Starting phenix.real_space_refine on Fri Mar 15 11:26:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/03_2024/7fd9_31537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/03_2024/7fd9_31537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/03_2024/7fd9_31537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/03_2024/7fd9_31537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/03_2024/7fd9_31537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/03_2024/7fd9_31537_updated.pdb" } resolution = 4.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 7384 2.51 5 N 1916 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 357": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5698 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 32, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 194 Chain: "B" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5698 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 32, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 194 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.99, per 1000 atoms: 0.52 Number of scatterers: 11476 At special positions: 0 Unit cell: (79.21, 112.14, 178.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 2066 8.00 N 1916 7.00 C 7384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.04 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.04 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.02 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.05 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.04 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 1.9 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 14 sheets defined 45.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 102 through 119 Processing helix chain 'A' and resid 152 through 165 removed outlier: 4.419A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.818A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.405A pdb=" N HIS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.509A pdb=" N GLN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 418 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 434 through 442 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 578 through 603 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 617 through 635 Processing helix chain 'A' and resid 641 through 672 removed outlier: 3.914A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 693 through 714 removed outlier: 3.573A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 761 Proline residue: A 743 - end of helix removed outlier: 3.985A pdb=" N LYS A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 No H-bonds generated for 'chain 'A' and resid 766 through 769' Processing helix chain 'A' and resid 771 through 793 Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 798 through 817 Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 102 through 119 Processing helix chain 'B' and resid 152 through 165 removed outlier: 4.419A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.817A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.405A pdb=" N HIS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.509A pdb=" N GLN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 418 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 434 through 442 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 578 through 603 Processing helix chain 'B' and resid 608 through 612 Processing helix chain 'B' and resid 617 through 635 Processing helix chain 'B' and resid 641 through 672 removed outlier: 3.913A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix Processing helix chain 'B' and resid 693 through 714 removed outlier: 3.573A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 761 Proline residue: B 743 - end of helix removed outlier: 3.986A pdb=" N LYS B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 769 No H-bonds generated for 'chain 'B' and resid 766 through 769' Processing helix chain 'B' and resid 771 through 793 Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 798 through 817 Processing helix chain 'B' and resid 819 through 825 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.392A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 38 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 146 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 40 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 245 through 248 removed outlier: 7.016A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 302 " --> pdb=" O CYS A 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 325 through 329 removed outlier: 3.627A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.838A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 469 through 472 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 558 Processing sheet with id= G, first strand: chain 'A' and resid 720 through 722 Processing sheet with id= H, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.393A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY B 38 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 146 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 40 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 245 through 248 removed outlier: 7.017A pdb=" N ALA B 216 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS B 218 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 302 " --> pdb=" O CYS B 276 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.626A pdb=" N GLY B 485 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 445 through 447 removed outlier: 3.838A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 469 through 472 Processing sheet with id= M, first strand: chain 'B' and resid 556 through 558 Processing sheet with id= N, first strand: chain 'B' and resid 720 through 722 532 hydrogen bonds defined for protein. 1464 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: 3.36 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: 1.22 - 1.34: 3604 1.34 - 1.47: 2964 1.47 - 1.59: 5018 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 11742 Sorted by residual: bond pdb=" CAS Z99 A 902 " pdb=" CAU Z99 A 902 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CAS Z99 B 902 " pdb=" CAU Z99 B 902 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CAT Z99 A 902 " pdb=" CAV Z99 A 902 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CAT Z99 B 902 " pdb=" CAV Z99 B 902 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C CYS B 419 " pdb=" N PRO B 420 " ideal model delta sigma weight residual 1.331 1.358 -0.026 7.90e-03 1.60e+04 1.10e+01 ... (remaining 11737 not shown) Histogram of bond angle deviations from ideal: 59.32 - 74.35: 6 74.35 - 89.38: 0 89.38 - 104.41: 213 104.41 - 119.43: 9429 119.43 - 134.46: 6356 Bond angle restraints: 16004 Sorted by residual: angle pdb=" CAN Z99 A 902 " pdb=" CAW Z99 A 902 " pdb=" CAV Z99 A 902 " ideal model delta sigma weight residual 108.20 130.06 -21.86 3.00e+00 1.11e-01 5.31e+01 angle pdb=" CAN Z99 B 902 " pdb=" CAW Z99 B 902 " pdb=" CAV Z99 B 902 " ideal model delta sigma weight residual 108.20 130.05 -21.85 3.00e+00 1.11e-01 5.30e+01 angle pdb=" CAW Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAY Z99 B 902 " ideal model delta sigma weight residual 117.71 131.39 -13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CAW Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAY Z99 A 902 " ideal model delta sigma weight residual 117.71 131.35 -13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CAT Z99 A 902 " pdb=" CAV Z99 A 902 " pdb=" CAW Z99 A 902 " ideal model delta sigma weight residual 118.77 106.06 12.71 3.00e+00 1.11e-01 1.80e+01 ... (remaining 15999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 6886 34.06 - 68.11: 102 68.11 - 102.17: 22 102.17 - 136.23: 6 136.23 - 170.28: 18 Dihedral angle restraints: 7034 sinusoidal: 2574 harmonic: 4460 Sorted by residual: dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -164.80 78.80 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -164.77 78.77 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 549 " pdb=" CB CYS B 549 " ideal model delta sinusoidal sigma weight residual 93.00 155.70 -62.70 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 7031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.536: 1844 0.536 - 1.072: 2 1.072 - 1.607: 0 1.607 - 2.143: 0 2.143 - 2.679: 2 Chirality restraints: 1848 Sorted by residual: chirality pdb=" CAW Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAU Z99 B 902 " pdb=" CAV Z99 B 902 " both_signs ideal model delta sigma weight residual False 2.61 -0.07 2.68 2.00e-01 2.50e+01 1.79e+02 chirality pdb=" CAW Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAU Z99 A 902 " pdb=" CAV Z99 A 902 " both_signs ideal model delta sigma weight residual False 2.61 -0.06 2.67 2.00e-01 2.50e+01 1.79e+02 chirality pdb=" CAY Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAR Z99 B 902 " pdb=" CAZ Z99 B 902 " both_signs ideal model delta sigma weight residual False -2.97 -2.38 -0.59 2.00e-01 2.50e+01 8.66e+00 ... (remaining 1845 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAG Z99 A 902 " 0.016 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CAI Z99 A 902 " 0.008 2.00e-02 2.50e+03 pdb=" CAK Z99 A 902 " 0.006 2.00e-02 2.50e+03 pdb=" CAM Z99 A 902 " -0.023 2.00e-02 2.50e+03 pdb=" CAT Z99 A 902 " 0.002 2.00e-02 2.50e+03 pdb=" CAV Z99 A 902 " -0.035 2.00e-02 2.50e+03 pdb=" CAW Z99 A 902 " 0.043 2.00e-02 2.50e+03 pdb=" OAP Z99 A 902 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAG Z99 B 902 " 0.016 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CAI Z99 B 902 " 0.008 2.00e-02 2.50e+03 pdb=" CAK Z99 B 902 " 0.005 2.00e-02 2.50e+03 pdb=" CAM Z99 B 902 " -0.022 2.00e-02 2.50e+03 pdb=" CAT Z99 B 902 " 0.003 2.00e-02 2.50e+03 pdb=" CAV Z99 B 902 " -0.034 2.00e-02 2.50e+03 pdb=" CAW Z99 B 902 " 0.042 2.00e-02 2.50e+03 pdb=" OAP Z99 B 902 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAF Z99 A 902 " 0.000 2.00e-02 2.50e+03 1.22e-02 3.00e+00 pdb=" CAH Z99 A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CAJ Z99 A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CAL Z99 A 902 " 0.011 2.00e-02 2.50e+03 pdb=" CAS Z99 A 902 " 0.007 2.00e-02 2.50e+03 pdb=" CAU Z99 A 902 " -0.030 2.00e-02 2.50e+03 pdb=" CAW Z99 A 902 " 0.011 2.00e-02 2.50e+03 pdb=" OAP Z99 A 902 " 0.001 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1891 2.79 - 3.32: 12126 3.32 - 3.85: 19164 3.85 - 4.37: 20848 4.37 - 4.90: 35974 Nonbonded interactions: 90003 Sorted by model distance: nonbonded pdb=" OE1 GLN A 198 " pdb=" OG SER A 304 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLN B 198 " pdb=" OG SER B 304 " model vdw 2.266 2.440 nonbonded pdb=" O SER A 116 " pdb=" OG SER A 119 " model vdw 2.288 2.440 nonbonded pdb=" O SER B 116 " pdb=" OG SER B 119 " model vdw 2.288 2.440 nonbonded pdb=" NH2 ARG B 648 " pdb=" OD1 ASN B 734 " model vdw 2.320 2.520 ... (remaining 89998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.210 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.230 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.007 0.090 11742 Z= 0.462 Angle : 1.283 21.858 16004 Z= 0.839 Chirality : 0.127 2.679 1848 Planarity : 0.003 0.023 2026 Dihedral : 17.544 170.285 4110 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.84 (0.21), residues: 1522 helix: 0.96 (0.19), residues: 700 sheet: -0.60 (0.47), residues: 124 loop : -2.22 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 532 HIS 0.004 0.002 HIS B 53 PHE 0.013 0.003 PHE B 165 TYR 0.012 0.002 TYR A 645 ARG 0.006 0.001 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 414 MET cc_start: 0.8629 (tmm) cc_final: 0.8350 (tmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1846 time to fit residues: 23.1581 Evaluate side-chains 60 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0970 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11742 Z= 0.164 Angle : 0.548 10.185 16004 Z= 0.271 Chirality : 0.043 0.233 1848 Planarity : 0.003 0.026 2026 Dihedral : 13.012 121.386 1742 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.97 % Allowed : 6.27 % Favored : 92.76 % 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: -0.41 (0.21), residues: 1522 helix: 1.29 (0.20), residues: 710 sheet: -0.62 (0.47), residues: 128 loop : -1.97 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 500 HIS 0.002 0.000 HIS A 361 PHE 0.022 0.001 PHE B 277 TYR 0.024 0.001 TYR A 340 ARG 0.003 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: A 414 MET cc_start: 0.8429 (tmm) cc_final: 0.8143 (tmm) REVERT: B 290 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7989 (mmm) REVERT: B 414 MET cc_start: 0.8572 (tmm) cc_final: 0.8077 (tmm) REVERT: B 768 PHE cc_start: 0.5738 (m-80) cc_final: 0.5513 (t80) outliers start: 11 outliers final: 1 residues processed: 70 average time/residue: 0.1689 time to fit residues: 19.1367 Evaluate side-chains 67 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 0.0670 chunk 138 optimal weight: 40.0000 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 47 optimal weight: 0.0470 chunk 110 optimal weight: 10.0000 overall best weight: 2.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11742 Z= 0.186 Angle : 0.518 8.623 16004 Z= 0.260 Chirality : 0.041 0.238 1848 Planarity : 0.003 0.026 2026 Dihedral : 9.902 124.917 1742 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.80 % Allowed : 8.39 % Favored : 90.81 % 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: -0.31 (0.21), residues: 1522 helix: 1.40 (0.19), residues: 710 sheet: -0.77 (0.45), residues: 138 loop : -1.93 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 500 HIS 0.002 0.001 HIS A 74 PHE 0.017 0.001 PHE B 277 TYR 0.015 0.001 TYR A 340 ARG 0.002 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: B 290 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8005 (mmm) REVERT: B 414 MET cc_start: 0.8585 (tmm) cc_final: 0.8196 (tmm) REVERT: B 768 PHE cc_start: 0.5769 (m-80) cc_final: 0.5561 (t80) outliers start: 9 outliers final: 2 residues processed: 66 average time/residue: 0.2010 time to fit residues: 21.9852 Evaluate side-chains 64 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.0370 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 overall best weight: 7.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 11742 Z= 0.504 Angle : 0.699 8.942 16004 Z= 0.357 Chirality : 0.045 0.247 1848 Planarity : 0.004 0.032 2026 Dihedral : 9.567 131.896 1742 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.94 % Allowed : 8.13 % Favored : 89.93 % 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: -0.64 (0.21), residues: 1522 helix: 1.10 (0.20), residues: 700 sheet: -0.88 (0.44), residues: 140 loop : -2.03 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 307 HIS 0.006 0.002 HIS A 74 PHE 0.018 0.002 PHE B 188 TYR 0.028 0.002 TYR B 340 ARG 0.006 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: A 802 MET cc_start: 0.9420 (mtt) cc_final: 0.9165 (mmm) REVERT: B 290 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8036 (mmm) REVERT: B 414 MET cc_start: 0.8649 (tmm) cc_final: 0.8298 (tmm) REVERT: B 768 PHE cc_start: 0.5737 (m-80) cc_final: 0.5499 (t80) outliers start: 22 outliers final: 8 residues processed: 77 average time/residue: 0.1827 time to fit residues: 23.3264 Evaluate side-chains 70 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 109 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 101 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 5.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11742 Z= 0.369 Angle : 0.619 9.754 16004 Z= 0.314 Chirality : 0.043 0.183 1848 Planarity : 0.004 0.027 2026 Dihedral : 9.469 133.808 1742 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.59 % Allowed : 9.36 % Favored : 89.05 % 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: -0.56 (0.21), residues: 1522 helix: 1.12 (0.19), residues: 706 sheet: -0.76 (0.44), residues: 138 loop : -1.98 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 500 HIS 0.005 0.001 HIS A 361 PHE 0.011 0.001 PHE A 277 TYR 0.024 0.001 TYR B 340 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: A 405 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 802 MET cc_start: 0.9403 (mtt) cc_final: 0.9147 (mmm) REVERT: B 290 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7991 (mmm) REVERT: B 405 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: B 414 MET cc_start: 0.8611 (tmm) cc_final: 0.8261 (tmm) REVERT: B 768 PHE cc_start: 0.5798 (m-80) cc_final: 0.5507 (t80) outliers start: 18 outliers final: 9 residues processed: 75 average time/residue: 0.1789 time to fit residues: 22.0005 Evaluate side-chains 72 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 10.0000 chunk 132 optimal weight: 40.0000 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN B 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11742 Z= 0.165 Angle : 0.536 10.284 16004 Z= 0.265 Chirality : 0.040 0.172 1848 Planarity : 0.003 0.028 2026 Dihedral : 9.155 133.504 1742 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.59 % Allowed : 9.81 % Favored : 88.60 % 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: -0.31 (0.21), residues: 1522 helix: 1.31 (0.19), residues: 716 sheet: -0.57 (0.44), residues: 138 loop : -1.88 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 500 HIS 0.003 0.001 HIS B 361 PHE 0.012 0.001 PHE A 277 TYR 0.012 0.001 TYR B 340 ARG 0.001 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 802 MET cc_start: 0.9381 (mtt) cc_final: 0.9106 (mmm) REVERT: B 290 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8013 (mmm) REVERT: B 405 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: B 414 MET cc_start: 0.8584 (tmm) cc_final: 0.8219 (tmm) outliers start: 18 outliers final: 9 residues processed: 74 average time/residue: 0.1977 time to fit residues: 23.8485 Evaluate side-chains 72 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11742 Z= 0.291 Angle : 0.585 10.261 16004 Z= 0.292 Chirality : 0.042 0.208 1848 Planarity : 0.003 0.027 2026 Dihedral : 9.056 134.946 1742 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.68 % Allowed : 10.16 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1522 helix: 1.28 (0.19), residues: 718 sheet: -0.54 (0.45), residues: 138 loop : -1.85 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 557 HIS 0.005 0.001 HIS A 74 PHE 0.010 0.001 PHE A 277 TYR 0.017 0.001 TYR B 340 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: A 802 MET cc_start: 0.9395 (mtt) cc_final: 0.9117 (mmm) REVERT: B 290 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8020 (mmm) REVERT: B 405 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: B 414 MET cc_start: 0.8599 (tmm) cc_final: 0.8227 (tmm) REVERT: B 768 PHE cc_start: 0.5808 (m-80) cc_final: 0.5500 (t80) outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.2066 time to fit residues: 24.6242 Evaluate side-chains 80 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 140 optimal weight: 40.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11742 Z= 0.262 Angle : 0.581 10.987 16004 Z= 0.287 Chirality : 0.041 0.163 1848 Planarity : 0.003 0.028 2026 Dihedral : 8.995 135.319 1742 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.68 % Allowed : 10.34 % Favored : 87.99 % 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: -0.31 (0.21), residues: 1522 helix: 1.27 (0.19), residues: 720 sheet: -0.57 (0.45), residues: 138 loop : -1.86 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 557 HIS 0.005 0.001 HIS B 74 PHE 0.009 0.001 PHE A 277 TYR 0.016 0.001 TYR B 340 ARG 0.002 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: A 405 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: B 290 MET cc_start: 0.8344 (mmp) cc_final: 0.8015 (mmm) REVERT: B 405 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: B 414 MET cc_start: 0.8601 (tmm) cc_final: 0.8230 (tmm) REVERT: B 802 MET cc_start: 0.9377 (mtt) cc_final: 0.9159 (mmm) outliers start: 19 outliers final: 14 residues processed: 76 average time/residue: 0.2071 time to fit residues: 24.7512 Evaluate side-chains 77 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11742 Z= 0.464 Angle : 0.714 12.057 16004 Z= 0.357 Chirality : 0.044 0.191 1848 Planarity : 0.004 0.029 2026 Dihedral : 9.174 136.649 1742 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.47 % Allowed : 10.42 % Favored : 87.10 % 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: -0.59 (0.22), residues: 1522 helix: 1.07 (0.20), residues: 714 sheet: -0.99 (0.46), residues: 128 loop : -1.92 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 359 HIS 0.008 0.002 HIS A 74 PHE 0.011 0.001 PHE B 363 TYR 0.025 0.002 TYR B 340 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 61 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8173 (mtt) cc_final: 0.7895 (mtt) REVERT: A 277 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: A 405 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: B 290 MET cc_start: 0.8354 (mmp) cc_final: 0.8007 (mmm) REVERT: B 405 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: B 768 PHE cc_start: 0.5762 (m-80) cc_final: 0.5439 (t80) REVERT: B 802 MET cc_start: 0.9386 (mtt) cc_final: 0.9154 (mmm) outliers start: 28 outliers final: 21 residues processed: 85 average time/residue: 0.1941 time to fit residues: 26.0013 Evaluate side-chains 84 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 60 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 50.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11742 Z= 0.161 Angle : 0.580 12.967 16004 Z= 0.283 Chirality : 0.041 0.193 1848 Planarity : 0.003 0.028 2026 Dihedral : 8.969 135.389 1742 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.12 % Allowed : 10.51 % Favored : 87.37 % 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: -0.31 (0.21), residues: 1522 helix: 1.26 (0.19), residues: 716 sheet: -0.60 (0.44), residues: 138 loop : -1.81 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 487 HIS 0.007 0.001 HIS B 218 PHE 0.008 0.001 PHE B 165 TYR 0.012 0.001 TYR A 187 ARG 0.001 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 59 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: A 405 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7326 (m-10) REVERT: B 290 MET cc_start: 0.8310 (mmp) cc_final: 0.7999 (mmm) REVERT: B 405 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: B 414 MET cc_start: 0.8545 (tmm) cc_final: 0.8281 (tmm) REVERT: B 802 MET cc_start: 0.9382 (mtt) cc_final: 0.9158 (mmm) outliers start: 24 outliers final: 16 residues processed: 79 average time/residue: 0.2113 time to fit residues: 26.0007 Evaluate side-chains 78 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 626 CYS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 50.0000 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.069651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.048384 restraints weight = 70964.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.049643 restraints weight = 36877.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050475 restraints weight = 24282.139| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11742 Z= 0.259 Angle : 0.604 12.911 16004 Z= 0.297 Chirality : 0.042 0.192 1848 Planarity : 0.003 0.028 2026 Dihedral : 8.843 136.192 1742 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.94 % Allowed : 10.51 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1522 helix: 1.25 (0.19), residues: 714 sheet: -0.63 (0.44), residues: 138 loop : -1.80 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 500 HIS 0.010 0.001 HIS B 218 PHE 0.007 0.001 PHE B 363 TYR 0.017 0.001 TYR B 340 ARG 0.002 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.18 seconds wall clock time: 33 minutes 33.82 seconds (2013.82 seconds total)