A 177 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 430 GLN A 433 HIS A 544 GLN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 157 GLN B 177 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 433 HIS ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9392 Z= 0.227 Angle : 0.618 7.597 12731 Z= 0.324 Chirality : 0.040 0.143 1416 Planarity : 0.006 0.060 1601 Dihedral : 9.103 88.584 1348 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.98 % Allowed : 12.68 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.20), residues: 1130 helix: -2.40 (0.14), residues: 759 sheet: -2.02 (0.51), residues: 88 loop : -2.64 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.003 0.001 HIS A 283 PHE 0.020 0.001 PHE A 252 TYR 0.017 0.002 TYR A 406 ARG 0.003 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.009 Fit side-chains REVERT: A 140 ILE cc_start: 0.8395 (tp) cc_final: 0.8156 (tt) REVERT: A 477 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7463 (mt-10) REVERT: B 140 ILE cc_start: 0.8425 (tp) cc_final: 0.8139 (tt) REVERT: B 565 ASP cc_start: 0.7142 (t0) cc_final: 0.6847 (t0) outliers start: 19 outliers final: 14 residues processed: 144 average time/residue: 0.2363 time to fit residues: 46.3945 Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 133 GLN A 192 ASN A 316 GLN A 502 HIS ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS B 97 HIS B 133 GLN B 192 ASN B 210 HIS B 316 GLN B 502 HIS ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9392 Z= 0.326 Angle : 0.618 10.749 12731 Z= 0.319 Chirality : 0.042 0.153 1416 Planarity : 0.005 0.051 1601 Dihedral : 8.707 89.859 1344 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.12 % Allowed : 13.72 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.23), residues: 1130 helix: -1.15 (0.17), residues: 759 sheet: -1.27 (0.57), residues: 88 loop : -2.46 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.004 0.001 HIS B 502 PHE 0.015 0.002 PHE B 252 TYR 0.033 0.002 TYR B 620 ARG 0.004 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 0.930 Fit side-chains REVERT: A 140 ILE cc_start: 0.8307 (tp) cc_final: 0.8064 (tt) REVERT: A 477 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7513 (mt-10) REVERT: A 584 HIS cc_start: 0.8528 (m-70) cc_final: 0.8200 (m170) REVERT: A 591 ARG cc_start: 0.7376 (mmt90) cc_final: 0.7133 (mmt90) REVERT: B 140 ILE cc_start: 0.8377 (tp) cc_final: 0.8100 (tt) REVERT: B 565 ASP cc_start: 0.7279 (t0) cc_final: 0.6790 (t0) outliers start: 30 outliers final: 25 residues processed: 147 average time/residue: 0.2323 time to fit residues: 47.0663 Evaluate side-chains 146 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 604 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN B 192 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.216 Angle : 0.567 7.731 12731 Z= 0.291 Chirality : 0.040 0.140 1416 Planarity : 0.004 0.047 1601 Dihedral : 8.406 89.615 1344 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.81 % Allowed : 15.90 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 1130 helix: -0.49 (0.18), residues: 760 sheet: -0.62 (0.60), residues: 87 loop : -2.32 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS A 283 PHE 0.014 0.001 PHE B 252 TYR 0.014 0.001 TYR A 310 ARG 0.004 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.126 Fit side-chains REVERT: A 140 ILE cc_start: 0.8253 (tp) cc_final: 0.7987 (tt) REVERT: A 477 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 580 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7169 (mp) REVERT: A 584 HIS cc_start: 0.8500 (m-70) cc_final: 0.8197 (m170) REVERT: B 140 ILE cc_start: 0.8273 (tp) cc_final: 0.7998 (tt) REVERT: B 501 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8064 (ttt) REVERT: B 565 ASP cc_start: 0.7321 (t0) cc_final: 0.6775 (t0) REVERT: B 580 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7066 (mp) outliers start: 27 outliers final: 18 residues processed: 154 average time/residue: 0.2190 time to fit residues: 46.6605 Evaluate side-chains 146 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.0040 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.7952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.192 Angle : 0.543 7.741 12731 Z= 0.276 Chirality : 0.039 0.164 1416 Planarity : 0.004 0.045 1601 Dihedral : 8.183 89.761 1344 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.01 % Allowed : 16.53 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.25), residues: 1130 helix: -0.04 (0.19), residues: 760 sheet: -0.29 (0.60), residues: 87 loop : -2.23 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS B 299 PHE 0.015 0.001 PHE B 252 TYR 0.025 0.002 TYR A 620 ARG 0.006 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.087 Fit side-chains REVERT: A 140 ILE cc_start: 0.8221 (tp) cc_final: 0.7969 (tt) REVERT: A 580 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7125 (mp) REVERT: A 584 HIS cc_start: 0.8485 (m-70) cc_final: 0.8187 (m170) REVERT: B 140 ILE cc_start: 0.8260 (tp) cc_final: 0.7979 (tt) REVERT: B 312 ASP cc_start: 0.7581 (m-30) cc_final: 0.7053 (m-30) REVERT: B 501 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8039 (ttt) REVERT: B 565 ASP cc_start: 0.7346 (t0) cc_final: 0.6772 (t0) REVERT: B 580 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7031 (mp) REVERT: B 584 HIS cc_start: 0.8474 (m-70) cc_final: 0.8170 (m170) outliers start: 29 outliers final: 17 residues processed: 146 average time/residue: 0.2236 time to fit residues: 44.9302 Evaluate side-chains 139 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.0050 chunk 57 optimal weight: 5.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9392 Z= 0.211 Angle : 0.547 7.167 12731 Z= 0.277 Chirality : 0.040 0.138 1416 Planarity : 0.004 0.044 1601 Dihedral : 8.082 89.230 1344 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.43 % Allowed : 16.63 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1130 helix: 0.23 (0.19), residues: 760 sheet: -0.31 (0.65), residues: 76 loop : -1.97 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS A 283 PHE 0.016 0.001 PHE B 252 TYR 0.012 0.001 TYR A 310 ARG 0.004 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 0.898 Fit side-chains REVERT: A 140 ILE cc_start: 0.8206 (tp) cc_final: 0.7947 (tt) REVERT: A 580 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7100 (mp) REVERT: A 584 HIS cc_start: 0.8472 (m-70) cc_final: 0.8149 (m170) REVERT: B 67 MET cc_start: 0.7384 (ttt) cc_final: 0.6929 (ttt) REVERT: B 140 ILE cc_start: 0.8267 (tp) cc_final: 0.7974 (tt) REVERT: B 312 ASP cc_start: 0.7578 (m-30) cc_final: 0.7050 (m-30) REVERT: B 501 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7958 (ttt) REVERT: B 565 ASP cc_start: 0.7304 (t0) cc_final: 0.6709 (t0) REVERT: B 580 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7025 (mp) REVERT: B 584 HIS cc_start: 0.8498 (m-70) cc_final: 0.8186 (m170) outliers start: 33 outliers final: 20 residues processed: 150 average time/residue: 0.2189 time to fit residues: 45.2926 Evaluate side-chains 153 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9392 Z= 0.230 Angle : 0.563 9.340 12731 Z= 0.283 Chirality : 0.040 0.145 1416 Planarity : 0.004 0.046 1601 Dihedral : 8.054 88.856 1344 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.53 % Allowed : 17.78 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1130 helix: 0.42 (0.19), residues: 760 sheet: -0.53 (0.70), residues: 62 loop : -1.72 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS B 299 PHE 0.017 0.001 PHE B 252 TYR 0.014 0.001 TYR B 620 ARG 0.004 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.930 Fit side-chains REVERT: A 140 ILE cc_start: 0.8164 (tp) cc_final: 0.7932 (tt) REVERT: A 580 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7061 (mp) REVERT: A 584 HIS cc_start: 0.8487 (m-70) cc_final: 0.8163 (m170) REVERT: B 67 MET cc_start: 0.7494 (ttt) cc_final: 0.7019 (ttt) REVERT: B 140 ILE cc_start: 0.8340 (tp) cc_final: 0.8055 (tt) REVERT: B 565 ASP cc_start: 0.7330 (t0) cc_final: 0.6744 (t0) REVERT: B 580 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7011 (mp) REVERT: B 584 HIS cc_start: 0.8458 (m-70) cc_final: 0.8119 (m170) REVERT: B 644 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6261 (t80) outliers start: 34 outliers final: 23 residues processed: 155 average time/residue: 0.2253 time to fit residues: 47.7532 Evaluate side-chains 155 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 644 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0030 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9392 Z= 0.247 Angle : 0.570 9.333 12731 Z= 0.285 Chirality : 0.040 0.139 1416 Planarity : 0.004 0.043 1601 Dihedral : 8.041 89.155 1344 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.60 % Allowed : 18.30 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1130 helix: 0.53 (0.19), residues: 760 sheet: -0.45 (0.72), residues: 56 loop : -1.64 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.005 0.001 HIS B 669 PHE 0.020 0.001 PHE B 252 TYR 0.012 0.002 TYR B 310 ARG 0.003 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.941 Fit side-chains REVERT: A 140 ILE cc_start: 0.8160 (tp) cc_final: 0.7960 (tt) REVERT: A 580 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7059 (mp) REVERT: A 584 HIS cc_start: 0.8465 (m-70) cc_final: 0.8126 (m170) REVERT: A 644 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.6255 (t80) REVERT: B 67 MET cc_start: 0.7498 (ttt) cc_final: 0.7051 (ttt) REVERT: B 140 ILE cc_start: 0.8274 (tp) cc_final: 0.8019 (tt) REVERT: B 191 ARG cc_start: 0.7398 (mmp80) cc_final: 0.7179 (mmm160) REVERT: B 565 ASP cc_start: 0.7294 (t0) cc_final: 0.6701 (t0) REVERT: B 580 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7052 (mp) REVERT: B 584 HIS cc_start: 0.8479 (m-70) cc_final: 0.8129 (m170) REVERT: B 644 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.6353 (t80) outliers start: 25 outliers final: 21 residues processed: 149 average time/residue: 0.2300 time to fit residues: 46.4754 Evaluate side-chains 153 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 644 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9392 Z= 0.206 Angle : 0.551 9.134 12731 Z= 0.275 Chirality : 0.039 0.138 1416 Planarity : 0.004 0.042 1601 Dihedral : 7.943 89.525 1344 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.01 % Allowed : 17.67 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1130 helix: 0.67 (0.19), residues: 762 sheet: -0.39 (0.72), residues: 56 loop : -1.61 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.003 0.001 HIS B 621 PHE 0.023 0.001 PHE B 252 TYR 0.014 0.001 TYR B 337 ARG 0.003 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.025 Fit side-chains REVERT: A 580 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7072 (mp) REVERT: A 584 HIS cc_start: 0.8453 (m-70) cc_final: 0.8100 (m170) REVERT: A 644 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.6258 (t80) REVERT: B 67 MET cc_start: 0.7488 (ttt) cc_final: 0.7067 (ttt) REVERT: B 140 ILE cc_start: 0.8215 (tp) cc_final: 0.7952 (tt) REVERT: B 282 MET cc_start: 0.8052 (mtp) cc_final: 0.7480 (mmt) REVERT: B 565 ASP cc_start: 0.7326 (t0) cc_final: 0.6736 (t0) REVERT: B 580 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7061 (mp) REVERT: B 584 HIS cc_start: 0.8453 (m-70) cc_final: 0.8088 (m170) REVERT: B 644 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6284 (t80) outliers start: 29 outliers final: 18 residues processed: 151 average time/residue: 0.2251 time to fit residues: 46.2565 Evaluate side-chains 147 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 644 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.0470 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9392 Z= 0.161 Angle : 0.541 9.288 12731 Z= 0.269 Chirality : 0.039 0.141 1416 Planarity : 0.004 0.043 1601 Dihedral : 7.811 87.319 1344 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.29 % Allowed : 18.30 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1130 helix: 0.81 (0.19), residues: 764 sheet: -0.38 (0.69), residues: 62 loop : -1.65 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 137 HIS 0.003 0.001 HIS A 283 PHE 0.025 0.001 PHE B 252 TYR 0.013 0.001 TYR B 337 ARG 0.003 0.000 ARG A 538 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.023 Fit side-chains REVERT: A 282 MET cc_start: 0.7989 (mtp) cc_final: 0.7451 (mmt) REVERT: A 532 TYR cc_start: 0.8369 (m-80) cc_final: 0.8127 (m-80) REVERT: A 580 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7043 (mp) REVERT: A 584 HIS cc_start: 0.8442 (m-70) cc_final: 0.8078 (m170) REVERT: A 644 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6246 (t80) REVERT: B 67 MET cc_start: 0.7462 (ttt) cc_final: 0.7067 (ttt) REVERT: B 140 ILE cc_start: 0.8096 (tp) cc_final: 0.7864 (tt) REVERT: B 580 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.6994 (mp) REVERT: B 584 HIS cc_start: 0.8413 (m-70) cc_final: 0.8042 (m170) REVERT: B 644 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6246 (t80) outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 0.2166 time to fit residues: 43.0993 Evaluate side-chains 144 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 644 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.196279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150756 restraints weight = 10068.508| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.77 r_work: 0.3602 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9392 Z= 0.179 Angle : 0.540 9.294 12731 Z= 0.268 Chirality : 0.039 0.142 1416 Planarity : 0.004 0.042 1601 Dihedral : 7.786 86.643 1344 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.08 % Allowed : 18.09 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1130 helix: 0.89 (0.19), residues: 764 sheet: -0.34 (0.69), residues: 62 loop : -1.64 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 339 HIS 0.004 0.001 HIS B 283 PHE 0.025 0.001 PHE B 252 TYR 0.016 0.001 TYR B 620 ARG 0.003 0.000 ARG B 538 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.60 seconds wall clock time: 38 minutes 50.59 seconds (2330.59 seconds total)