Starting phenix.real_space_refine on Mon Mar 18 00:13:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/03_2024/7t6j_25716.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/03_2024/7t6j_25716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/03_2024/7t6j_25716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/03_2024/7t6j_25716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/03_2024/7t6j_25716.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/03_2024/7t6j_25716.pdb" } resolution = 3.2 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= 0.005 sd= 0.038 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 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 627": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 10.04, per 1000 atoms: 0.52 Number of scatterers: 19412 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 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 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 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: 6.05 Conformation dependent library (CDL) restraints added in 3.4 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 66.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.871A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.644A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.616A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.345A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.518A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.539A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 4.050A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.782A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.811A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.607A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 402 removed outlier: 3.948A pdb=" N LEU A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.890A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.536A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.896A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.604A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.878A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.565A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 605 removed outlier: 4.114A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.567A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.856A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.696A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.531A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 193 through 197 removed outlier: 4.342A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.531A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.520A pdb=" N GLY B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 4.039A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.770A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 308 removed outlier: 3.811A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.614A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 402 removed outlier: 3.971A pdb=" N LEU B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.883A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.536A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.959A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.605A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.884A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 536 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.523A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 605 removed outlier: 4.067A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.560A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.863A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.642A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.517A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 193 through 197 removed outlier: 4.331A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 210 through 222 removed outlier: 4.512A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.517A pdb=" N GLY C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 4.051A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.783A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 308 removed outlier: 3.797A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.592A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 402 removed outlier: 3.962A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.891A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.538A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.968A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.597A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.878A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 536 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.548A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 605 removed outlier: 4.084A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.565A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 106 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.856A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.695A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.538A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 193 through 197 removed outlier: 4.343A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 210 through 222 removed outlier: 4.528A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.511A pdb=" N GLY D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 removed outlier: 4.046A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.771A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.809A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.595A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 402 removed outlier: 3.952A pdb=" N LEU D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.884A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.537A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.934A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.602A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.887A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 536 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.603A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 605 removed outlier: 4.104A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.810A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 268 removed outlier: 6.814A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.813A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 268 removed outlier: 6.814A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1061 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 6.65 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: 6145 1.34 - 1.46: 4426 1.46 - 1.58: 9061 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" SD MET A 554 " pdb=" CE MET A 554 " ideal model delta sigma weight residual 1.791 1.728 0.063 2.50e-02 1.60e+03 6.44e+00 bond pdb=" C VAL D 452 " pdb=" N PRO D 453 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.23e-02 6.61e+03 6.31e+00 bond pdb=" C ILE D 404 " pdb=" N PRO D 405 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.15e+00 bond pdb=" C ILE B 404 " pdb=" N PRO B 405 " ideal model delta sigma weight residual 1.335 1.369 -0.033 1.36e-02 5.41e+03 6.03e+00 bond pdb=" C ILE C 404 " pdb=" N PRO C 405 " ideal model delta sigma weight residual 1.335 1.369 -0.033 1.36e-02 5.41e+03 5.97e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 95.17 - 103.40: 226 103.40 - 111.64: 8424 111.64 - 119.88: 9284 119.88 - 128.11: 8833 128.11 - 136.35: 197 Bond angle restraints: 26964 Sorted by residual: angle pdb=" CA LEU A 536 " pdb=" CB LEU A 536 " pdb=" CG LEU A 536 " ideal model delta sigma weight residual 116.30 134.74 -18.44 3.50e+00 8.16e-02 2.78e+01 angle pdb=" CA LEU C 536 " pdb=" CB LEU C 536 " pdb=" CG LEU C 536 " ideal model delta sigma weight residual 116.30 134.55 -18.25 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU D 536 " pdb=" CB LEU D 536 " pdb=" CG LEU D 536 " ideal model delta sigma weight residual 116.30 134.40 -18.10 3.50e+00 8.16e-02 2.67e+01 angle pdb=" CA LEU B 536 " pdb=" CB LEU B 536 " pdb=" CG LEU B 536 " ideal model delta sigma weight residual 116.30 134.26 -17.96 3.50e+00 8.16e-02 2.63e+01 angle pdb=" C GLU B 403 " pdb=" N ILE B 404 " pdb=" CA ILE B 404 " ideal model delta sigma weight residual 120.24 123.47 -3.23 6.30e-01 2.52e+00 2.63e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10523 18.00 - 35.99: 1041 35.99 - 53.99: 188 53.99 - 71.98: 44 71.98 - 89.98: 16 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ASP B 406 " pdb=" C ASP B 406 " pdb=" N ILE B 407 " pdb=" CA ILE B 407 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP C 406 " pdb=" C ASP C 406 " pdb=" N ILE C 407 " pdb=" CA ILE C 407 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASP D 406 " pdb=" C ASP D 406 " pdb=" N ILE D 407 " pdb=" CA ILE D 407 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2915 0.117 - 0.234: 140 0.234 - 0.350: 11 0.350 - 0.467: 2 0.467 - 0.584: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL A 585 " pdb=" CA VAL A 585 " pdb=" CG1 VAL A 585 " pdb=" CG2 VAL A 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" CB VAL B 585 " pdb=" CA VAL B 585 " pdb=" CG1 VAL B 585 " pdb=" CG2 VAL B 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CB VAL D 585 " pdb=" CA VAL D 585 " pdb=" CG1 VAL D 585 " pdb=" CG2 VAL D 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.24e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 487 " 0.018 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE A 487 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 487 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 487 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 487 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 487 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 487 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 574 " 0.020 2.00e-02 2.50e+03 1.83e-02 5.86e+00 pdb=" CG PHE B 574 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 574 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 574 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 574 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 574 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 311 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 312 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.035 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6276 2.85 - 3.36: 17954 3.36 - 3.88: 32373 3.88 - 4.39: 37671 4.39 - 4.90: 64067 Nonbonded interactions: 158341 Sorted by model distance: nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.340 2.440 nonbonded pdb=" O MET C 577 " pdb=" OG1 THR C 581 " model vdw 2.342 2.440 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.342 2.440 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.351 2.440 nonbonded pdb=" O MET A 577 " pdb=" OG1 THR A 581 " model vdw 2.361 2.440 ... (remaining 158336 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 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.030 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 47.640 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.005 0.065 19860 Z= 0.340 Angle : 1.093 18.443 26964 Z= 0.556 Chirality : 0.061 0.584 3072 Planarity : 0.008 0.060 3416 Dihedral : 14.919 89.976 7236 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.16 % Favored : 96.68 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.09 % 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: -3.33 (0.13), residues: 2408 helix: -2.38 (0.10), residues: 1420 sheet: -0.78 (0.48), residues: 92 loop : -1.75 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 268 HIS 0.005 0.001 HIS C 201 PHE 0.055 0.003 PHE A 487 TYR 0.017 0.002 TYR B 547 ARG 0.005 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 339 time to evaluate : 1.934 Fit side-chains REVERT: A 177 GLU cc_start: 0.7814 (mp0) cc_final: 0.7501 (pm20) REVERT: A 255 MET cc_start: 0.8830 (tpp) cc_final: 0.8623 (tpp) REVERT: A 302 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7474 (ttm-80) REVERT: A 481 MET cc_start: 0.8743 (tpt) cc_final: 0.8306 (tpt) REVERT: B 55 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 177 GLU cc_start: 0.7800 (mp0) cc_final: 0.7535 (pm20) REVERT: B 302 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7467 (ttm-80) REVERT: B 440 MET cc_start: 0.7935 (ttp) cc_final: 0.7628 (ttp) REVERT: B 481 MET cc_start: 0.8731 (tpt) cc_final: 0.8273 (tpt) REVERT: C 177 GLU cc_start: 0.7822 (mp0) cc_final: 0.7514 (pm20) REVERT: C 302 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7479 (ttm-80) REVERT: D 177 GLU cc_start: 0.7801 (mp0) cc_final: 0.7532 (pm20) REVERT: D 302 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7470 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.2811 time to fit residues: 149.3192 Evaluate side-chains 244 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 261 GLN A 513 GLN A 635 ASN B 197 ASN B 208 ASN B 261 GLN B 513 GLN B 635 ASN C 197 ASN C 208 ASN C 214 GLN C 261 GLN C 513 GLN D 197 ASN D 208 ASN D 261 GLN D 513 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19860 Z= 0.399 Angle : 0.706 11.747 26964 Z= 0.353 Chirality : 0.046 0.228 3072 Planarity : 0.005 0.040 3416 Dihedral : 4.842 22.560 2644 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.53 % Allowed : 8.78 % Favored : 89.69 % 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: -1.03 (0.16), residues: 2408 helix: -0.31 (0.13), residues: 1472 sheet: -0.70 (0.51), residues: 92 loop : -1.13 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 321 HIS 0.008 0.001 HIS C 426 PHE 0.019 0.002 PHE B 574 TYR 0.011 0.002 TYR A 526 ARG 0.005 0.000 ARG D 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 242 time to evaluate : 2.166 Fit side-chains REVERT: A 288 GLU cc_start: 0.7220 (tp30) cc_final: 0.6991 (tp30) REVERT: B 481 MET cc_start: 0.8825 (tpt) cc_final: 0.8485 (tpt) REVERT: B 603 MET cc_start: 0.8297 (tmm) cc_final: 0.8082 (ttp) REVERT: C 177 GLU cc_start: 0.7896 (mp0) cc_final: 0.7685 (pm20) REVERT: C 288 GLU cc_start: 0.7240 (tp30) cc_final: 0.7015 (tp30) REVERT: D 55 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7516 (mm-30) outliers start: 32 outliers final: 16 residues processed: 260 average time/residue: 0.2790 time to fit residues: 115.4089 Evaluate side-chains 231 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 252 ASN C 252 ASN C 596 GLN D 252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19860 Z= 0.166 Angle : 0.558 10.133 26964 Z= 0.273 Chirality : 0.039 0.198 3072 Planarity : 0.004 0.037 3416 Dihedral : 4.390 19.919 2644 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.10 % Allowed : 12.60 % Favored : 86.31 % 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: -0.03 (0.17), residues: 2408 helix: 0.56 (0.13), residues: 1464 sheet: -0.81 (0.47), residues: 92 loop : -0.82 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.004 0.001 HIS D 426 PHE 0.015 0.001 PHE C 574 TYR 0.007 0.001 TYR A 547 ARG 0.002 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 2.408 Fit side-chains REVERT: D 262 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8435 (mtmt) REVERT: D 554 MET cc_start: 0.8690 (tpp) cc_final: 0.8475 (tpt) outliers start: 23 outliers final: 15 residues processed: 252 average time/residue: 0.2696 time to fit residues: 107.7538 Evaluate side-chains 224 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 310 GLN A 596 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 596 GLN C 635 ASN D 310 GLN D 635 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19860 Z= 0.257 Angle : 0.578 9.757 26964 Z= 0.286 Chirality : 0.041 0.197 3072 Planarity : 0.004 0.036 3416 Dihedral : 4.338 19.686 2644 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.57 % Allowed : 14.60 % Favored : 83.83 % 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: 0.32 (0.17), residues: 2408 helix: 0.85 (0.13), residues: 1488 sheet: -0.90 (0.45), residues: 92 loop : -0.69 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 593 HIS 0.004 0.001 HIS B 426 PHE 0.020 0.001 PHE B 574 TYR 0.008 0.001 TYR D 89 ARG 0.003 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 213 time to evaluate : 2.181 Fit side-chains REVERT: A 262 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8358 (mtmt) REVERT: A 481 MET cc_start: 0.8841 (tpp) cc_final: 0.8546 (tpt) REVERT: C 262 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8351 (mtmt) REVERT: D 262 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8313 (mtmt) outliers start: 33 outliers final: 20 residues processed: 234 average time/residue: 0.2820 time to fit residues: 105.1415 Evaluate side-chains 233 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 213 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 419 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.0870 chunk 131 optimal weight: 0.0050 chunk 3 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 0.0270 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 overall best weight: 0.2830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19860 Z= 0.122 Angle : 0.503 7.732 26964 Z= 0.248 Chirality : 0.038 0.174 3072 Planarity : 0.003 0.037 3416 Dihedral : 4.015 18.018 2644 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.10 % Allowed : 15.74 % 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: 0.85 (0.17), residues: 2408 helix: 1.32 (0.14), residues: 1476 sheet: -0.88 (0.45), residues: 92 loop : -0.53 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.002 0.000 HIS D 426 PHE 0.026 0.001 PHE C 574 TYR 0.005 0.001 TYR A 547 ARG 0.001 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 2.160 Fit side-chains REVERT: A 262 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8317 (mtmt) REVERT: A 481 MET cc_start: 0.8818 (tpp) cc_final: 0.8576 (tpt) REVERT: B 481 MET cc_start: 0.8852 (tpp) cc_final: 0.8603 (tpt) REVERT: B 554 MET cc_start: 0.8260 (tpt) cc_final: 0.8052 (tpt) REVERT: C 262 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8328 (mtmt) REVERT: D 262 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8343 (mtmt) REVERT: D 522 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8159 (mp0) outliers start: 23 outliers final: 12 residues processed: 256 average time/residue: 0.2723 time to fit residues: 111.0501 Evaluate side-chains 231 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 218 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19860 Z= 0.143 Angle : 0.503 7.617 26964 Z= 0.247 Chirality : 0.038 0.174 3072 Planarity : 0.003 0.039 3416 Dihedral : 3.924 17.223 2644 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.57 % Allowed : 16.51 % Favored : 81.92 % 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: 1.14 (0.18), residues: 2408 helix: 1.63 (0.14), residues: 1464 sheet: -0.82 (0.45), residues: 92 loop : -0.55 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 593 HIS 0.002 0.000 HIS B 426 PHE 0.013 0.001 PHE D 115 TYR 0.006 0.001 TYR C 89 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 2.227 Fit side-chains REVERT: A 262 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8319 (mtmt) REVERT: A 481 MET cc_start: 0.8877 (tpp) cc_final: 0.8646 (tpt) REVERT: A 522 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: B 481 MET cc_start: 0.8858 (tpp) cc_final: 0.8583 (tpt) REVERT: B 501 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8567 (mp) REVERT: B 522 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: C 262 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8324 (mtmt) REVERT: C 481 MET cc_start: 0.8879 (tpp) cc_final: 0.8625 (tpt) REVERT: C 522 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: D 501 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8598 (mp) outliers start: 33 outliers final: 20 residues processed: 257 average time/residue: 0.2803 time to fit residues: 114.4480 Evaluate side-chains 251 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 501 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.188 Angle : 0.528 7.476 26964 Z= 0.259 Chirality : 0.039 0.180 3072 Planarity : 0.003 0.040 3416 Dihedral : 3.970 17.810 2644 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.57 % Allowed : 16.79 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2408 helix: 1.67 (0.14), residues: 1472 sheet: -0.88 (0.44), residues: 92 loop : -0.49 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 593 HIS 0.002 0.000 HIS C 426 PHE 0.025 0.001 PHE B 574 TYR 0.007 0.001 TYR A 547 ARG 0.002 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 219 time to evaluate : 2.154 Fit side-chains REVERT: A 262 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8414 (mtmt) REVERT: A 481 MET cc_start: 0.8903 (tpp) cc_final: 0.8612 (tpt) REVERT: A 522 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: B 481 MET cc_start: 0.8865 (tpp) cc_final: 0.8611 (tpt) REVERT: B 501 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8586 (mp) REVERT: B 522 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: C 262 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8298 (mtmt) REVERT: C 481 MET cc_start: 0.8883 (tpp) cc_final: 0.8629 (tpt) REVERT: C 522 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: D 501 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8611 (mp) outliers start: 33 outliers final: 23 residues processed: 244 average time/residue: 0.2796 time to fit residues: 108.3548 Evaluate side-chains 243 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 501 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19860 Z= 0.197 Angle : 0.541 10.348 26964 Z= 0.264 Chirality : 0.039 0.182 3072 Planarity : 0.003 0.040 3416 Dihedral : 4.017 20.174 2644 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.57 % Allowed : 16.79 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2408 helix: 1.68 (0.14), residues: 1484 sheet: -0.91 (0.43), residues: 92 loop : -0.45 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 583 HIS 0.003 0.001 HIS B 201 PHE 0.012 0.001 PHE A 574 TYR 0.008 0.001 TYR A 547 ARG 0.002 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 2.466 Fit side-chains REVERT: A 262 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8277 (mtmt) REVERT: A 481 MET cc_start: 0.8917 (tpp) cc_final: 0.8670 (tpt) REVERT: A 522 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: B 262 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8437 (mtmt) REVERT: B 481 MET cc_start: 0.8861 (tpp) cc_final: 0.8548 (tpt) REVERT: B 501 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8564 (mp) REVERT: B 522 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: C 262 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8423 (mtmt) REVERT: C 481 MET cc_start: 0.8886 (tpp) cc_final: 0.8615 (tpt) REVERT: C 522 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: D 501 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8571 (mp) REVERT: D 522 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8188 (mp0) outliers start: 33 outliers final: 23 residues processed: 243 average time/residue: 0.2836 time to fit residues: 109.3675 Evaluate side-chains 243 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 522 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 202 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19860 Z= 0.182 Angle : 0.539 10.032 26964 Z= 0.262 Chirality : 0.039 0.180 3072 Planarity : 0.003 0.040 3416 Dihedral : 4.001 18.941 2644 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.57 % Allowed : 16.89 % Favored : 81.54 % 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: 1.33 (0.18), residues: 2408 helix: 1.77 (0.14), residues: 1476 sheet: -0.94 (0.43), residues: 92 loop : -0.45 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 593 HIS 0.002 0.001 HIS C 426 PHE 0.028 0.001 PHE C 574 TYR 0.007 0.001 TYR D 547 ARG 0.002 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 215 time to evaluate : 2.352 Fit side-chains REVERT: A 262 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8410 (mtmt) REVERT: A 481 MET cc_start: 0.8913 (tpp) cc_final: 0.8641 (tpt) REVERT: A 522 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 262 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8262 (mtmt) REVERT: B 481 MET cc_start: 0.8828 (tpp) cc_final: 0.8514 (tpt) REVERT: B 501 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8539 (mp) REVERT: B 522 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: C 262 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8419 (mtmt) REVERT: C 481 MET cc_start: 0.8885 (tpp) cc_final: 0.8611 (tpt) REVERT: C 522 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: D 501 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8551 (mp) REVERT: D 522 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8184 (mp0) outliers start: 33 outliers final: 24 residues processed: 240 average time/residue: 0.2942 time to fit residues: 111.9220 Evaluate side-chains 244 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 522 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 108 optimal weight: 0.2980 chunk 158 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19860 Z= 0.157 Angle : 0.526 9.369 26964 Z= 0.255 Chirality : 0.038 0.175 3072 Planarity : 0.003 0.040 3416 Dihedral : 3.946 18.347 2644 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.48 % Allowed : 17.08 % Favored : 81.44 % 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: 1.39 (0.18), residues: 2408 helix: 1.82 (0.14), residues: 1476 sheet: -0.86 (0.44), residues: 92 loop : -0.43 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 593 HIS 0.002 0.000 HIS C 426 PHE 0.026 0.001 PHE C 574 TYR 0.007 0.001 TYR D 555 ARG 0.002 0.000 ARG A 589 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 224 time to evaluate : 2.322 Fit side-chains REVERT: A 262 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8386 (mtmt) REVERT: A 481 MET cc_start: 0.8907 (tpp) cc_final: 0.8643 (tpt) REVERT: A 522 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: B 262 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8219 (mtmt) REVERT: B 501 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8506 (mp) REVERT: B 522 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: C 262 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8374 (mtmt) REVERT: C 481 MET cc_start: 0.8892 (tpp) cc_final: 0.8609 (tpt) REVERT: C 522 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: D 501 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 522 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8182 (mp0) outliers start: 31 outliers final: 22 residues processed: 245 average time/residue: 0.2875 time to fit residues: 112.2494 Evaluate side-chains 236 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 522 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 58 optimal weight: 0.0570 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 0.0570 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 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 = 0.3399 r_free = 0.3399 target = 0.120138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099702 restraints weight = 28204.137| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.52 r_work: 0.3006 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19860 Z= 0.132 Angle : 0.510 8.869 26964 Z= 0.247 Chirality : 0.037 0.169 3072 Planarity : 0.003 0.040 3416 Dihedral : 3.838 17.136 2644 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.29 % Allowed : 17.46 % Favored : 81.25 % 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: 1.52 (0.18), residues: 2408 helix: 1.93 (0.14), residues: 1472 sheet: -0.69 (0.45), residues: 92 loop : -0.40 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 593 HIS 0.002 0.000 HIS C 426 PHE 0.026 0.001 PHE C 574 TYR 0.007 0.001 TYR B 555 ARG 0.002 0.000 ARG B 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3716.18 seconds wall clock time: 68 minutes 6.64 seconds (4086.64 seconds total)