Starting phenix.real_space_refine on Sun Apr 7 13:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2024/7kcl_22812_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2024/7kcl_22812.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/7kcl_22812/04_2024/7kcl_22812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2024/7kcl_22812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2024/7kcl_22812_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2024/7kcl_22812_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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 522 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 6358 2.51 5 N 1742 2.21 5 O 1903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B ASP 557": "OD1" <-> "OD2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 658": "NH1" <-> "NH2" Residue "C GLU 154": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10057 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 186 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.78, per 1000 atoms: 0.57 Number of scatterers: 10057 At special positions: 0 Unit cell: (92.796, 91.982, 132.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 44 16.00 P 6 15.00 Mg 2 11.99 O 1903 8.00 N 1742 7.00 C 6358 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: 4.07 Conformation dependent library (CDL) restraints added in 1.7 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 8 sheets defined 41.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 109 through 134 removed outlier: 4.277A pdb=" N PHE A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 113 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 179 through 186 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 409 through 432 Processing helix chain 'A' and resid 434 through 454 removed outlier: 6.299A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 removed outlier: 4.001A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.606A pdb=" N LYS A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'A' and resid 576 through 589 removed outlier: 3.509A pdb=" N TRP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.638A pdb=" N HIS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 658 removed outlier: 3.783A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 Processing helix chain 'A' and resid 686 through 700 removed outlier: 3.512A pdb=" N VAL A 690 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 691 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 698 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 700 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 109 through 131 removed outlier: 4.004A pdb=" N PHE B 112 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 113 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 115 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 117 " --> pdb=" O ARG B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 262 through 265 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 352 through 355 No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 382 through 386 removed outlier: 4.399A pdb=" N PHE B 386 " --> pdb=" O TRP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 432 Processing helix chain 'B' and resid 434 through 454 removed outlier: 6.812A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 4.085A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 removed outlier: 3.629A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 512 through 519 removed outlier: 4.588A pdb=" N LYS B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 576 through 589 Processing helix chain 'B' and resid 615 through 624 removed outlier: 3.504A pdb=" N HIS B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 removed outlier: 3.964A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 657 removed outlier: 3.886A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 680 removed outlier: 3.512A pdb=" N GLN B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.754A pdb=" N LYS B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.197A pdb=" N TYR C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) Proline residue: C 155 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 284 through 287 removed outlier: 3.810A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 387 through 392 removed outlier: 3.548A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 546 through 549 removed outlier: 3.580A pdb=" N TYR A 499 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 608 through 611 removed outlier: 3.689A pdb=" N THR A 595 " --> pdb=" O PRO A 640 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 642 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 597 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 644 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL A 599 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 284 through 287 removed outlier: 3.899A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 363 through 366 removed outlier: 7.018A pdb=" N GLY B 389 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N TYR B 366 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 391 " --> pdb=" O TYR B 366 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 546 through 549 removed outlier: 3.601A pdb=" N TYR B 499 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 596 through 599 404 hydrogen bonds defined for protein. 1020 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: 3.10 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3313 1.34 - 1.46: 2175 1.46 - 1.58: 4658 1.58 - 1.70: 8 1.70 - 1.81: 80 Bond restraints: 10234 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 10229 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.21: 162 105.21 - 112.42: 5294 112.42 - 119.64: 3324 119.64 - 126.86: 4925 126.86 - 134.08: 108 Bond angle restraints: 13813 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 110.65 16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.80 16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 108.92 11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " pdb=" O2G ANP A 801 " ideal model delta sigma weight residual 101.05 109.79 -8.74 3.00e+00 1.11e-01 8.48e+00 ... (remaining 13808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5587 17.96 - 35.92: 547 35.92 - 53.87: 114 53.87 - 71.83: 31 71.83 - 89.79: 17 Dihedral angle restraints: 6296 sinusoidal: 2627 harmonic: 3669 Sorted by residual: dihedral pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " pdb=" CD GLU A 216 " pdb=" OE1 GLU A 216 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 415 " pdb=" CD ARG A 415 " pdb=" NE ARG A 415 " pdb=" CZ ARG A 415 " ideal model delta sinusoidal sigma weight residual 90.00 134.20 -44.20 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CB GLU A 578 " pdb=" CG GLU A 578 " pdb=" CD GLU A 578 " pdb=" OE1 GLU A 578 " ideal model delta sinusoidal sigma weight residual 0.00 -87.66 87.66 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 6293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1304 0.055 - 0.109: 227 0.109 - 0.164: 23 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE B 156 " pdb=" CA ILE B 156 " pdb=" CG1 ILE B 156 " pdb=" CG2 ILE B 156 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1554 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 639 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO B 640 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 640 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 640 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 123 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ALA A 123 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 123 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 124 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 121 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C SER A 121 " -0.022 2.00e-02 2.50e+03 pdb=" O SER A 121 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 122 " 0.007 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.63: 165 2.63 - 3.26: 10463 3.26 - 3.89: 20571 3.89 - 4.51: 28258 4.51 - 5.14: 43560 Nonbonded interactions: 103017 Sorted by model distance: nonbonded pdb=" O3G ANP B 801 " pdb="MG MG B 802 " model vdw 2.009 2.170 nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 2.011 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 802 " model vdw 2.029 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 802 " model vdw 2.061 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.089 2.170 ... (remaining 103012 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' and (resid 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 704 or resid 801 through 803)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 704 or resid 801 through 803)) } 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 7.500 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.490 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 10234 Z= 0.244 Angle : 0.621 16.305 13813 Z= 0.306 Chirality : 0.042 0.274 1557 Planarity : 0.003 0.053 1752 Dihedral : 15.769 89.789 3912 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.08 (0.24), residues: 1231 helix: 0.53 (0.23), residues: 531 sheet: 0.60 (0.41), residues: 175 loop : -0.82 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.004 0.001 HIS A 311 PHE 0.019 0.001 PHE C 146 TYR 0.010 0.001 TYR A 317 ARG 0.006 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.168 Fit side-chains REVERT: A 643 GLU cc_start: 0.7549 (mp0) cc_final: 0.7133 (mp0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2415 time to fit residues: 50.3789 Evaluate side-chains 128 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10234 Z= 0.209 Angle : 0.494 7.761 13813 Z= 0.253 Chirality : 0.041 0.181 1557 Planarity : 0.003 0.036 1752 Dihedral : 5.654 58.448 1427 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.46 % Allowed : 9.44 % Favored : 90.10 % 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: -0.02 (0.24), residues: 1231 helix: 0.60 (0.23), residues: 522 sheet: 0.56 (0.40), residues: 174 loop : -0.75 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.003 0.001 HIS A 538 PHE 0.010 0.001 PHE C 146 TYR 0.015 0.001 TYR B 218 ARG 0.004 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.249 Fit side-chains REVERT: A 643 GLU cc_start: 0.7538 (mp0) cc_final: 0.7128 (mp0) outliers start: 5 outliers final: 4 residues processed: 139 average time/residue: 0.2404 time to fit residues: 46.8103 Evaluate side-chains 127 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 379 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.0050 chunk 90 optimal weight: 2.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10234 Z= 0.206 Angle : 0.484 7.211 13813 Z= 0.248 Chirality : 0.040 0.146 1557 Planarity : 0.003 0.036 1752 Dihedral : 5.606 59.696 1427 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.82 % Allowed : 13.20 % Favored : 85.98 % 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: -0.04 (0.24), residues: 1231 helix: 0.59 (0.23), residues: 521 sheet: 0.54 (0.40), residues: 174 loop : -0.76 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 585 HIS 0.003 0.001 HIS A 538 PHE 0.007 0.001 PHE C 146 TYR 0.013 0.001 TYR B 218 ARG 0.005 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.248 Fit side-chains REVERT: A 317 TYR cc_start: 0.7904 (t80) cc_final: 0.7665 (t80) REVERT: A 643 GLU cc_start: 0.7475 (mp0) cc_final: 0.7068 (mp0) REVERT: B 156 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8402 (mt) outliers start: 9 outliers final: 5 residues processed: 132 average time/residue: 0.2328 time to fit residues: 43.5237 Evaluate side-chains 127 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 379 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10234 Z= 0.204 Angle : 0.481 6.907 13813 Z= 0.249 Chirality : 0.040 0.198 1557 Planarity : 0.003 0.029 1752 Dihedral : 5.505 57.458 1427 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.28 % Allowed : 14.30 % Favored : 84.42 % 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: -0.01 (0.24), residues: 1231 helix: 0.65 (0.23), residues: 523 sheet: 0.54 (0.40), residues: 174 loop : -0.79 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 585 HIS 0.004 0.001 HIS A 538 PHE 0.013 0.001 PHE A 112 TYR 0.012 0.001 TYR B 218 ARG 0.003 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.241 Fit side-chains REVERT: A 643 GLU cc_start: 0.7390 (mp0) cc_final: 0.6959 (mp0) REVERT: A 682 LEU cc_start: 0.8543 (mt) cc_final: 0.8339 (mt) REVERT: B 156 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8360 (mt) REVERT: B 301 MET cc_start: 0.7057 (pmm) cc_final: 0.6629 (ptt) REVERT: B 693 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8605 (tt) REVERT: B 701 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7407 (pp) outliers start: 14 outliers final: 8 residues processed: 137 average time/residue: 0.2378 time to fit residues: 45.9021 Evaluate side-chains 133 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 HIS B 530 GLN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 10234 Z= 0.458 Angle : 0.622 8.451 13813 Z= 0.318 Chirality : 0.045 0.208 1557 Planarity : 0.004 0.034 1752 Dihedral : 6.083 59.038 1427 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.38 % Allowed : 15.95 % Favored : 81.67 % 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: -0.37 (0.24), residues: 1231 helix: 0.37 (0.23), residues: 518 sheet: 0.14 (0.38), residues: 187 loop : -0.92 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 585 HIS 0.004 0.001 HIS A 606 PHE 0.014 0.002 PHE C 146 TYR 0.019 0.002 TYR B 218 ARG 0.004 0.001 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.356 Fit side-chains REVERT: A 620 HIS cc_start: 0.7982 (t-170) cc_final: 0.7625 (t-170) REVERT: A 643 GLU cc_start: 0.7353 (mp0) cc_final: 0.6955 (mp0) REVERT: B 110 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: B 693 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8625 (tt) REVERT: B 701 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7735 (pp) outliers start: 26 outliers final: 16 residues processed: 141 average time/residue: 0.2361 time to fit residues: 46.8600 Evaluate side-chains 133 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 293 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10234 Z= 0.180 Angle : 0.490 6.559 13813 Z= 0.254 Chirality : 0.040 0.185 1557 Planarity : 0.003 0.026 1752 Dihedral : 5.621 58.121 1427 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.65 % Allowed : 16.77 % Favored : 81.58 % 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: -0.27 (0.24), residues: 1231 helix: 0.38 (0.23), residues: 538 sheet: 0.30 (0.39), residues: 186 loop : -0.88 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 585 HIS 0.003 0.001 HIS A 538 PHE 0.007 0.001 PHE A 386 TYR 0.012 0.001 TYR B 437 ARG 0.004 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.195 Fit side-chains REVERT: A 682 LEU cc_start: 0.8631 (mt) cc_final: 0.8417 (mt) REVERT: B 110 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: B 156 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8337 (mt) REVERT: B 657 LEU cc_start: 0.7913 (mm) cc_final: 0.7416 (tt) REVERT: B 693 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8581 (tt) REVERT: B 701 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7496 (pp) outliers start: 18 outliers final: 9 residues processed: 149 average time/residue: 0.2332 time to fit residues: 49.3067 Evaluate side-chains 134 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10234 Z= 0.373 Angle : 0.583 7.056 13813 Z= 0.299 Chirality : 0.044 0.190 1557 Planarity : 0.004 0.027 1752 Dihedral : 5.951 58.466 1427 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.66 % Allowed : 16.87 % Favored : 80.48 % 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: -0.43 (0.24), residues: 1231 helix: 0.26 (0.22), residues: 527 sheet: 0.11 (0.38), residues: 187 loop : -0.90 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 585 HIS 0.005 0.001 HIS A 538 PHE 0.011 0.002 PHE B 264 TYR 0.022 0.002 TYR B 218 ARG 0.005 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.240 Fit side-chains REVERT: B 352 MET cc_start: 0.7815 (tpp) cc_final: 0.7611 (tpt) REVERT: B 657 LEU cc_start: 0.8042 (mm) cc_final: 0.7814 (mm) REVERT: B 693 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8613 (tt) REVERT: B 701 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7710 (pp) outliers start: 29 outliers final: 17 residues processed: 139 average time/residue: 0.2362 time to fit residues: 45.8870 Evaluate side-chains 133 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 279 ASN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10234 Z= 0.160 Angle : 0.510 6.804 13813 Z= 0.263 Chirality : 0.040 0.166 1557 Planarity : 0.003 0.026 1752 Dihedral : 5.531 55.871 1427 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.83 % Allowed : 17.78 % Favored : 80.38 % 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: -0.29 (0.24), residues: 1231 helix: 0.34 (0.22), residues: 536 sheet: 0.29 (0.39), residues: 186 loop : -0.85 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 585 HIS 0.008 0.001 HIS A 620 PHE 0.007 0.001 PHE A 386 TYR 0.031 0.001 TYR B 218 ARG 0.003 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.341 Fit side-chains REVERT: A 643 GLU cc_start: 0.7430 (mp0) cc_final: 0.6994 (mp0) REVERT: A 682 LEU cc_start: 0.8603 (mt) cc_final: 0.8395 (mt) REVERT: B 156 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 657 LEU cc_start: 0.7917 (mm) cc_final: 0.7414 (tt) REVERT: B 693 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8550 (tt) REVERT: B 701 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7489 (pp) outliers start: 20 outliers final: 11 residues processed: 146 average time/residue: 0.2360 time to fit residues: 48.4801 Evaluate side-chains 136 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.0000 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 636 GLN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10234 Z= 0.278 Angle : 0.558 8.739 13813 Z= 0.283 Chirality : 0.042 0.190 1557 Planarity : 0.003 0.024 1752 Dihedral : 5.699 58.354 1427 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.92 % Allowed : 18.24 % Favored : 79.84 % 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: -0.30 (0.24), residues: 1231 helix: 0.35 (0.22), residues: 531 sheet: 0.26 (0.38), residues: 186 loop : -0.86 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 585 HIS 0.025 0.001 HIS A 620 PHE 0.019 0.001 PHE C 146 TYR 0.026 0.002 TYR B 218 ARG 0.003 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.282 Fit side-chains REVERT: A 295 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8430 (tt) REVERT: B 580 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7171 (mm-30) REVERT: B 657 LEU cc_start: 0.7983 (mm) cc_final: 0.7456 (tt) REVERT: B 693 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8605 (tt) REVERT: B 701 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7589 (pp) outliers start: 21 outliers final: 15 residues processed: 139 average time/residue: 0.2585 time to fit residues: 49.7892 Evaluate side-chains 134 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10234 Z= 0.245 Angle : 0.547 8.285 13813 Z= 0.278 Chirality : 0.041 0.182 1557 Planarity : 0.003 0.026 1752 Dihedral : 5.678 58.044 1427 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.92 % Allowed : 18.24 % Favored : 79.84 % 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: -0.30 (0.24), residues: 1231 helix: 0.34 (0.23), residues: 532 sheet: 0.27 (0.38), residues: 186 loop : -0.85 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 585 HIS 0.023 0.001 HIS A 620 PHE 0.009 0.001 PHE A 112 TYR 0.022 0.001 TYR B 218 ARG 0.003 0.000 ARG B 495 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.243 Fit side-chains REVERT: A 295 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 517 MET cc_start: 0.6349 (tpp) cc_final: 0.5888 (tpp) REVERT: B 580 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7200 (mm-30) REVERT: B 657 LEU cc_start: 0.7977 (mm) cc_final: 0.7449 (tt) REVERT: B 693 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8596 (tt) REVERT: B 701 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7566 (pp) outliers start: 21 outliers final: 17 residues processed: 136 average time/residue: 0.2460 time to fit residues: 46.7501 Evaluate side-chains 138 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.4980 chunk 30 optimal weight: 0.0010 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106821 restraints weight = 14004.072| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.28 r_work: 0.3173 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10234 Z= 0.174 Angle : 0.524 8.054 13813 Z= 0.266 Chirality : 0.040 0.169 1557 Planarity : 0.003 0.026 1752 Dihedral : 5.509 54.946 1427 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.02 % Allowed : 18.06 % Favored : 79.93 % 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: -0.20 (0.24), residues: 1231 helix: 0.40 (0.23), residues: 531 sheet: 0.35 (0.39), residues: 186 loop : -0.79 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 585 HIS 0.022 0.001 HIS A 620 PHE 0.009 0.001 PHE A 112 TYR 0.028 0.001 TYR B 218 ARG 0.003 0.000 ARG B 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.04 seconds wall clock time: 47 minutes 10.92 seconds (2830.92 seconds total)