Starting phenix.real_space_refine on Wed May 8 17:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/05_2024/8wos_37697_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/05_2024/8wos_37697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/05_2024/8wos_37697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/05_2024/8wos_37697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/05_2024/8wos_37697_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/05_2024/8wos_37697_neut_updated.pdb" } resolution = 3.37 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 58 5.16 5 C 7106 2.51 5 N 1644 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 786": "OE1" <-> "OE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 625": "OD1" <-> "OD2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 819": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "B" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 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: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.44, per 1000 atoms: 0.51 Number of scatterers: 10672 At special positions: 0 Unit cell: (97.865, 86.802, 137.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1862 8.00 N 1644 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 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 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 901 " - " ASN A 67 " " NAG A 902 " - " ASN A 136 " " NAG B 901 " - " ASN B 67 " " NAG B 902 " - " ASN B 136 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 57 " " NAG E 1 " - " ASN B 83 " " NAG F 1 " - " ASN B 57 " Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 907 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 907 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 800 " 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 46.2% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 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 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 303 through 335 removed outlier: 3.822A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 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 495 through 528 removed outlier: 4.882A pdb=" N ASN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLY A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N HIS A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 removed outlier: 4.429A pdb=" N GLU A 535 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 564 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 576 through 593 removed outlier: 3.808A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 621 Processing helix chain 'A' and resid 627 through 648 Processing helix chain 'A' and resid 689 through 708 Processing helix chain 'A' and resid 714 through 739 Processing helix chain 'A' and resid 746 through 767 Processing helix chain 'A' and resid 777 through 782 removed outlier: 3.746A pdb=" N GLU A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 819 removed outlier: 5.129A pdb=" N ASP A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASP A 819 " --> pdb=" O LEU A 815 " (cutoff:3.500A) 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 303 through 335 removed outlier: 3.814A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 473 removed outlier: 3.564A pdb=" N VAL B 453 " --> pdb=" O ILE B 449 " (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 528 removed outlier: 4.849A pdb=" N ASN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N HIS B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.958A pdb=" N GLU B 535 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 564 removed outlier: 3.635A pdb=" N VAL B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 576 through 593 removed outlier: 3.926A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 621 Processing helix chain 'B' and resid 627 through 648 Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 714 through 740 Processing helix chain 'B' and resid 746 through 767 Processing helix chain 'B' and resid 777 through 780 No H-bonds generated for 'chain 'B' and resid 777 through 780' Processing helix chain 'B' and resid 795 through 816 Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing sheet with id= A, first strand: chain 'A' and resid 52 through 56 Processing sheet with id= B, first strand: chain 'A' and resid 61 through 70 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 114 Processing sheet with id= D, first strand: chain 'A' and resid 178 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 52 through 56 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 114 Processing sheet with id= I, first strand: chain 'B' and resid 178 through 181 Processing sheet with id= J, first strand: chain 'B' and resid 187 through 192 573 hydrogen bonds defined for protein. 1653 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: 3.32 Time building geometry restraints manager: 4.95 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: 3170 1.34 - 1.46: 2808 1.46 - 1.58: 4908 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 10976 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.93: 316 106.93 - 113.70: 6190 113.70 - 120.48: 4302 120.48 - 127.25: 4069 127.25 - 134.03: 103 Bond angle restraints: 14980 Sorted by residual: angle pdb=" C SER B 600 " pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 116.54 110.30 6.24 1.15e+00 7.56e-01 2.94e+01 angle pdb=" C LEU A 789 " pdb=" CA LEU A 789 " pdb=" CB LEU A 789 " ideal model delta sigma weight residual 116.63 111.62 5.01 1.16e+00 7.43e-01 1.87e+01 angle pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N ALA B 601 " ideal model delta sigma weight residual 119.52 116.43 3.09 7.90e-01 1.60e+00 1.53e+01 angle pdb=" C LEU A 704 " pdb=" N PHE A 705 " pdb=" CA PHE A 705 " ideal model delta sigma weight residual 122.06 114.81 7.25 1.86e+00 2.89e-01 1.52e+01 angle pdb=" C LEU B 789 " pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " ideal model delta sigma weight residual 117.23 112.78 4.45 1.36e+00 5.41e-01 1.07e+01 ... (remaining 14975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 6322 25.77 - 51.54: 518 51.54 - 77.30: 55 77.30 - 103.07: 23 103.07 - 128.84: 10 Dihedral angle restraints: 6928 sinusoidal: 3148 harmonic: 3780 Sorted by residual: 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 93.00 128.21 -35.21 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" C2 NAG B 901 " pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C5 NAG B 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.88 -128.84 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.20 -128.16 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1612 0.074 - 0.149: 135 0.149 - 0.223: 3 0.223 - 0.298: 0 0.298 - 0.372: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1749 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.001 2.00e-02 2.50e+03 2.76e-02 9.53e+00 pdb=" CG ASN B 83 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 702 " -0.024 2.00e-02 2.50e+03 2.16e-02 8.15e+00 pdb=" CG PHE A 702 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 702 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 702 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 702 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 702 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 702 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 717 " -0.023 2.00e-02 2.50e+03 1.43e-02 4.10e+00 pdb=" CG TYR A 717 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 717 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 717 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 717 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 717 " -0.007 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 100 2.53 - 3.13: 8860 3.13 - 3.72: 16174 3.72 - 4.31: 21282 4.31 - 4.90: 36544 Nonbonded interactions: 82960 Sorted by model distance: nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 1.943 2.440 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 1.961 2.440 nonbonded pdb=" OG SER B 701 " pdb=" OH TYR B 717 " model vdw 1.981 2.440 nonbonded pdb=" OG SER A 740 " pdb=" OE2 GLU A 742 " model vdw 2.036 2.440 nonbonded pdb=" OH TYR A 321 " pdb=" O LEU A 506 " model vdw 2.086 2.440 ... (remaining 82955 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' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.000 Extract box with map and model: 10.180 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 33.210 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.003 0.053 10976 Z= 0.199 Angle : 0.552 7.753 14980 Z= 0.301 Chirality : 0.041 0.372 1752 Planarity : 0.003 0.049 1802 Dihedral : 18.351 128.840 4470 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.35 % Allowed : 33.39 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1256 helix: 2.71 (0.21), residues: 568 sheet: 0.51 (0.33), residues: 272 loop : -2.17 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.050 0.001 PHE A 702 TYR 0.032 0.001 TYR A 717 ARG 0.001 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 767 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.6557 (m-80) outliers start: 4 outliers final: 3 residues processed: 148 average time/residue: 0.1736 time to fit residues: 40.7513 Evaluate side-chains 143 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 767 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 594 HIS ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10976 Z= 0.315 Angle : 0.693 9.356 14980 Z= 0.338 Chirality : 0.049 0.531 1752 Planarity : 0.004 0.049 1802 Dihedral : 12.798 114.387 2162 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.64 % Favored : 92.28 % Rotamer: Outliers : 4.42 % Allowed : 29.33 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.33 (0.24), residues: 1256 helix: 1.88 (0.21), residues: 560 sheet: 0.41 (0.32), residues: 280 loop : -2.36 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 446 HIS 0.010 0.001 HIS B 636 PHE 0.022 0.002 PHE A 702 TYR 0.043 0.002 TYR A 717 ARG 0.004 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 154 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5217 (mt) REVERT: A 605 TYR cc_start: 0.8510 (m-80) cc_final: 0.8286 (m-80) REVERT: B 36 ARG cc_start: 0.5096 (OUTLIER) cc_final: 0.3373 (mtt180) REVERT: B 208 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.5694 (ppp) REVERT: B 572 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: B 613 MET cc_start: 0.8501 (mmm) cc_final: 0.8254 (mmm) REVERT: B 722 PHE cc_start: 0.8607 (m-10) cc_final: 0.8352 (m-10) REVERT: B 736 MET cc_start: 0.8021 (mmt) cc_final: 0.7785 (mmt) REVERT: B 767 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7623 (m-80) outliers start: 50 outliers final: 22 residues processed: 192 average time/residue: 0.1927 time to fit residues: 55.7038 Evaluate side-chains 170 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 0.0970 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10976 Z= 0.194 Angle : 0.618 9.633 14980 Z= 0.299 Chirality : 0.046 0.484 1752 Planarity : 0.004 0.048 1802 Dihedral : 12.272 113.341 2158 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 4.77 % Allowed : 30.04 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.35 (0.24), residues: 1256 helix: 1.84 (0.22), residues: 560 sheet: 0.56 (0.32), residues: 280 loop : -2.36 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 446 HIS 0.008 0.001 HIS B 636 PHE 0.024 0.001 PHE A 445 TYR 0.040 0.001 TYR A 717 ARG 0.003 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 153 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: A 326 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5214 (mt) REVERT: A 617 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8845 (pp) REVERT: A 702 PHE cc_start: 0.8011 (m-80) cc_final: 0.7337 (m-80) REVERT: A 713 ASP cc_start: 0.8070 (t0) cc_final: 0.7860 (t0) REVERT: B 36 ARG cc_start: 0.5064 (OUTLIER) cc_final: 0.3329 (mtt180) REVERT: B 208 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.5580 (ppp) REVERT: B 613 MET cc_start: 0.8460 (mmm) cc_final: 0.8183 (mmm) REVERT: B 709 TYR cc_start: 0.7083 (t80) cc_final: 0.6684 (t80) REVERT: B 722 PHE cc_start: 0.8610 (m-10) cc_final: 0.8340 (m-10) REVERT: B 736 MET cc_start: 0.8055 (mmt) cc_final: 0.7791 (mmt) REVERT: B 767 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7564 (m-80) outliers start: 54 outliers final: 24 residues processed: 198 average time/residue: 0.1849 time to fit residues: 56.1842 Evaluate side-chains 172 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10976 Z= 0.381 Angle : 0.721 10.059 14980 Z= 0.352 Chirality : 0.050 0.535 1752 Planarity : 0.004 0.050 1802 Dihedral : 11.995 115.361 2156 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.64 % Favored : 92.20 % Rotamer: Outliers : 6.10 % Allowed : 28.89 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.06 (0.24), residues: 1256 helix: 1.62 (0.22), residues: 548 sheet: 0.47 (0.33), residues: 268 loop : -2.39 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 629 HIS 0.006 0.001 HIS B 636 PHE 0.026 0.002 PHE A 445 TYR 0.037 0.002 TYR A 717 ARG 0.005 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 150 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: A 326 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5334 (mm) REVERT: A 455 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: A 702 PHE cc_start: 0.8073 (m-80) cc_final: 0.7410 (m-80) REVERT: A 713 ASP cc_start: 0.8274 (t0) cc_final: 0.8047 (t0) REVERT: B 36 ARG cc_start: 0.5055 (OUTLIER) cc_final: 0.3398 (mtt-85) REVERT: B 208 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.5777 (ppp) REVERT: B 536 TYR cc_start: 0.6470 (OUTLIER) cc_final: 0.6247 (t80) REVERT: B 613 MET cc_start: 0.8431 (mmm) cc_final: 0.8151 (mmm) REVERT: B 709 TYR cc_start: 0.7335 (t80) cc_final: 0.7090 (t80) REVERT: B 722 PHE cc_start: 0.8730 (m-10) cc_final: 0.8421 (m-10) REVERT: B 767 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7641 (m-80) outliers start: 69 outliers final: 37 residues processed: 201 average time/residue: 0.2577 time to fit residues: 82.5397 Evaluate side-chains 185 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10976 Z= 0.205 Angle : 0.648 11.334 14980 Z= 0.308 Chirality : 0.047 0.512 1752 Planarity : 0.004 0.038 1802 Dihedral : 11.555 114.821 2156 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.75 % Rotamer: Outliers : 4.06 % Allowed : 30.39 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.21 (0.24), residues: 1256 helix: 1.76 (0.22), residues: 548 sheet: 0.52 (0.32), residues: 280 loop : -2.38 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 446 HIS 0.006 0.001 HIS B 636 PHE 0.023 0.001 PHE A 445 TYR 0.037 0.001 TYR A 717 ARG 0.003 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 151 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: A 326 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5181 (mt) REVERT: A 702 PHE cc_start: 0.7935 (m-80) cc_final: 0.7483 (m-80) REVERT: A 713 ASP cc_start: 0.8283 (t0) cc_final: 0.8022 (t0) REVERT: B 36 ARG cc_start: 0.5055 (OUTLIER) cc_final: 0.3385 (mtt-85) REVERT: B 208 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.5567 (ppp) REVERT: B 613 MET cc_start: 0.8504 (mmm) cc_final: 0.8195 (mmm) REVERT: B 709 TYR cc_start: 0.7118 (t80) cc_final: 0.6772 (t80) REVERT: B 722 PHE cc_start: 0.8718 (m-10) cc_final: 0.8375 (m-10) REVERT: B 736 MET cc_start: 0.7984 (mmt) cc_final: 0.7749 (mmt) REVERT: B 767 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7583 (m-80) outliers start: 46 outliers final: 34 residues processed: 185 average time/residue: 0.2058 time to fit residues: 58.2496 Evaluate side-chains 181 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.0470 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN B 461 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10976 Z= 0.248 Angle : 0.662 11.426 14980 Z= 0.315 Chirality : 0.048 0.508 1752 Planarity : 0.004 0.040 1802 Dihedral : 11.287 115.067 2156 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 5.21 % Allowed : 29.86 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1256 helix: 1.74 (0.22), residues: 548 sheet: 0.67 (0.33), residues: 268 loop : -2.42 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 446 HIS 0.006 0.001 HIS B 636 PHE 0.028 0.001 PHE A 445 TYR 0.029 0.001 TYR A 717 ARG 0.005 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 147 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: A 455 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: A 702 PHE cc_start: 0.7919 (m-80) cc_final: 0.7485 (m-80) REVERT: A 713 ASP cc_start: 0.8311 (t0) cc_final: 0.8026 (t0) REVERT: B 36 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.3470 (mtt-85) REVERT: B 208 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.5535 (ppp) REVERT: B 536 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.6301 (t80) REVERT: B 580 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7407 (tpp) REVERT: B 613 MET cc_start: 0.8482 (mmm) cc_final: 0.8174 (mmm) REVERT: B 709 TYR cc_start: 0.6982 (t80) cc_final: 0.6753 (t80) REVERT: B 722 PHE cc_start: 0.8750 (m-10) cc_final: 0.8405 (m-10) REVERT: B 736 MET cc_start: 0.8040 (mmt) cc_final: 0.7790 (mmt) REVERT: B 767 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7605 (m-80) outliers start: 59 outliers final: 41 residues processed: 190 average time/residue: 0.1797 time to fit residues: 53.0271 Evaluate side-chains 189 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 572 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10976 Z= 0.198 Angle : 0.644 12.211 14980 Z= 0.305 Chirality : 0.047 0.501 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.965 114.782 2156 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 5.04 % Allowed : 30.04 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.23 (0.24), residues: 1256 helix: 1.67 (0.22), residues: 560 sheet: 0.72 (0.33), residues: 268 loop : -2.42 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.027 0.001 PHE A 445 TYR 0.039 0.001 TYR A 717 ARG 0.003 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 147 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: A 326 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5241 (mt) REVERT: A 455 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: A 702 PHE cc_start: 0.7775 (m-80) cc_final: 0.7409 (m-80) REVERT: A 713 ASP cc_start: 0.8352 (t0) cc_final: 0.8076 (t0) REVERT: B 36 ARG cc_start: 0.5144 (OUTLIER) cc_final: 0.3427 (mtt-85) REVERT: B 160 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7870 (mttp) REVERT: B 208 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.5382 (ppp) REVERT: B 536 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.6243 (t80) REVERT: B 613 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8166 (mmm) REVERT: B 722 PHE cc_start: 0.8751 (m-10) cc_final: 0.8412 (m-10) REVERT: B 736 MET cc_start: 0.8006 (mmt) cc_final: 0.7750 (mmt) REVERT: B 767 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7613 (m-80) outliers start: 57 outliers final: 41 residues processed: 193 average time/residue: 0.2088 time to fit residues: 61.5268 Evaluate side-chains 196 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.0030 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10976 Z= 0.173 Angle : 0.639 12.022 14980 Z= 0.299 Chirality : 0.046 0.492 1752 Planarity : 0.004 0.036 1802 Dihedral : 10.616 114.471 2156 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 4.06 % Allowed : 30.74 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.24), residues: 1256 helix: 1.73 (0.22), residues: 560 sheet: 0.81 (0.33), residues: 268 loop : -2.39 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 799 HIS 0.005 0.001 HIS B 636 PHE 0.026 0.001 PHE B 705 TYR 0.027 0.001 TYR A 717 ARG 0.004 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 149 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: A 555 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8142 (tp30) REVERT: A 689 MET cc_start: 0.8777 (mmt) cc_final: 0.8482 (mmp) REVERT: A 702 PHE cc_start: 0.7819 (m-80) cc_final: 0.7478 (m-80) REVERT: A 713 ASP cc_start: 0.8335 (t0) cc_final: 0.8044 (t0) REVERT: B 36 ARG cc_start: 0.5104 (OUTLIER) cc_final: 0.3344 (mtt180) REVERT: B 160 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7860 (mttp) REVERT: B 208 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.5333 (ppp) REVERT: B 221 MET cc_start: 0.7801 (mmm) cc_final: 0.7481 (mmm) REVERT: B 613 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: B 722 PHE cc_start: 0.8754 (m-10) cc_final: 0.8448 (m-10) REVERT: B 736 MET cc_start: 0.8082 (mmt) cc_final: 0.7784 (mmt) REVERT: B 767 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7364 (m-80) outliers start: 46 outliers final: 37 residues processed: 186 average time/residue: 0.1687 time to fit residues: 48.5227 Evaluate side-chains 188 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 799 TRP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 112 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10976 Z= 0.171 Angle : 0.644 12.276 14980 Z= 0.299 Chirality : 0.046 0.495 1752 Planarity : 0.004 0.036 1802 Dihedral : 10.407 114.329 2156 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 4.33 % Allowed : 30.57 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.39 (0.24), residues: 1256 helix: 1.84 (0.22), residues: 548 sheet: 0.87 (0.34), residues: 268 loop : -2.34 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 759 HIS 0.004 0.001 HIS B 636 PHE 0.027 0.001 PHE A 732 TYR 0.040 0.001 TYR A 717 ARG 0.003 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: A 326 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5426 (mt) REVERT: A 555 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8256 (tp30) REVERT: A 590 TYR cc_start: 0.8570 (t80) cc_final: 0.8301 (t80) REVERT: A 689 MET cc_start: 0.8841 (mmt) cc_final: 0.8544 (mmp) REVERT: A 702 PHE cc_start: 0.7840 (m-80) cc_final: 0.7493 (m-80) REVERT: A 713 ASP cc_start: 0.8355 (t0) cc_final: 0.8061 (t0) REVERT: B 36 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.3305 (mtt180) REVERT: B 208 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.5303 (ppp) REVERT: B 536 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6402 (t80) REVERT: B 613 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8134 (mmm) REVERT: B 641 LEU cc_start: 0.9260 (mt) cc_final: 0.8968 (tp) REVERT: B 722 PHE cc_start: 0.8745 (m-10) cc_final: 0.8415 (m-10) REVERT: B 736 MET cc_start: 0.8011 (mmt) cc_final: 0.7712 (mmt) REVERT: B 767 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7342 (m-80) outliers start: 49 outliers final: 39 residues processed: 188 average time/residue: 0.1902 time to fit residues: 54.8126 Evaluate side-chains 189 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10976 Z= 0.175 Angle : 0.649 12.028 14980 Z= 0.301 Chirality : 0.046 0.492 1752 Planarity : 0.004 0.036 1802 Dihedral : 10.250 114.319 2156 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 4.24 % Allowed : 30.83 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.45 (0.24), residues: 1256 helix: 1.88 (0.22), residues: 548 sheet: 0.94 (0.34), residues: 268 loop : -2.32 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 759 HIS 0.004 0.001 HIS B 636 PHE 0.035 0.001 PHE A 705 TYR 0.021 0.001 TYR A 188 ARG 0.012 0.000 ARG B 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 144 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: A 326 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5470 (mt) REVERT: A 555 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8241 (tp30) REVERT: A 590 TYR cc_start: 0.8577 (t80) cc_final: 0.8321 (t80) REVERT: A 689 MET cc_start: 0.8877 (mmt) cc_final: 0.8563 (mmp) REVERT: A 702 PHE cc_start: 0.7723 (m-80) cc_final: 0.7410 (m-80) REVERT: A 713 ASP cc_start: 0.8323 (t0) cc_final: 0.8017 (t0) REVERT: B 208 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.5324 (ppp) REVERT: B 221 MET cc_start: 0.7828 (mmm) cc_final: 0.7462 (mmm) REVERT: B 536 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6512 (t80) REVERT: B 613 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: B 722 PHE cc_start: 0.8767 (m-10) cc_final: 0.8466 (m-10) REVERT: B 736 MET cc_start: 0.8015 (mmt) cc_final: 0.7717 (mmt) REVERT: B 767 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7384 (m-80) outliers start: 48 outliers final: 39 residues processed: 183 average time/residue: 0.1701 time to fit residues: 48.8078 Evaluate side-chains 186 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** 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 = 0.4118 r_free = 0.4118 target = 0.141888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104414 restraints weight = 19809.613| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.04 r_work: 0.3461 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10976 Z= 0.224 Angle : 0.665 11.898 14980 Z= 0.313 Chirality : 0.047 0.505 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.207 114.765 2156 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.13 % Favored : 93.71 % Rotamer: Outliers : 4.06 % Allowed : 30.92 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1256 helix: 1.82 (0.22), residues: 548 sheet: 0.85 (0.34), residues: 268 loop : -2.32 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 446 HIS 0.004 0.001 HIS B 636 PHE 0.039 0.002 PHE A 705 TYR 0.037 0.001 TYR A 717 ARG 0.008 0.000 ARG B 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.08 seconds wall clock time: 44 minutes 22.53 seconds (2662.53 seconds total)