Starting phenix.real_space_refine on Wed Feb 14 11:42:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo9_14087/02_2024/7qo9_14087.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo9_14087/02_2024/7qo9_14087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo9_14087/02_2024/7qo9_14087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo9_14087/02_2024/7qo9_14087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo9_14087/02_2024/7qo9_14087.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qo9_14087/02_2024/7qo9_14087.pdb" } resolution = 3.88 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 5830 2.51 5 N 1523 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A ASP 976": "OD1" <-> "OD2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9180 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4568 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 562} Chain breaks: 14 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4486 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 26, 'TRANS': 551} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 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: "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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.25, per 1000 atoms: 0.57 Number of scatterers: 9180 At special positions: 0 Unit cell: (87.5022, 112.046, 122.717, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1782 8.00 N 1523 7.00 C 5830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 231 " " NAG A1302 " - " ASN A 279 " " NAG C 1 " - " ASN A 160 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 135 " Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 17 sheets defined 26.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.661A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.500A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.589A pdb=" N PHE A 852 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 874 Processing helix chain 'A' and resid 943 through 962 removed outlier: 4.873A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1022 removed outlier: 4.599A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.769A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 removed outlier: 3.762A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 757 through 779 removed outlier: 3.565A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 825 through 827 No H-bonds generated for 'chain 'B' and resid 825 through 827' Processing helix chain 'B' and resid 863 through 864 No H-bonds generated for 'chain 'B' and resid 863 through 864' Processing helix chain 'B' and resid 866 through 868 No H-bonds generated for 'chain 'B' and resid 866 through 868' Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.739A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1022 removed outlier: 4.466A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.205A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.508A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA6, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.861A pdb=" N SER A 114 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 126 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE A 163 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL A 128 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS A 161 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER A 157 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.626A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 651 through 657 removed outlier: 6.058A pdb=" N THR A 693 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN A 655 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 724 through 725 Processing sheet with id=AB1, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 316 removed outlier: 3.807A pdb=" N THR B 312 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.500A pdb=" N ASN B 539 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 355 removed outlier: 3.836A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.547A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.708A pdb=" N ARG B 506 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.593A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 732 through 733 300 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1899 1.33 - 1.45: 2235 1.45 - 1.58: 5160 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 9349 Sorted by residual: bond pdb=" N GLN A 625 " pdb=" CA GLN A 625 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.31e+01 bond pdb=" CA SER B 491 " pdb=" CB SER B 491 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.39e-02 5.18e+03 1.30e+01 bond pdb=" N VAL B 480 " pdb=" CA VAL B 480 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N ASP A 624 " pdb=" CA ASP A 624 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.20e-02 6.94e+03 9.24e+00 bond pdb=" N CYS B 485 " pdb=" CA CYS B 485 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.26e-02 6.30e+03 7.82e+00 ... (remaining 9344 not shown) Histogram of bond angle deviations from ideal: 92.75 - 101.00: 11 101.00 - 109.25: 686 109.25 - 117.50: 6311 117.50 - 125.75: 5582 125.75 - 134.00: 100 Bond angle restraints: 12690 Sorted by residual: angle pdb=" N PRO A 628 " pdb=" CA PRO A 628 " pdb=" CB PRO A 628 " ideal model delta sigma weight residual 103.25 92.75 10.50 1.05e+00 9.07e-01 1.00e+02 angle pdb=" C TYR B 448 " pdb=" CA TYR B 448 " pdb=" CB TYR B 448 " ideal model delta sigma weight residual 110.88 99.97 10.91 1.57e+00 4.06e-01 4.83e+01 angle pdb=" C TYR B 486 " pdb=" CA TYR B 486 " pdb=" CB TYR B 486 " ideal model delta sigma weight residual 109.83 97.99 11.84 1.75e+00 3.27e-01 4.58e+01 angle pdb=" C TYR B 446 " pdb=" CA TYR B 446 " pdb=" CB TYR B 446 " ideal model delta sigma weight residual 114.87 104.90 9.97 1.51e+00 4.39e-01 4.36e+01 angle pdb=" CA ASP A 624 " pdb=" C ASP A 624 " pdb=" O ASP A 624 " ideal model delta sigma weight residual 121.31 116.01 5.30 1.07e+00 8.73e-01 2.45e+01 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 5320 23.74 - 47.48: 327 47.48 - 71.21: 45 71.21 - 94.95: 24 94.95 - 118.69: 13 Dihedral angle restraints: 5729 sinusoidal: 2346 harmonic: 3383 Sorted by residual: dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual -86.00 -167.55 81.55 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 535 " pdb=" SG CYS B 535 " pdb=" SG CYS B 587 " pdb=" CB CYS B 587 " ideal model delta sinusoidal sigma weight residual -86.00 -5.51 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -11.72 -74.28 1 1.00e+01 1.00e-02 7.00e+01 ... (remaining 5726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1436 0.110 - 0.219: 48 0.219 - 0.329: 8 0.329 - 0.438: 3 0.438 - 0.548: 3 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA TYR B 448 " pdb=" N TYR B 448 " pdb=" C TYR B 448 " pdb=" CB TYR B 448 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 160 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA TYR B 446 " pdb=" N TYR B 446 " pdb=" C TYR B 446 " pdb=" CB TYR B 446 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 4.96e+00 ... (remaining 1495 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 627 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C THR A 627 " -0.055 2.00e-02 2.50e+03 pdb=" O THR A 627 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 628 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 226 " 0.043 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A 227 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 79 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 80 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " 0.035 5.00e-02 4.00e+02 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 528 2.72 - 3.27: 9666 3.27 - 3.81: 14147 3.81 - 4.36: 16230 4.36 - 4.90: 27275 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OE1 GLU A 186 " model vdw 2.179 2.440 nonbonded pdb=" O THR B 863 " pdb=" N MET B 866 " model vdw 2.201 2.520 nonbonded pdb=" O VAL A 619 " pdb=" ND1 HIS A 622 " model vdw 2.232 2.520 nonbonded pdb=" OG SER A 110 " pdb=" OE1 GLN A 132 " model vdw 2.237 2.440 nonbonded pdb=" OG SER A 755 " pdb=" OG1 THR A 758 " model vdw 2.251 2.440 ... (remaining 67841 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 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.380 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.870 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 0.053 9349 Z= 0.271 Angle : 0.757 11.839 12690 Z= 0.435 Chirality : 0.056 0.548 1498 Planarity : 0.005 0.066 1615 Dihedral : 16.656 118.691 3490 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.16 % Favored : 90.30 % Rotamer: Outliers : 1.29 % Allowed : 0.50 % Favored : 98.22 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1124 helix: 1.37 (0.33), residues: 272 sheet: -0.07 (0.39), residues: 181 loop : -2.05 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 433 HIS 0.004 0.001 HIS B 951 PHE 0.037 0.001 PHE B 371 TYR 0.031 0.001 TYR B 450 ARG 0.015 0.001 ARG B1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.093 Fit side-chains REVERT: A 290 LEU cc_start: 0.8808 (tt) cc_final: 0.8282 (tt) REVERT: B 446 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6471 (t80) REVERT: B 490 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7178 (tpm170) REVERT: B 770 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6274 (tm-30) REVERT: B 999 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7871 (tm-30) outliers start: 13 outliers final: 4 residues processed: 120 average time/residue: 0.1984 time to fit residues: 33.9215 Evaluate side-chains 75 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 PRO Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 491 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 46 optimal weight: 10.0000 chunk 90 optimal weight: 0.0470 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9349 Z= 0.232 Angle : 0.655 10.668 12690 Z= 0.330 Chirality : 0.046 0.320 1498 Planarity : 0.005 0.068 1615 Dihedral : 12.782 105.107 1434 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.70 % Favored : 90.04 % Rotamer: Outliers : 1.29 % Allowed : 10.01 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.25), residues: 1124 helix: 1.53 (0.33), residues: 263 sheet: -0.11 (0.40), residues: 169 loop : -2.20 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 630 HIS 0.003 0.001 HIS B 502 PHE 0.021 0.001 PHE B 371 TYR 0.011 0.001 TYR B 348 ARG 0.003 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 296 THR cc_start: 0.9118 (m) cc_final: 0.8785 (p) REVERT: A 629 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8012 (t) REVERT: A 773 LYS cc_start: 0.9067 (tptt) cc_final: 0.8163 (tptt) REVERT: A 777 GLU cc_start: 0.8644 (tt0) cc_final: 0.8393 (pt0) REVERT: A 833 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7958 (tp-100) REVERT: A 987 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8667 (tm-30) REVERT: A 991 ASP cc_start: 0.8440 (t70) cc_final: 0.8178 (t70) REVERT: B 446 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6657 (t80) REVERT: B 490 ARG cc_start: 0.8109 (mtt90) cc_final: 0.6932 (tpm170) REVERT: B 737 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7823 (tpp) REVERT: B 770 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6600 (tp30) REVERT: B 999 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 1009 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8965 (mt) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 0.1910 time to fit residues: 25.2529 Evaluate side-chains 80 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9349 Z= 0.217 Angle : 0.627 9.235 12690 Z= 0.313 Chirality : 0.045 0.358 1498 Planarity : 0.004 0.065 1615 Dihedral : 11.987 109.215 1428 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.32 % Favored : 89.41 % Rotamer: Outliers : 1.68 % Allowed : 13.68 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.25), residues: 1124 helix: 1.66 (0.33), residues: 263 sheet: 0.07 (0.41), residues: 165 loop : -2.24 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 630 HIS 0.002 0.001 HIS B 502 PHE 0.016 0.001 PHE B 556 TYR 0.011 0.001 TYR B 448 ARG 0.004 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 773 LYS cc_start: 0.9101 (tptt) cc_final: 0.8086 (tptt) REVERT: A 777 GLU cc_start: 0.8633 (tt0) cc_final: 0.8311 (pt0) REVERT: A 833 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7829 (tp-100) REVERT: A 987 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8638 (tm-30) REVERT: B 446 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6672 (t80) REVERT: B 490 ARG cc_start: 0.7992 (mtt90) cc_final: 0.6814 (tpm170) REVERT: B 737 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7860 (tpp) REVERT: B 999 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7862 (tm-30) outliers start: 17 outliers final: 9 residues processed: 90 average time/residue: 0.1850 time to fit residues: 24.7273 Evaluate side-chains 79 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 104 optimal weight: 0.0030 chunk 111 optimal weight: 0.0670 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9349 Z= 0.160 Angle : 0.596 9.869 12690 Z= 0.294 Chirality : 0.044 0.341 1498 Planarity : 0.004 0.061 1615 Dihedral : 11.169 107.892 1428 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.70 % Favored : 90.04 % Rotamer: Outliers : 1.59 % Allowed : 16.25 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1124 helix: 1.78 (0.33), residues: 263 sheet: 0.65 (0.46), residues: 133 loop : -2.14 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 630 HIS 0.003 0.001 HIS B 502 PHE 0.012 0.001 PHE B 487 TYR 0.009 0.001 TYR B 348 ARG 0.004 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 625 GLN cc_start: 0.4898 (OUTLIER) cc_final: 0.4662 (pt0) REVERT: A 773 LYS cc_start: 0.9114 (tptt) cc_final: 0.8107 (tptt) REVERT: A 777 GLU cc_start: 0.8638 (tt0) cc_final: 0.8318 (pt0) REVERT: A 833 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7733 (tp-100) REVERT: A 987 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8849 (pp20) REVERT: B 446 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6701 (t80) REVERT: B 490 ARG cc_start: 0.7932 (mtt90) cc_final: 0.6923 (tpm170) REVERT: B 737 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7821 (tpp) REVERT: B 770 GLU cc_start: 0.7927 (tt0) cc_final: 0.6562 (tm-30) REVERT: B 999 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7700 (tm-30) outliers start: 16 outliers final: 8 residues processed: 97 average time/residue: 0.2038 time to fit residues: 28.9159 Evaluate side-chains 83 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 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: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9349 Z= 0.338 Angle : 0.702 9.262 12690 Z= 0.352 Chirality : 0.046 0.311 1498 Planarity : 0.005 0.066 1615 Dihedral : 10.744 110.322 1428 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.39 % Favored : 88.35 % Rotamer: Outliers : 2.78 % Allowed : 19.03 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.24), residues: 1124 helix: 1.51 (0.33), residues: 269 sheet: 0.14 (0.41), residues: 151 loop : -2.40 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 630 HIS 0.003 0.001 HIS A 622 PHE 0.020 0.002 PHE B 556 TYR 0.012 0.002 TYR A 276 ARG 0.004 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 773 LYS cc_start: 0.9158 (tptt) cc_final: 0.8117 (tptt) REVERT: A 777 GLU cc_start: 0.8695 (tt0) cc_final: 0.8443 (pt0) REVERT: A 833 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7845 (tp-100) REVERT: A 987 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 991 ASP cc_start: 0.7833 (m-30) cc_final: 0.6659 (m-30) REVERT: B 415 ILE cc_start: 0.8310 (mp) cc_final: 0.7849 (tp) REVERT: B 425 ASP cc_start: 0.7995 (t0) cc_final: 0.7716 (t70) REVERT: B 446 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6746 (t80) REVERT: B 490 ARG cc_start: 0.8093 (mtt90) cc_final: 0.6981 (tpm170) REVERT: B 999 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 1009 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9012 (mt) outliers start: 28 outliers final: 16 residues processed: 100 average time/residue: 0.2022 time to fit residues: 28.8099 Evaluate side-chains 87 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 107 optimal weight: 5.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9349 Z= 0.193 Angle : 0.638 10.692 12690 Z= 0.317 Chirality : 0.045 0.322 1498 Planarity : 0.004 0.053 1615 Dihedral : 10.249 108.852 1428 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.70 % Favored : 90.04 % Rotamer: Outliers : 2.58 % Allowed : 19.82 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1124 helix: 1.71 (0.33), residues: 269 sheet: 0.36 (0.45), residues: 139 loop : -2.27 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 630 HIS 0.003 0.001 HIS B 502 PHE 0.014 0.001 PHE B 487 TYR 0.009 0.001 TYR B 348 ARG 0.012 0.001 ARG B1016 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 622 HIS cc_start: 0.4237 (p-80) cc_final: 0.3925 (p-80) REVERT: A 773 LYS cc_start: 0.9173 (tptt) cc_final: 0.8160 (tptt) REVERT: A 777 GLU cc_start: 0.8695 (tt0) cc_final: 0.8345 (pt0) REVERT: A 833 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7772 (tp-100) REVERT: A 987 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 415 ILE cc_start: 0.8297 (mp) cc_final: 0.7846 (tp) REVERT: B 446 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6830 (t80) REVERT: B 490 ARG cc_start: 0.8123 (mtt90) cc_final: 0.7018 (tpm170) REVERT: B 737 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7906 (tpp) REVERT: B 999 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7847 (tm-30) outliers start: 26 outliers final: 19 residues processed: 100 average time/residue: 0.2201 time to fit residues: 31.0619 Evaluate side-chains 95 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 0.0070 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9349 Z= 0.172 Angle : 0.620 10.998 12690 Z= 0.306 Chirality : 0.044 0.320 1498 Planarity : 0.005 0.065 1615 Dihedral : 9.791 107.841 1428 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.14 % Favored : 89.59 % Rotamer: Outliers : 1.78 % Allowed : 20.91 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.25), residues: 1124 helix: 1.95 (0.34), residues: 257 sheet: 0.45 (0.46), residues: 133 loop : -2.21 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 630 HIS 0.002 0.001 HIS A 202 PHE 0.012 0.001 PHE B 487 TYR 0.009 0.001 TYR B 348 ARG 0.006 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 HIS cc_start: 0.4215 (p-80) cc_final: 0.3873 (p-80) REVERT: A 773 LYS cc_start: 0.9127 (tptt) cc_final: 0.8111 (tptt) REVERT: A 777 GLU cc_start: 0.8695 (tt0) cc_final: 0.8350 (pt0) REVERT: A 987 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 415 ILE cc_start: 0.8349 (mp) cc_final: 0.7861 (tp) REVERT: B 446 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6682 (t80) REVERT: B 490 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7023 (tpm170) REVERT: B 737 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7818 (tpp) REVERT: B 999 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7793 (tm-30) outliers start: 18 outliers final: 12 residues processed: 97 average time/residue: 0.1987 time to fit residues: 27.9778 Evaluate side-chains 90 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 6.9990 chunk 33 optimal weight: 0.0020 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.0040 chunk 96 optimal weight: 2.9990 overall best weight: 0.5804 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9349 Z= 0.168 Angle : 0.623 11.133 12690 Z= 0.305 Chirality : 0.045 0.321 1498 Planarity : 0.004 0.046 1615 Dihedral : 9.405 106.985 1427 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.43 % Favored : 90.30 % Rotamer: Outliers : 2.38 % Allowed : 20.71 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1124 helix: 2.00 (0.34), residues: 257 sheet: 0.47 (0.46), residues: 133 loop : -2.18 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 630 HIS 0.002 0.001 HIS B 502 PHE 0.013 0.001 PHE A 272 TYR 0.009 0.001 TYR B 492 ARG 0.009 0.000 ARG B 980 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7948 (tpt) cc_final: 0.7562 (tpp) REVERT: A 622 HIS cc_start: 0.4135 (p-80) cc_final: 0.3785 (p-80) REVERT: A 773 LYS cc_start: 0.9141 (tptt) cc_final: 0.8916 (tptp) REVERT: A 987 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8357 (tm-30) REVERT: B 412 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7547 (p) REVERT: B 415 ILE cc_start: 0.8300 (mp) cc_final: 0.7823 (tp) REVERT: B 446 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.6652 (t80) REVERT: B 490 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7006 (tpm170) REVERT: B 737 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7783 (tpp) REVERT: B 999 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7803 (tm-30) outliers start: 24 outliers final: 16 residues processed: 98 average time/residue: 0.1871 time to fit residues: 27.0862 Evaluate side-chains 95 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0570 chunk 106 optimal weight: 0.0030 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9349 Z= 0.177 Angle : 0.631 11.806 12690 Z= 0.309 Chirality : 0.044 0.316 1498 Planarity : 0.005 0.061 1615 Dihedral : 9.180 106.791 1427 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.70 % Favored : 90.04 % Rotamer: Outliers : 2.08 % Allowed : 21.31 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.13 (0.25), residues: 1124 helix: 1.99 (0.34), residues: 257 sheet: 0.48 (0.46), residues: 133 loop : -2.18 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 630 HIS 0.002 0.001 HIS B 502 PHE 0.022 0.001 PHE A 272 TYR 0.021 0.001 TYR B 492 ARG 0.011 0.000 ARG B 980 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7932 (tpt) cc_final: 0.7551 (tpp) REVERT: A 622 HIS cc_start: 0.4207 (p-80) cc_final: 0.3768 (p-80) REVERT: A 773 LYS cc_start: 0.9170 (tptt) cc_final: 0.8940 (tptp) REVERT: A 987 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 412 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7557 (p) REVERT: B 415 ILE cc_start: 0.8317 (mp) cc_final: 0.7858 (tp) REVERT: B 490 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7039 (tpm170) REVERT: B 737 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7779 (tpp) REVERT: B 999 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7795 (tm-30) outliers start: 21 outliers final: 17 residues processed: 98 average time/residue: 0.1972 time to fit residues: 28.6456 Evaluate side-chains 95 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 114 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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: 0.7786 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9349 Z= 0.180 Angle : 0.648 13.434 12690 Z= 0.316 Chirality : 0.045 0.379 1498 Planarity : 0.004 0.053 1615 Dihedral : 9.050 106.723 1425 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.61 % Favored : 90.12 % Rotamer: Outliers : 1.98 % Allowed : 21.41 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.16 (0.25), residues: 1124 helix: 1.84 (0.34), residues: 257 sheet: 0.51 (0.46), residues: 133 loop : -2.16 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 630 HIS 0.002 0.001 HIS A 202 PHE 0.025 0.001 PHE B 389 TYR 0.015 0.001 TYR B 492 ARG 0.009 0.000 ARG B 980 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7784 (tpt) cc_final: 0.7441 (tpp) REVERT: A 622 HIS cc_start: 0.4175 (p-80) cc_final: 0.3747 (p-80) REVERT: A 773 LYS cc_start: 0.9166 (tptt) cc_final: 0.8938 (tptp) REVERT: A 987 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 412 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7565 (p) REVERT: B 415 ILE cc_start: 0.8311 (mp) cc_final: 0.7852 (tp) REVERT: B 490 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7009 (tpm170) REVERT: B 737 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7759 (tpp) REVERT: B 999 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7825 (tm-30) outliers start: 20 outliers final: 17 residues processed: 96 average time/residue: 0.1814 time to fit residues: 25.8115 Evaluate side-chains 96 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 0.0270 chunk 5 optimal weight: 4.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.117214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.089747 restraints weight = 28329.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.091661 restraints weight = 18473.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094042 restraints weight = 13131.757| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9349 Z= 0.192 Angle : 0.651 14.406 12690 Z= 0.320 Chirality : 0.045 0.345 1498 Planarity : 0.004 0.052 1615 Dihedral : 8.910 105.690 1425 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.70 % Favored : 90.04 % Rotamer: Outliers : 1.88 % Allowed : 21.61 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1124 helix: 1.79 (0.33), residues: 263 sheet: 0.49 (0.47), residues: 133 loop : -2.16 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 630 HIS 0.002 0.001 HIS A1055 PHE 0.024 0.001 PHE B 389 TYR 0.014 0.001 TYR B 492 ARG 0.009 0.000 ARG A 762 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.28 seconds wall clock time: 32 minutes 59.32 seconds (1979.32 seconds total)