Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 20:58:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2023/7kcl_22812_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2023/7kcl_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_2023/7kcl_22812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2023/7kcl_22812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2023/7kcl_22812_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcl_22812/04_2023/7kcl_22812_updated.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.75, 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: 4.35 Conformation dependent library (CDL) restraints added in 1.5 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: 1.24 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: 2.88 Time building geometry restraints manager: 4.56 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: 5539 17.96 - 35.92: 545 35.92 - 53.87: 109 53.87 - 71.83: 30 71.83 - 89.79: 17 Dihedral angle restraints: 6240 sinusoidal: 2571 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 6237 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: 2.590 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: 7.940 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.870 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- 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 : 15.740 89.789 3856 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 % 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 *********************** 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 : 1.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2326 time to fit residues: 48.6607 Evaluate side-chains 129 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6846 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.0684 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= 0.183 Angle : 0.482 7.662 13813 Z= 0.247 Chirality : 0.041 0.175 1557 Planarity : 0.003 0.034 1752 Dihedral : 4.786 59.620 1371 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.24), residues: 1231 helix: 0.61 (0.23), residues: 522 sheet: 0.55 (0.40), residues: 175 loop : -0.75 (0.28), residues: 534 *********************** 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 142 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.191 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 141 average time/residue: 0.2356 time to fit residues: 46.8700 Evaluate side-chains 127 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1039 time to fit residues: 2.4539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10234 Z= 0.249 Angle : 0.510 7.237 13813 Z= 0.262 Chirality : 0.041 0.161 1557 Planarity : 0.003 0.037 1752 Dihedral : 4.855 58.467 1371 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.64 % 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: 0.60 (0.23), residues: 525 sheet: 0.50 (0.40), residues: 174 loop : -0.77 (0.27), residues: 532 *********************** 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 139 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.274 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 137 average time/residue: 0.2454 time to fit residues: 47.1539 Evaluate side-chains 119 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1011 time to fit residues: 2.2582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8208 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10234 Z= 0.182 Angle : 0.487 7.104 13813 Z= 0.250 Chirality : 0.040 0.169 1557 Planarity : 0.003 0.029 1752 Dihedral : 4.689 59.027 1371 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.92 % 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: -0.10 (0.24), residues: 1231 helix: 0.50 (0.23), residues: 539 sheet: 0.54 (0.39), residues: 180 loop : -0.82 (0.28), residues: 512 *********************** 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 136 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.226 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 134 average time/residue: 0.2426 time to fit residues: 45.6042 Evaluate side-chains 128 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0914 time to fit residues: 2.3928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 10234 Z= 0.372 Angle : 0.574 7.365 13813 Z= 0.292 Chirality : 0.043 0.193 1557 Planarity : 0.004 0.028 1752 Dihedral : 5.028 59.182 1371 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.92 % 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: -0.30 (0.24), residues: 1231 helix: 0.38 (0.22), residues: 535 sheet: 0.21 (0.37), residues: 187 loop : -0.88 (0.28), residues: 509 *********************** 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 132 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.177 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 131 average time/residue: 0.2435 time to fit residues: 44.9455 Evaluate side-chains 119 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0990 time to fit residues: 2.3922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10234 Z= 0.155 Angle : 0.491 6.818 13813 Z= 0.250 Chirality : 0.040 0.134 1557 Planarity : 0.003 0.027 1752 Dihedral : 4.725 58.597 1371 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.92 % 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: -0.19 (0.24), residues: 1231 helix: 0.44 (0.23), residues: 538 sheet: 0.34 (0.38), residues: 186 loop : -0.83 (0.28), residues: 507 *********************** 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 141 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.356 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 139 average time/residue: 0.2502 time to fit residues: 49.0339 Evaluate side-chains 125 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0966 time to fit residues: 2.0440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 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: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8300 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 10234 Z= 0.353 Angle : 0.584 9.311 13813 Z= 0.294 Chirality : 0.043 0.144 1557 Planarity : 0.003 0.026 1752 Dihedral : 5.014 59.533 1371 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.92 % 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: -0.24 (0.24), residues: 1231 helix: 0.38 (0.22), residues: 536 sheet: 0.20 (0.38), residues: 187 loop : -0.78 (0.28), residues: 508 *********************** 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 128 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.247 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 122 average time/residue: 0.2641 time to fit residues: 44.6016 Evaluate side-chains 120 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1039 time to fit residues: 2.4664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.0370 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.0470 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10234 Z= 0.144 Angle : 0.509 9.882 13813 Z= 0.257 Chirality : 0.040 0.137 1557 Planarity : 0.003 0.026 1752 Dihedral : 4.680 56.699 1371 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.55 % 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: -0.13 (0.24), residues: 1231 helix: 0.46 (0.23), residues: 536 sheet: 0.41 (0.39), residues: 186 loop : -0.77 (0.28), residues: 509 *********************** 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 139 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.294 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 138 average time/residue: 0.2523 time to fit residues: 48.7401 Evaluate side-chains 123 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0938 time to fit residues: 1.8327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- 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 636 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: 0.8274 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10234 Z= 0.274 Angle : 0.568 9.703 13813 Z= 0.283 Chirality : 0.041 0.142 1557 Planarity : 0.003 0.049 1752 Dihedral : 4.869 59.129 1371 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.37 % 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: -0.25 (0.24), residues: 1231 helix: 0.37 (0.22), residues: 544 sheet: 0.30 (0.38), residues: 187 loop : -0.84 (0.28), residues: 500 *********************** 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 125 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.247 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 123 average time/residue: 0.2602 time to fit residues: 44.4858 Evaluate side-chains 118 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0941 time to fit residues: 1.8960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8231 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10234 Z= 0.177 Angle : 0.535 9.983 13813 Z= 0.266 Chirality : 0.040 0.137 1557 Planarity : 0.003 0.052 1752 Dihedral : 4.687 57.278 1371 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.09 % 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: -0.13 (0.24), residues: 1231 helix: 0.47 (0.23), residues: 530 sheet: 0.42 (0.39), residues: 186 loop : -0.77 (0.28), residues: 515 ********************** 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 124 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.245 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.2602 time to fit residues: 44.5142 Evaluate side-chains 123 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1345 time to fit residues: 1.9201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108718 restraints weight = 13995.467| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.16 r_work: 0.3212 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10234 Z= 0.162 Angle : 0.530 10.553 13813 Z= 0.262 Chirality : 0.040 0.136 1557 Planarity : 0.003 0.047 1752 Dihedral : 4.507 53.908 1371 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.18 % 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: -0.07 (0.24), residues: 1231 helix: 0.52 (0.23), residues: 530 sheet: 0.49 (0.39), residues: 186 loop : -0.76 (0.28), residues: 515 =============================================================================== Job complete usr+sys time: 2298.95 seconds wall clock time: 42 minutes 39.38 seconds (2559.38 seconds total)