Starting phenix.real_space_refine on Wed May 8 21:46:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woq_37695/05_2024/8woq_37695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woq_37695/05_2024/8woq_37695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woq_37695/05_2024/8woq_37695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woq_37695/05_2024/8woq_37695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woq_37695/05_2024/8woq_37695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woq_37695/05_2024/8woq_37695_updated.pdb" } resolution = 2.85 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= 0.013 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 S 60 5.16 5 C 7539 2.51 5 N 1696 2.21 5 O 1919 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 ASP 196": "OD1" <-> "OD2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 791": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11218 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "B" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.85, per 1000 atoms: 0.97 Number of scatterers: 11218 At special positions: 0 Unit cell: (94.461, 89.355, 135.309, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 60 16.00 O 1919 8.00 N 1696 7.00 C 7539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 787 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 903 " - " ASN A 67 " " NAG A 904 " - " ASN A 136 " " NAG B 903 " - " ASN B 67 " " NAG B 904 " - " ASN B 136 " " NAG C 1 " - " ASN A 57 " " NAG D 1 " - " ASN A 83 " " NAG E 1 " - " ASN B 57 " " NAG F 1 " - " ASN B 83 " Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 46.0% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 303 through 334 removed outlier: 3.888A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 473 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 496 through 526 removed outlier: 4.895A pdb=" N ASN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 564 removed outlier: 3.592A pdb=" N VAL A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 593 removed outlier: 3.994A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 620 Processing helix chain 'A' and resid 625 through 649 removed outlier: 4.358A pdb=" N TRP A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 708 Processing helix chain 'A' and resid 714 through 737 Processing helix chain 'A' and resid 746 through 767 removed outlier: 3.805A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 783 removed outlier: 3.880A pdb=" N LYS A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 815 Processing helix chain 'A' and resid 820 through 823 Processing helix chain 'B' and resid 39 through 42 No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 303 through 334 removed outlier: 3.856A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 473 removed outlier: 4.137A pdb=" N ILE B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 496 through 526 removed outlier: 4.701A pdb=" N ASN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 564 removed outlier: 3.597A pdb=" N VAL B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 593 removed outlier: 3.985A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 579 " --> pdb=" O THR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 620 Processing helix chain 'B' and resid 625 through 649 removed outlier: 4.442A pdb=" N TRP B 629 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 708 Processing helix chain 'B' and resid 714 through 737 Processing helix chain 'B' and resid 746 through 767 removed outlier: 3.560A pdb=" N PHE B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 783 removed outlier: 3.934A pdb=" N LYS B 783 " --> pdb=" O GLU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 815 Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing sheet with id= A, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.473A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 62 through 70 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 113 Processing sheet with id= D, first strand: chain 'A' and resid 177 through 181 Processing sheet with id= E, first strand: chain 'A' and resid 187 through 192 Processing sheet with id= F, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.625A pdb=" N ALA B 77 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 61 through 70 Processing sheet with id= H, first strand: chain 'B' and resid 110 through 113 Processing sheet with id= I, first strand: chain 'B' and resid 177 through 181 Processing sheet with id= J, first strand: chain 'B' and resid 187 through 192 590 hydrogen bonds defined for protein. 1708 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: 3.03 Time building geometry restraints manager: 5.05 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: 3251 1.34 - 1.46: 2724 1.46 - 1.58: 5472 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 11541 Sorted by residual: bond pdb=" C10 OLA B 914 " pdb=" C9 OLA B 914 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C10 OLA A 912 " pdb=" C9 OLA A 912 " ideal model delta sigma weight residual 1.332 1.467 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C1 OLA A 912 " pdb=" C2 OLA A 912 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 OLA B 914 " pdb=" C2 OLA B 914 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 11536 not shown) Histogram of bond angle deviations from ideal: 94.79 - 103.14: 110 103.14 - 111.48: 5311 111.48 - 119.83: 4774 119.83 - 128.17: 5465 128.17 - 136.52: 88 Bond angle restraints: 15748 Sorted by residual: angle pdb=" C ASN B 598 " pdb=" N ALA B 599 " pdb=" CA ALA B 599 " ideal model delta sigma weight residual 121.70 133.71 -12.01 1.80e+00 3.09e-01 4.45e+01 angle pdb=" C ASN A 598 " pdb=" N ALA A 599 " pdb=" CA ALA A 599 " ideal model delta sigma weight residual 121.70 133.55 -11.85 1.80e+00 3.09e-01 4.33e+01 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 136.52 -20.22 3.50e+00 8.16e-02 3.34e+01 angle pdb=" CA MET B 613 " pdb=" CB MET B 613 " pdb=" CG MET B 613 " ideal model delta sigma weight residual 114.10 124.06 -9.96 2.00e+00 2.50e-01 2.48e+01 angle pdb=" C ILE A 612 " pdb=" N MET A 613 " pdb=" CA MET A 613 " ideal model delta sigma weight residual 121.58 112.24 9.34 1.95e+00 2.63e-01 2.29e+01 ... (remaining 15743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 6571 17.39 - 34.78: 801 34.78 - 52.17: 217 52.17 - 69.56: 54 69.56 - 86.95: 8 Dihedral angle restraints: 7651 sinusoidal: 3791 harmonic: 3860 Sorted by residual: dihedral pdb=" CA TYR B 210 " pdb=" C TYR B 210 " pdb=" N PRO B 211 " pdb=" CA PRO B 211 " ideal model delta harmonic sigma weight residual 0.00 24.23 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 0.00 21.40 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 58.11 34.89 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 7648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1590 0.064 - 0.128: 229 0.128 - 0.192: 15 0.192 - 0.256: 4 0.256 - 0.320: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C2 SPL B 906 " pdb=" C1 SPL B 906 " pdb=" C3 SPL B 906 " pdb=" N2 SPL B 906 " both_signs ideal model delta sigma weight residual False -2.45 -2.20 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1837 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 914 " 0.200 2.00e-02 2.50e+03 1.55e-01 2.42e+02 pdb=" C11 OLA B 914 " -0.090 2.00e-02 2.50e+03 pdb=" C8 OLA B 914 " 0.091 2.00e-02 2.50e+03 pdb=" C9 OLA B 914 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 912 " -0.186 2.00e-02 2.50e+03 1.44e-01 2.09e+02 pdb=" C11 OLA A 912 " 0.085 2.00e-02 2.50e+03 pdb=" C8 OLA A 912 " -0.085 2.00e-02 2.50e+03 pdb=" C9 OLA A 912 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.214 9.50e-02 1.11e+02 9.57e-02 5.64e+00 pdb=" NE ARG A 710 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " -0.007 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 105 2.62 - 3.19: 9567 3.19 - 3.76: 16361 3.76 - 4.33: 22558 4.33 - 4.90: 37918 Nonbonded interactions: 86509 Sorted by model distance: nonbonded pdb="ZN ZN B 901 " pdb=" O HOH B1002 " model vdw 2.046 2.230 nonbonded pdb="ZN ZN A 901 " pdb=" O HOH A1002 " model vdw 2.052 2.230 nonbonded pdb=" OG1 THR A 135 " pdb=" OE1 GLU A 137 " model vdw 2.128 2.440 nonbonded pdb=" O LYS B 265 " pdb=" NH1 ARG B 289 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.246 2.440 ... (remaining 86504 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 35 through 80 or resid 82 through 830 or resid 901 through \ 905 or resid 907 through 911)) selection = (chain 'B' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 905 or resid 907 through 911)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.21 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 9.910 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 40.860 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 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:14.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 0.136 11541 Z= 0.249 Angle : 0.820 20.220 15748 Z= 0.375 Chirality : 0.046 0.320 1840 Planarity : 0.007 0.155 1850 Dihedral : 15.764 86.946 5135 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 3.96 % Allowed : 27.37 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1276 helix: 1.94 (0.21), residues: 590 sheet: 1.85 (0.28), residues: 260 loop : -2.11 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 PHE 0.030 0.001 PHE B 275 TYR 0.021 0.001 TYR A 332 ARG 0.007 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 103 time to evaluate : 1.219 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 40 residues processed: 145 average time/residue: 0.7616 time to fit residues: 125.4526 Evaluate side-chains 142 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 102 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 768 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11541 Z= 0.300 Angle : 0.710 16.712 15748 Z= 0.335 Chirality : 0.045 0.289 1840 Planarity : 0.004 0.056 1850 Dihedral : 9.457 59.926 2786 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 4.99 % Allowed : 25.56 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1276 helix: 1.82 (0.21), residues: 604 sheet: 1.74 (0.28), residues: 272 loop : -2.06 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 106 HIS 0.004 0.001 HIS A 636 PHE 0.016 0.001 PHE B 276 TYR 0.018 0.001 TYR A 188 ARG 0.006 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 101 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: A 208 MET cc_start: 0.8483 (ttm) cc_final: 0.8167 (ttm) REVERT: A 443 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7321 (tt) REVERT: A 461 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: A 591 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6944 (pp30) outliers start: 58 outliers final: 27 residues processed: 150 average time/residue: 0.7996 time to fit residues: 135.5844 Evaluate side-chains 129 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN B 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 11541 Z= 0.433 Angle : 0.756 15.064 15748 Z= 0.360 Chirality : 0.047 0.291 1840 Planarity : 0.004 0.050 1850 Dihedral : 9.002 59.702 2753 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 4.99 % Allowed : 25.90 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 0.90 (0.23), residues: 1276 helix: 1.76 (0.21), residues: 604 sheet: 1.75 (0.29), residues: 260 loop : -2.09 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 106 HIS 0.005 0.001 HIS A 636 PHE 0.035 0.002 PHE B 722 TYR 0.021 0.002 TYR A 188 ARG 0.007 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 97 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: A 443 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7399 (tt) REVERT: A 461 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: B 513 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8176 (mp) REVERT: B 590 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7565 (t80) REVERT: B 781 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7916 (ttm170) outliers start: 58 outliers final: 32 residues processed: 144 average time/residue: 0.8327 time to fit residues: 135.4016 Evaluate side-chains 134 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8188 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11541 Z= 0.184 Angle : 0.685 14.283 15748 Z= 0.319 Chirality : 0.044 0.288 1840 Planarity : 0.004 0.048 1850 Dihedral : 8.306 59.696 2752 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 3.61 % Allowed : 27.02 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1276 helix: 1.87 (0.21), residues: 604 sheet: 1.82 (0.28), residues: 272 loop : -2.04 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 PHE 0.049 0.001 PHE A 732 TYR 0.014 0.001 TYR B 188 ARG 0.005 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 107 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: A 443 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7253 (tt) REVERT: B 513 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 781 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7906 (ttm170) outliers start: 42 outliers final: 14 residues processed: 139 average time/residue: 0.8294 time to fit residues: 129.8515 Evaluate side-chains 119 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 105 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 0.3980 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11541 Z= 0.209 Angle : 0.698 14.579 15748 Z= 0.324 Chirality : 0.044 0.293 1840 Planarity : 0.004 0.047 1850 Dihedral : 7.883 58.910 2741 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 3.61 % Allowed : 27.19 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1276 helix: 2.01 (0.21), residues: 592 sheet: 1.88 (0.28), residues: 272 loop : -2.15 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 PHE 0.010 0.001 PHE B 722 TYR 0.019 0.001 TYR A 332 ARG 0.004 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: A 208 MET cc_start: 0.8340 (ttm) cc_final: 0.7980 (ttm) REVERT: A 443 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7260 (tt) REVERT: B 513 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 781 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7917 (ttm170) outliers start: 42 outliers final: 21 residues processed: 140 average time/residue: 0.8060 time to fit residues: 127.4698 Evaluate side-chains 132 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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: 0.8180 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11541 Z= 0.190 Angle : 0.695 14.671 15748 Z= 0.321 Chirality : 0.044 0.293 1840 Planarity : 0.004 0.047 1850 Dihedral : 7.625 59.618 2738 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 3.44 % Allowed : 27.02 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1276 helix: 2.03 (0.21), residues: 592 sheet: 1.90 (0.28), residues: 272 loop : -2.12 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 PHE 0.050 0.001 PHE A 732 TYR 0.015 0.001 TYR B 188 ARG 0.004 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: A 829 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8389 (tp) REVERT: B 513 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8196 (mp) REVERT: B 781 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7918 (ttm170) outliers start: 40 outliers final: 24 residues processed: 138 average time/residue: 0.8065 time to fit residues: 126.3396 Evaluate side-chains 128 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0170 chunk 13 optimal weight: 0.0980 chunk 70 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 0.0270 chunk 76 optimal weight: 0.8980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11541 Z= 0.143 Angle : 0.687 17.705 15748 Z= 0.313 Chirality : 0.043 0.303 1840 Planarity : 0.004 0.045 1850 Dihedral : 7.180 58.185 2736 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 2.93 % Allowed : 27.62 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1276 helix: 2.08 (0.21), residues: 590 sheet: 2.00 (0.28), residues: 272 loop : -2.06 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 PHE 0.049 0.001 PHE A 732 TYR 0.012 0.001 TYR B 188 ARG 0.004 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8375 (tt0) cc_final: 0.8070 (pt0) REVERT: A 461 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8555 (mp-120) REVERT: A 829 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8339 (tp) REVERT: B 513 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8192 (mp) REVERT: B 781 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7950 (ttm170) outliers start: 34 outliers final: 16 residues processed: 139 average time/residue: 0.7832 time to fit residues: 123.5865 Evaluate side-chains 125 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11541 Z= 0.192 Angle : 0.706 17.879 15748 Z= 0.324 Chirality : 0.043 0.302 1840 Planarity : 0.004 0.046 1850 Dihedral : 7.041 57.720 2733 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 2.32 % Allowed : 28.74 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1276 helix: 2.09 (0.21), residues: 592 sheet: 2.02 (0.28), residues: 272 loop : -2.07 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 PHE 0.030 0.001 PHE B 329 TYR 0.020 0.001 TYR A 332 ARG 0.004 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 318 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 461 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8560 (mp-120) REVERT: A 829 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8345 (tp) REVERT: B 513 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8187 (mp) REVERT: B 689 MET cc_start: 0.7428 (pmm) cc_final: 0.5679 (pp-130) outliers start: 27 outliers final: 15 residues processed: 129 average time/residue: 0.8318 time to fit residues: 120.8532 Evaluate side-chains 122 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11541 Z= 0.421 Angle : 0.783 18.620 15748 Z= 0.370 Chirality : 0.048 0.301 1840 Planarity : 0.004 0.049 1850 Dihedral : 7.431 58.143 2733 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 2.41 % Allowed : 28.23 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1276 helix: 1.96 (0.21), residues: 592 sheet: 1.98 (0.29), residues: 260 loop : -2.16 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 799 HIS 0.004 0.001 HIS A 50 PHE 0.051 0.002 PHE A 732 TYR 0.024 0.002 TYR A 188 ARG 0.008 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.9129 (ptmm) cc_final: 0.8926 (tmmm) REVERT: A 461 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8617 (mp-120) REVERT: A 829 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8398 (tp) REVERT: B 513 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 781 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7835 (ttm170) outliers start: 28 outliers final: 14 residues processed: 120 average time/residue: 0.8938 time to fit residues: 120.2066 Evaluate side-chains 113 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11541 Z= 0.180 Angle : 0.722 18.749 15748 Z= 0.331 Chirality : 0.044 0.295 1840 Planarity : 0.004 0.046 1850 Dihedral : 7.168 58.743 2733 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 1.64 % Allowed : 29.17 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1276 helix: 1.99 (0.21), residues: 588 sheet: 1.95 (0.28), residues: 272 loop : -2.16 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 446 HIS 0.004 0.001 HIS A 636 PHE 0.028 0.001 PHE B 329 TYR 0.020 0.001 TYR A 332 ARG 0.003 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8385 (tt0) cc_final: 0.8102 (pt0) REVERT: A 461 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8565 (mp-120) REVERT: A 829 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8323 (tp) REVERT: B 513 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 781 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7901 (ttm170) outliers start: 19 outliers final: 12 residues processed: 119 average time/residue: 0.9247 time to fit residues: 123.0031 Evaluate side-chains 118 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077413 restraints weight = 25124.432| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.47 r_work: 0.2887 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11541 Z= 0.178 Angle : 0.717 18.699 15748 Z= 0.330 Chirality : 0.044 0.300 1840 Planarity : 0.004 0.046 1850 Dihedral : 7.046 58.915 2733 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.46 % Allowed : 29.26 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1276 helix: 2.01 (0.21), residues: 588 sheet: 2.00 (0.28), residues: 272 loop : -2.13 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 PHE 0.053 0.001 PHE A 732 TYR 0.014 0.001 TYR B 188 ARG 0.004 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3268.00 seconds wall clock time: 59 minutes 59.89 seconds (3599.89 seconds total)