Starting phenix.real_space_refine on Sun Apr 7 14:07:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/04_2024/8wot_37698_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/04_2024/8wot_37698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/04_2024/8wot_37698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/04_2024/8wot_37698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/04_2024/8wot_37698_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/04_2024/8wot_37698_neut_updated.pdb" } resolution = 3.18 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= 0.014 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 41": "OD1" <-> "OD2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 791": "OD1" <-> "OD2" Residue "B ASP 795": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.84, per 1000 atoms: 0.55 Number of scatterers: 10672 At special positions: 0 Unit cell: (98.716, 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: 4.64 Conformation dependent library (CDL) restraints added in 1.8 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 800 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 796 " 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: 32 helices and 10 sheets defined 45.5% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 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 303 through 335 removed outlier: 3.767A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 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: 4.768A pdb=" N ASN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLY A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 removed outlier: 4.410A 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: 3.878A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.658A 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 690 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 Processing helix chain 'A' and resid 795 through 816 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: 3.777A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 473 removed outlier: 3.549A 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: 4.935A pdb=" N ASN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 4.009A pdb=" N GLU B 535 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 564 removed outlier: 3.782A 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: 3.853A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.597A 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 782 Processing helix chain 'B' and resid 795 through 816 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: 3.08 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3170 1.34 - 1.46: 2831 1.46 - 1.58: 4885 1.58 - 1.70: 0 1.70 - 1.81: 90 Bond restraints: 10976 Sorted by residual: bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 318 106.95 - 113.72: 6180 113.72 - 120.48: 4315 120.48 - 127.25: 4061 127.25 - 134.01: 106 Bond angle restraints: 14980 Sorted by residual: angle pdb=" C SER A 600 " pdb=" CA SER A 600 " pdb=" CB SER A 600 " ideal model delta sigma weight residual 116.54 110.44 6.10 1.15e+00 7.56e-01 2.81e+01 angle pdb=" C SER B 600 " pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 116.54 110.48 6.06 1.15e+00 7.56e-01 2.78e+01 angle pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " pdb=" CG LEU B 789 " ideal model delta sigma weight residual 116.30 129.42 -13.12 3.50e+00 8.16e-02 1.41e+01 angle pdb=" CA SER A 600 " pdb=" C SER A 600 " pdb=" N ALA A 601 " ideal model delta sigma weight residual 119.52 116.57 2.95 7.90e-01 1.60e+00 1.39e+01 angle pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N ALA B 601 " ideal model delta sigma weight residual 119.52 116.63 2.89 7.90e-01 1.60e+00 1.33e+01 ... (remaining 14975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.66: 6356 25.66 - 51.33: 481 51.33 - 76.99: 59 76.99 - 102.66: 22 102.66 - 128.32: 10 Dihedral angle restraints: 6928 sinusoidal: 3148 harmonic: 3780 Sorted by residual: 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 65.36 -128.32 1 3.00e+01 1.11e-03 1.73e+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 65.32 -128.28 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sinusoidal sigma weight residual 175.11 62.53 112.58 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1596 0.069 - 0.138: 151 0.138 - 0.207: 3 0.207 - 0.276: 0 0.276 - 0.345: 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 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+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 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+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 -2.21 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1749 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.002 2.00e-02 2.50e+03 1.90e-02 4.50e+00 pdb=" CG ASN B 83 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 747 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 748 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 748 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 748 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 747 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 748 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " -0.023 5.00e-02 4.00e+02 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 116 2.60 - 3.17: 9695 3.17 - 3.75: 15909 3.75 - 4.32: 20999 4.32 - 4.90: 35975 Nonbonded interactions: 82694 Sorted by model distance: nonbonded pdb=" OG SER B 701 " pdb=" OH TYR B 717 " model vdw 2.020 2.440 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.073 2.440 nonbonded pdb=" OG SER A 740 " pdb=" OE2 GLU A 742 " model vdw 2.097 2.440 nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 2.103 2.440 nonbonded pdb=" N GLU B 137 " pdb=" OE1 GLU B 137 " model vdw 2.121 2.520 ... (remaining 82689 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: 3.180 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: 9.970 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.130 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 0.052 10976 Z= 0.193 Angle : 0.519 13.124 14980 Z= 0.273 Chirality : 0.040 0.345 1752 Planarity : 0.003 0.045 1802 Dihedral : 17.953 128.319 4470 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.27 % Allowed : 29.86 % Favored : 69.88 % 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: 1.30 (0.25), residues: 1256 helix: 3.00 (0.21), residues: 580 sheet: 0.62 (0.33), residues: 268 loop : -2.36 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 446 HIS 0.001 0.000 HIS B 636 PHE 0.025 0.001 PHE B 705 TYR 0.016 0.001 TYR B 709 ARG 0.002 0.000 ARG B 37 *********************** 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 132 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 689 MET cc_start: 0.8366 (pmm) cc_final: 0.7892 (pmm) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 0.2039 time to fit residues: 40.0895 Evaluate side-chains 131 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 714 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: 0.5980 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 0.0770 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10976 Z= 0.218 Angle : 0.613 10.133 14980 Z= 0.297 Chirality : 0.047 0.489 1752 Planarity : 0.004 0.050 1802 Dihedral : 12.728 112.581 2158 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.69 % Favored : 93.15 % Rotamer: Outliers : 3.09 % Allowed : 26.24 % Favored : 70.67 % 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: 0.66 (0.24), residues: 1256 helix: 2.13 (0.21), residues: 584 sheet: 0.68 (0.32), residues: 268 loop : -2.45 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.025 0.001 PHE A 705 TYR 0.029 0.001 TYR A 717 ARG 0.003 0.000 ARG A 712 *********************** 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 177 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.189 Fit side-chains REVERT: A 287 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6938 (tt) REVERT: A 520 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8359 (tp) REVERT: A 540 LYS cc_start: 0.6101 (tmtt) cc_final: 0.5786 (tmtt) REVERT: A 586 MET cc_start: 0.8125 (mmp) cc_final: 0.7882 (mmp) REVERT: A 689 MET cc_start: 0.8453 (pmm) cc_final: 0.8038 (pmm) REVERT: B 708 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7105 (pt) outliers start: 35 outliers final: 20 residues processed: 167 average time/residue: 0.1992 time to fit residues: 50.7879 Evaluate side-chains 158 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU 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 B residue 75 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 724 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.0570 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10976 Z= 0.242 Angle : 0.611 10.093 14980 Z= 0.298 Chirality : 0.047 0.497 1752 Planarity : 0.004 0.047 1802 Dihedral : 12.044 110.510 2154 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 3.71 % Allowed : 26.06 % Favored : 70.23 % 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: 0.44 (0.24), residues: 1256 helix: 1.90 (0.22), residues: 584 sheet: 0.61 (0.32), residues: 276 loop : -2.56 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.027 0.001 PHE B 705 TYR 0.031 0.001 TYR A 717 ARG 0.002 0.000 ARG A 712 *********************** 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 184 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6947 (tt) REVERT: A 520 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8398 (tp) REVERT: A 540 LYS cc_start: 0.6163 (tmtt) cc_final: 0.5657 (tmtt) REVERT: A 689 MET cc_start: 0.8469 (pmm) cc_final: 0.8076 (pmm) outliers start: 42 outliers final: 31 residues processed: 171 average time/residue: 0.1984 time to fit residues: 51.1264 Evaluate side-chains 165 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0170 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 0.0670 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 0.0270 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10976 Z= 0.144 Angle : 0.587 11.735 14980 Z= 0.280 Chirality : 0.045 0.488 1752 Planarity : 0.004 0.047 1802 Dihedral : 11.414 108.665 2154 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.70 % Favored : 95.14 % Rotamer: Outliers : 3.00 % Allowed : 27.03 % Favored : 69.96 % 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: 0.58 (0.24), residues: 1256 helix: 1.96 (0.22), residues: 580 sheet: 0.77 (0.32), residues: 276 loop : -2.42 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 446 HIS 0.003 0.000 HIS A 636 PHE 0.027 0.001 PHE B 705 TYR 0.030 0.001 TYR A 717 ARG 0.002 0.000 ARG A 712 *********************** 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 170 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.057 Fit side-chains REVERT: A 287 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6929 (tt) REVERT: A 520 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8385 (tp) REVERT: A 540 LYS cc_start: 0.6078 (tmtt) cc_final: 0.5561 (tmtt) REVERT: A 580 MET cc_start: 0.8096 (tpp) cc_final: 0.7671 (tpp) outliers start: 34 outliers final: 20 residues processed: 158 average time/residue: 0.1879 time to fit residues: 45.0818 Evaluate side-chains 150 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU 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 B residue 75 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10976 Z= 0.164 Angle : 0.596 12.149 14980 Z= 0.281 Chirality : 0.045 0.489 1752 Planarity : 0.004 0.047 1802 Dihedral : 11.084 108.201 2154 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 3.09 % Allowed : 26.94 % Favored : 69.96 % 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: 0.56 (0.24), residues: 1256 helix: 1.90 (0.22), residues: 580 sheet: 0.83 (0.32), residues: 276 loop : -2.41 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 446 HIS 0.003 0.000 HIS A 636 PHE 0.026 0.001 PHE B 705 TYR 0.032 0.001 TYR B 717 ARG 0.002 0.000 ARG A 712 *********************** 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 173 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6928 (tt) REVERT: A 520 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8416 (tp) REVERT: A 540 LYS cc_start: 0.6128 (tmtt) cc_final: 0.5584 (tmtt) REVERT: A 602 TYR cc_start: 0.7354 (m-10) cc_final: 0.7138 (m-10) REVERT: B 526 LEU cc_start: 0.8287 (tt) cc_final: 0.7926 (pp) outliers start: 35 outliers final: 25 residues processed: 164 average time/residue: 0.1913 time to fit residues: 48.1483 Evaluate side-chains 159 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU 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 B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.0170 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10976 Z= 0.154 Angle : 0.595 11.522 14980 Z= 0.279 Chirality : 0.045 0.485 1752 Planarity : 0.004 0.047 1802 Dihedral : 10.737 107.433 2154 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 3.18 % Allowed : 27.21 % Favored : 69.61 % 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: 0.56 (0.24), residues: 1256 helix: 1.88 (0.21), residues: 580 sheet: 0.86 (0.32), residues: 276 loop : -2.39 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 629 HIS 0.003 0.001 HIS A 636 PHE 0.032 0.001 PHE B 705 TYR 0.038 0.001 TYR B 717 ARG 0.003 0.000 ARG A 712 *********************** 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 172 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6913 (tt) REVERT: A 520 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8410 (tp) REVERT: A 540 LYS cc_start: 0.6087 (tmtt) cc_final: 0.5485 (tmtt) REVERT: A 602 TYR cc_start: 0.7350 (m-10) cc_final: 0.7116 (m-10) REVERT: B 596 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7130 (p0) outliers start: 36 outliers final: 27 residues processed: 164 average time/residue: 0.1860 time to fit residues: 46.2191 Evaluate side-chains 160 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU 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 B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS 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: 1.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10976 Z= 0.244 Angle : 0.630 12.333 14980 Z= 0.298 Chirality : 0.046 0.504 1752 Planarity : 0.004 0.049 1802 Dihedral : 10.524 107.249 2154 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 3.98 % Allowed : 26.50 % Favored : 69.52 % 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: 0.47 (0.24), residues: 1256 helix: 1.82 (0.22), residues: 580 sheet: 0.77 (0.32), residues: 276 loop : -2.42 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 446 HIS 0.004 0.001 HIS A 796 PHE 0.030 0.001 PHE A 705 TYR 0.039 0.001 TYR B 717 ARG 0.003 0.000 ARG A 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 178 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 133 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8494 (pt) cc_final: 0.8078 (tt) REVERT: A 287 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6980 (tt) REVERT: A 520 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8456 (tp) REVERT: A 602 TYR cc_start: 0.7466 (m-10) cc_final: 0.7197 (m-10) outliers start: 45 outliers final: 37 residues processed: 166 average time/residue: 0.1905 time to fit residues: 48.6306 Evaluate side-chains 168 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1561 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= 0.171 Angle : 0.614 11.811 14980 Z= 0.288 Chirality : 0.045 0.494 1752 Planarity : 0.004 0.048 1802 Dihedral : 10.339 106.752 2154 Min Nonbonded Distance : 1.594 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 3.36 % Allowed : 27.56 % Favored : 69.08 % 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: 0.50 (0.24), residues: 1256 helix: 1.81 (0.22), residues: 582 sheet: 0.80 (0.32), residues: 276 loop : -2.39 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.026 0.001 PHE B 732 TYR 0.039 0.001 TYR B 717 ARG 0.003 0.000 ARG A 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 173 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8488 (pt) cc_final: 0.8066 (tt) REVERT: A 287 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6911 (tt) REVERT: A 520 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 602 TYR cc_start: 0.7449 (m-10) cc_final: 0.7183 (m-10) REVERT: B 596 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7099 (p0) REVERT: B 745 LEU cc_start: 0.6179 (tp) cc_final: 0.5682 (tt) outliers start: 38 outliers final: 30 residues processed: 164 average time/residue: 0.1826 time to fit residues: 45.8184 Evaluate side-chains 162 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 697 LEU 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 B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0980 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 88 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10976 Z= 0.168 Angle : 0.629 12.355 14980 Z= 0.292 Chirality : 0.045 0.498 1752 Planarity : 0.004 0.047 1802 Dihedral : 10.107 106.006 2154 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 3.27 % Allowed : 28.18 % Favored : 68.55 % 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: 0.55 (0.24), residues: 1256 helix: 1.86 (0.22), residues: 578 sheet: 0.86 (0.32), residues: 276 loop : -2.35 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.035 0.001 PHE A 573 TYR 0.033 0.001 TYR A 717 ARG 0.004 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 177 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8469 (pt) cc_final: 0.8054 (tt) REVERT: A 287 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6834 (tt) REVERT: A 326 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7857 (mt) REVERT: A 520 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8489 (tp) REVERT: A 602 TYR cc_start: 0.7429 (m-10) cc_final: 0.7126 (m-10) REVERT: B 596 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7101 (p0) REVERT: B 745 LEU cc_start: 0.6144 (tp) cc_final: 0.5719 (tt) outliers start: 37 outliers final: 30 residues processed: 166 average time/residue: 0.1848 time to fit residues: 46.5482 Evaluate side-chains 169 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 697 LEU 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 B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1655 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= 0.242 Angle : 0.662 11.454 14980 Z= 0.311 Chirality : 0.047 0.514 1752 Planarity : 0.004 0.048 1802 Dihedral : 10.008 105.735 2154 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.63 % Rotamer: Outliers : 3.27 % Allowed : 28.00 % Favored : 68.73 % 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: 0.49 (0.24), residues: 1256 helix: 1.86 (0.22), residues: 568 sheet: 0.78 (0.32), residues: 276 loop : -2.34 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 446 HIS 0.003 0.001 HIS A 636 PHE 0.055 0.001 PHE B 705 TYR 0.049 0.001 TYR A 717 ARG 0.004 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 165 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8464 (pt) cc_final: 0.8050 (tt) REVERT: A 287 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6879 (tt) REVERT: A 326 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7863 (mt) REVERT: A 520 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8531 (tp) REVERT: A 602 TYR cc_start: 0.7453 (m-10) cc_final: 0.7163 (m-10) outliers start: 37 outliers final: 32 residues processed: 156 average time/residue: 0.1840 time to fit residues: 43.6413 Evaluate side-chains 162 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 697 LEU 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 791 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 5 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 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 = 0.4071 r_free = 0.4071 target = 0.142793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.097222 restraints weight = 17036.298| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.82 r_work: 0.3320 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10976 Z= 0.381 Angle : 0.723 10.381 14980 Z= 0.349 Chirality : 0.050 0.552 1752 Planarity : 0.004 0.048 1802 Dihedral : 10.097 106.096 2154 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.07 % Rotamer: Outliers : 3.71 % Allowed : 27.47 % Favored : 68.82 % 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: 0.11 (0.24), residues: 1256 helix: 1.52 (0.22), residues: 580 sheet: 0.53 (0.31), residues: 276 loop : -2.53 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 446 HIS 0.003 0.001 HIS A 800 PHE 0.020 0.002 PHE A 705 TYR 0.033 0.002 TYR A 717 ARG 0.005 0.000 ARG B 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.34 seconds wall clock time: 42 minutes 19.99 seconds (2539.99 seconds total)