Starting phenix.real_space_refine on Thu Feb 15 13:54:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysw_34084/02_2024/7ysw_34084_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysw_34084/02_2024/7ysw_34084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysw_34084/02_2024/7ysw_34084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysw_34084/02_2024/7ysw_34084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysw_34084/02_2024/7ysw_34084_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysw_34084/02_2024/7ysw_34084_updated.pdb" } resolution = 3.03 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= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 S 63 5.16 5 C 7924 2.51 5 N 2129 2.21 5 O 2289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 327": "OD1" <-> "OD2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ASP 480": "OD1" <-> "OD2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 535": "OD1" <-> "OD2" Residue "A ASP 598": "OD1" <-> "OD2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A ASP 769": "OD1" <-> "OD2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "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: 12407 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Chain: "E" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1597 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 7523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7523 Classifications: {'peptide': 921} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 869} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1442 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 16, 'TRANS': 162} Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 176 Unusual residues: {'IDS': 5, 'SGN': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8830 SG CYS A 739 38.710 77.102 99.185 1.00 62.48 S Time building chain proxies: 6.43, per 1000 atoms: 0.52 Number of scatterers: 12407 At special positions: 0 Unit cell: (85.488, 123.848, 141.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 63 16.00 O 2289 8.00 N 2129 7.00 C 7924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 271 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 224 " distance=2.03 Simple disulfide: pdb=" SG CYS E 271 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 963 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 621 " distance=2.03 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 970 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 113 " 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 Atom "HETATM12365 O5 SGN F 8 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=10, symmetry=0 Links applied ALPHA1-4 " IDS F 1 " - " SGN F 2 " " IDS F 3 " - " SGN F 4 " " IDS F 5 " - " SGN F 6 " " IDS F 7 " - " SGN F 8 " " IDS F 9 " - " SGN F 10 " BETA1-4 " SGN F 2 " - " IDS F 3 " ~> Even though IDS is an alpha isomer, a beta linkage is required... " SGN F 4 " - " IDS F 5 " " SGN F 6 " - " IDS F 7 " " SGN F 8 " - " IDS F 9 " Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 739 " 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 18 sheets defined 24.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'E' and resid 152 through 155 No H-bonds generated for 'chain 'E' and resid 152 through 155' Processing helix chain 'E' and resid 216 through 218 No H-bonds generated for 'chain 'E' and resid 216 through 218' Processing helix chain 'A' and resid 37 through 46 removed outlier: 3.873A pdb=" N GLN A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP A 42 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 45 " --> pdb=" O TRP A 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 46 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.821A pdb=" N HIS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 167 through 183 removed outlier: 3.633A pdb=" N TYR A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.769A pdb=" N ALA A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 217 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 218 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 225 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A 226 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 325 through 332 Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 382 through 385 Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 578 through 588 Processing helix chain 'A' and resid 599 through 602 No H-bonds generated for 'chain 'A' and resid 599 through 602' Processing helix chain 'A' and resid 613 through 628 Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 660 through 679 removed outlier: 4.929A pdb=" N HIS A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 717 Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 758 through 765 Proline residue: A 763 - end of helix Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 849 through 863 removed outlier: 4.108A pdb=" N ARG A 853 " --> pdb=" O PRO A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 903 removed outlier: 3.516A pdb=" N TYR A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 950 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 166 through 169 Processing sheet with id= A, first strand: chain 'C' and resid 168 through 171 removed outlier: 4.167A pdb=" N ARG C 203 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL C 210 " --> pdb=" O ARG C 201 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 201 " --> pdb=" O VAL C 210 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 266 through 270 Processing sheet with id= C, first strand: chain 'C' and resid 302 through 304 removed outlier: 3.561A pdb=" N HIS C 286 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU C 330 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 168 through 171 removed outlier: 3.540A pdb=" N ARG E 201 " --> pdb=" O VAL E 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 181 through 186 removed outlier: 3.670A pdb=" N GLY E 220 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU E 239 " --> pdb=" O GLY E 220 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 267 through 271 removed outlier: 3.641A pdb=" N VAL E 267 " --> pdb=" O LEU E 320 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 280 through 282 Processing sheet with id= H, first strand: chain 'A' and resid 293 through 295 removed outlier: 4.251A pdb=" N TYR A 233 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE A 410 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A 455 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 412 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA A 457 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU A 414 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE A 367 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 413 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU A 369 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 302 through 304 removed outlier: 3.643A pdb=" N TRP A 302 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 912 through 914 removed outlier: 6.557A pdb=" N HIS A 592 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ASP A 529 " --> pdb=" O HIS A 592 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG A 594 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A 632 " --> pdb=" O PHE A 593 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 595 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 634 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 683 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS A 725 " --> pdb=" O TRP A 684 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 729 through 731 removed outlier: 6.569A pdb=" N ALA A 805 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 734 through 737 Processing sheet with id= M, first strand: chain 'A' and resid 928 through 931 Processing sheet with id= N, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.024A pdb=" N VAL A 546 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 563 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N LEU A 548 " --> pdb=" O ASP A 561 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N ASP A 561 " --> pdb=" O LEU A 548 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 158 through 161 removed outlier: 13.017A pdb=" N ILE B 40 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ILE B 55 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU B 42 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 93 through 96 Processing sheet with id= Q, first strand: chain 'B' and resid 115 through 119 Processing sheet with id= R, first strand: chain 'B' and resid 75 through 79 removed outlier: 6.798A pdb=" N PHE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 861 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: 3.86 Time building geometry restraints manager: 6.06 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: 3979 1.34 - 1.46: 3105 1.46 - 1.58: 5618 1.58 - 1.69: 5 1.69 - 1.81: 74 Bond restraints: 12781 Sorted by residual: bond pdb=" O6 SGN F 6 " pdb=" S2 SGN F 6 " ideal model delta sigma weight residual 1.660 1.519 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" O6 SGN F 4 " pdb=" S2 SGN F 4 " ideal model delta sigma weight residual 1.660 1.522 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" O6 SGN F 10 " pdb=" S2 SGN F 10 " ideal model delta sigma weight residual 1.660 1.524 0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" O6 SGN F 2 " pdb=" S2 SGN F 2 " ideal model delta sigma weight residual 1.660 1.524 0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" O6 SGN F 8 " pdb=" S2 SGN F 8 " ideal model delta sigma weight residual 1.660 1.525 0.135 2.00e-02 2.50e+03 4.57e+01 ... (remaining 12776 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.50: 324 105.50 - 113.27: 6908 113.27 - 121.04: 6224 121.04 - 128.81: 3822 128.81 - 136.59: 152 Bond angle restraints: 17430 Sorted by residual: angle pdb=" C3 IDS F 1 " pdb=" C4 IDS F 1 " pdb=" O4 IDS F 1 " ideal model delta sigma weight residual 108.24 135.78 -27.54 3.00e+00 1.11e-01 8.43e+01 angle pdb=" C3 IDS F 7 " pdb=" C4 IDS F 7 " pdb=" O4 IDS F 7 " ideal model delta sigma weight residual 108.24 135.42 -27.18 3.00e+00 1.11e-01 8.21e+01 angle pdb=" C3 SGN F 6 " pdb=" C4 SGN F 6 " pdb=" O4 SGN F 6 " ideal model delta sigma weight residual 108.83 135.26 -26.43 3.00e+00 1.11e-01 7.76e+01 angle pdb=" C5 SGN F 8 " pdb=" C4 SGN F 8 " pdb=" O4 SGN F 8 " ideal model delta sigma weight residual 108.84 133.83 -24.99 3.00e+00 1.11e-01 6.94e+01 angle pdb=" O1S SGN F 2 " pdb=" S1 SGN F 2 " pdb=" O2S SGN F 2 " ideal model delta sigma weight residual 101.21 125.33 -24.12 3.00e+00 1.11e-01 6.47e+01 ... (remaining 17425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.23: 7089 31.23 - 62.46: 388 62.46 - 93.68: 56 93.68 - 124.91: 74 124.91 - 156.14: 19 Dihedral angle restraints: 7626 sinusoidal: 3215 harmonic: 4411 Sorted by residual: dihedral pdb=" C2 SGN F 8 " pdb=" C3 SGN F 8 " pdb=" C4 SGN F 8 " pdb=" O4 SGN F 8 " ideal model delta sinusoidal sigma weight residual 67.57 -136.29 -156.14 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O3 SGN F 8 " pdb=" C3 SGN F 8 " pdb=" C4 SGN F 8 " pdb=" O4 SGN F 8 " ideal model delta sinusoidal sigma weight residual -172.07 -17.53 -154.54 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C6 SGN F 6 " pdb=" C4 SGN F 6 " pdb=" C5 SGN F 6 " pdb=" O4 SGN F 6 " ideal model delta sinusoidal sigma weight residual -171.98 -21.86 -150.12 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 7623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.943: 1843 0.943 - 1.885: 3 1.885 - 2.828: 2 2.828 - 3.770: 0 3.770 - 4.713: 3 Chirality restraints: 1851 Sorted by residual: chirality pdb=" C4 SGN F 4 " pdb=" C3 SGN F 4 " pdb=" C5 SGN F 4 " pdb=" O4 SGN F 4 " both_signs ideal model delta sigma weight residual False -2.48 2.23 -4.71 2.00e-01 2.50e+01 5.55e+02 chirality pdb=" C4 IDS F 5 " pdb=" C3 IDS F 5 " pdb=" C5 IDS F 5 " pdb=" O4 IDS F 5 " both_signs ideal model delta sigma weight residual False -2.41 2.02 -4.43 2.00e-01 2.50e+01 4.91e+02 chirality pdb=" C4 IDS F 7 " pdb=" C3 IDS F 7 " pdb=" C5 IDS F 7 " pdb=" O4 IDS F 7 " both_signs ideal model delta sigma weight residual False -2.41 1.68 -4.09 2.00e-01 2.50e+01 4.18e+02 ... (remaining 1848 not shown) Planarity restraints: 2228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 215 " 0.063 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO C 216 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 772 " 0.014 2.00e-02 2.50e+03 1.09e-02 3.00e+00 pdb=" CG TRP A 772 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 772 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 772 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 772 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 772 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 772 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 772 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 772 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 772 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 649 " 0.119 9.50e-02 1.11e+02 5.40e-02 2.77e+00 pdb=" NE ARG A 649 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 649 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 649 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 649 " -0.001 2.00e-02 2.50e+03 ... (remaining 2225 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 124 2.54 - 3.13: 9328 3.13 - 3.72: 19923 3.72 - 4.31: 28212 4.31 - 4.90: 47582 Nonbonded interactions: 105169 Sorted by model distance: nonbonded pdb=" OD1 ASP A 815 " pdb="ZN ZN A1001 " model vdw 1.948 2.230 nonbonded pdb=" OD1 ASP A 426 " pdb="ZN ZN A1001 " model vdw 1.995 2.230 nonbonded pdb=" CZ ARG E 203 " pdb=" O5 SGN F 8 " model vdw 2.050 2.616 nonbonded pdb=" OD2 ASP A 745 " pdb="ZN ZN A1001 " model vdw 2.098 2.230 nonbonded pdb=" OH TYR A 697 " pdb=" OH TYR A 827 " model vdw 2.104 2.440 ... (remaining 105164 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' and (resid 142 through 308 or resid 315 through 351)) selection = (chain 'E' and resid 142 through 351) } 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: 3.340 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: 0.020 Extract box with map and model: 14.140 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.120 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 12781 Z= 0.472 Angle : 1.013 27.545 17430 Z= 0.394 Chirality : 0.203 4.713 1851 Planarity : 0.004 0.094 2228 Dihedral : 24.629 156.141 4778 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.77 % Allowed : 22.63 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.74 (0.21), residues: 1505 helix: -0.02 (0.27), residues: 383 sheet: -1.24 (0.30), residues: 314 loop : -1.69 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 772 HIS 0.004 0.001 HIS A 407 PHE 0.013 0.001 PHE B 115 TYR 0.016 0.001 TYR A 827 ARG 0.018 0.001 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 124 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: E 320 LEU cc_start: 0.4021 (OUTLIER) cc_final: 0.3524 (tt) REVERT: A 608 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: A 649 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7903 (ttm110) REVERT: B 101 ASN cc_start: 0.8168 (p0) cc_final: 0.7924 (p0) outliers start: 62 outliers final: 56 residues processed: 181 average time/residue: 0.2217 time to fit residues: 59.9733 Evaluate side-chains 180 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 122 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 173 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 HIS B 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12781 Z= 0.277 Angle : 0.638 11.002 17430 Z= 0.296 Chirality : 0.049 0.447 1851 Planarity : 0.004 0.059 2228 Dihedral : 25.649 138.454 1998 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.16 % Rotamer: Outliers : 4.93 % Allowed : 21.94 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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 (0.22), residues: 1505 helix: 0.49 (0.27), residues: 382 sheet: -1.07 (0.31), residues: 307 loop : -1.65 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 772 HIS 0.004 0.001 HIS E 206 PHE 0.009 0.001 PHE A 595 TYR 0.015 0.001 TYR A 432 ARG 0.008 0.000 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 129 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: C 240 ASP cc_start: 0.7619 (t0) cc_final: 0.7385 (t0) REVERT: E 192 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.7110 (m-70) REVERT: E 326 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: A 148 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8348 (tpt90) REVERT: A 308 MET cc_start: 0.8322 (mmm) cc_final: 0.8096 (tpp) REVERT: A 572 CYS cc_start: 0.6853 (m) cc_final: 0.6542 (m) REVERT: A 649 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7894 (ttm110) REVERT: A 687 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8187 (mpm) REVERT: A 722 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7162 (pt0) REVERT: A 936 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: A 942 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7862 (mtpp) outliers start: 64 outliers final: 42 residues processed: 183 average time/residue: 0.2434 time to fit residues: 65.5756 Evaluate side-chains 174 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 173 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN A 608 GLN A 943 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12781 Z= 0.232 Angle : 0.579 9.834 17430 Z= 0.271 Chirality : 0.048 0.436 1851 Planarity : 0.004 0.054 2228 Dihedral : 22.927 121.903 1961 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 5.16 % Allowed : 21.17 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.39 (0.22), residues: 1505 helix: 0.59 (0.27), residues: 382 sheet: -1.04 (0.31), residues: 297 loop : -1.64 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 772 HIS 0.004 0.001 HIS A 280 PHE 0.008 0.001 PHE A 595 TYR 0.013 0.001 TYR B 43 ARG 0.004 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 131 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: C 151 HIS cc_start: 0.7820 (m-70) cc_final: 0.7561 (m-70) REVERT: C 240 ASP cc_start: 0.7705 (t0) cc_final: 0.7354 (t0) REVERT: E 194 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7109 (tp30) REVERT: E 239 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7948 (tp) REVERT: E 326 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7331 (pm20) REVERT: A 572 CYS cc_start: 0.6817 (m) cc_final: 0.6510 (m) REVERT: A 687 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8118 (mpm) REVERT: A 868 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: A 919 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: A 936 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: A 942 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7898 (mtpp) REVERT: B 89 MET cc_start: 0.8282 (mmm) cc_final: 0.7889 (mmm) outliers start: 67 outliers final: 40 residues processed: 184 average time/residue: 0.2462 time to fit residues: 66.5864 Evaluate side-chains 173 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 126 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 206 HIS Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 963 CYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 199 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 39 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN A 943 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12781 Z= 0.232 Angle : 0.579 10.975 17430 Z= 0.272 Chirality : 0.048 0.441 1851 Planarity : 0.004 0.052 2228 Dihedral : 21.670 117.157 1946 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 5.00 % Allowed : 21.17 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.38 (0.22), residues: 1505 helix: 0.65 (0.27), residues: 382 sheet: -1.06 (0.30), residues: 297 loop : -1.65 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 772 HIS 0.003 0.001 HIS A 407 PHE 0.008 0.001 PHE A 595 TYR 0.012 0.001 TYR A 827 ARG 0.005 0.000 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 133 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: C 240 ASP cc_start: 0.7774 (t0) cc_final: 0.7396 (t0) REVERT: E 194 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7107 (tp30) REVERT: E 211 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.5539 (mmm) REVERT: E 239 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7906 (tp) REVERT: E 326 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: A 148 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8178 (tpt90) REVERT: A 535 ASP cc_start: 0.8092 (p0) cc_final: 0.7647 (p0) REVERT: A 572 CYS cc_start: 0.6878 (m) cc_final: 0.6545 (m) REVERT: A 687 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8180 (mpm) REVERT: A 868 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8311 (mtm) REVERT: A 919 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: A 936 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: A 942 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7815 (mtpp) REVERT: B 89 MET cc_start: 0.8335 (mmm) cc_final: 0.7797 (mmm) outliers start: 65 outliers final: 47 residues processed: 182 average time/residue: 0.2554 time to fit residues: 66.9086 Evaluate side-chains 185 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 129 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.6980 chunk 82 optimal weight: 0.0970 chunk 2 optimal weight: 0.0670 chunk 107 optimal weight: 0.0060 chunk 59 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 overall best weight: 0.2532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12781 Z= 0.163 Angle : 0.562 10.286 17430 Z= 0.261 Chirality : 0.047 0.454 1851 Planarity : 0.004 0.053 2228 Dihedral : 20.265 115.664 1943 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 4.46 % Allowed : 21.56 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.26 (0.22), residues: 1505 helix: 0.84 (0.28), residues: 383 sheet: -0.99 (0.30), residues: 299 loop : -1.63 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 772 HIS 0.003 0.001 HIS A 407 PHE 0.015 0.001 PHE B 115 TYR 0.011 0.001 TYR B 43 ARG 0.006 0.000 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 126 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: C 155 MET cc_start: 0.6669 (mmt) cc_final: 0.6303 (mmt) REVERT: C 240 ASP cc_start: 0.7737 (t0) cc_final: 0.7329 (t0) REVERT: E 194 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7051 (tp30) REVERT: E 211 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.5457 (mmm) REVERT: E 239 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7879 (tp) REVERT: E 326 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: A 342 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6359 (ttmt) REVERT: A 535 ASP cc_start: 0.7907 (p0) cc_final: 0.7496 (p0) REVERT: A 572 CYS cc_start: 0.6850 (m) cc_final: 0.6521 (m) REVERT: A 649 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7764 (ttt-90) REVERT: A 687 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8123 (mpm) REVERT: A 868 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8227 (mtm) REVERT: A 919 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: A 936 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 942 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7818 (mtpp) REVERT: B 89 MET cc_start: 0.8335 (mmm) cc_final: 0.7771 (mmm) outliers start: 58 outliers final: 41 residues processed: 171 average time/residue: 0.2498 time to fit residues: 62.6527 Evaluate side-chains 174 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 199 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12781 Z= 0.309 Angle : 0.618 9.911 17430 Z= 0.289 Chirality : 0.050 0.452 1851 Planarity : 0.004 0.055 2228 Dihedral : 18.842 117.528 1940 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.82 % Rotamer: Outliers : 5.31 % Allowed : 20.86 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.42 (0.22), residues: 1505 helix: 0.68 (0.28), residues: 376 sheet: -1.13 (0.30), residues: 303 loop : -1.68 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 772 HIS 0.004 0.001 HIS A 275 PHE 0.018 0.001 PHE B 98 TYR 0.015 0.001 TYR A 432 ARG 0.006 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 126 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: C 155 MET cc_start: 0.6644 (mmt) cc_final: 0.6272 (mmt) REVERT: C 240 ASP cc_start: 0.7648 (t0) cc_final: 0.7239 (t0) REVERT: E 194 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7044 (tp30) REVERT: E 211 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5599 (mmm) REVERT: E 222 TYR cc_start: 0.7018 (m-80) cc_final: 0.6421 (m-80) REVERT: E 239 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7463 (tt) REVERT: E 326 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: A 148 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8218 (tpt90) REVERT: A 196 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8120 (tp) REVERT: A 342 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6148 (ttmt) REVERT: A 687 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8171 (mpm) REVERT: A 868 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: A 919 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: A 936 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: A 942 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7903 (mtpp) REVERT: B 89 MET cc_start: 0.8318 (mmm) cc_final: 0.7751 (mmm) outliers start: 69 outliers final: 47 residues processed: 181 average time/residue: 0.2606 time to fit residues: 68.5369 Evaluate side-chains 182 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 124 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 199 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.5980 chunk 82 optimal weight: 0.0970 chunk 105 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.0970 chunk 57 optimal weight: 0.5980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12781 Z= 0.185 Angle : 0.589 9.974 17430 Z= 0.270 Chirality : 0.049 0.425 1851 Planarity : 0.004 0.055 2228 Dihedral : 16.648 117.445 1940 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 4.93 % Allowed : 21.40 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.31 (0.22), residues: 1505 helix: 0.87 (0.28), residues: 378 sheet: -1.09 (0.30), residues: 305 loop : -1.66 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 772 HIS 0.004 0.001 HIS C 151 PHE 0.016 0.001 PHE B 98 TYR 0.011 0.001 TYR B 43 ARG 0.008 0.000 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 129 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: C 155 MET cc_start: 0.6660 (mmt) cc_final: 0.6338 (mmt) REVERT: C 240 ASP cc_start: 0.7608 (t0) cc_final: 0.7195 (t0) REVERT: E 194 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6991 (tp30) REVERT: E 211 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.5589 (mmm) REVERT: E 222 TYR cc_start: 0.6970 (m-80) cc_final: 0.6402 (m-80) REVERT: E 239 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7441 (tt) REVERT: E 326 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: A 148 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8114 (tpt90) REVERT: A 342 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6371 (ttmt) REVERT: A 535 ASP cc_start: 0.7943 (p0) cc_final: 0.7504 (p0) REVERT: A 687 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8192 (mpm) REVERT: A 868 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8212 (mtm) REVERT: A 919 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: A 936 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: A 942 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7870 (mtpp) REVERT: B 89 MET cc_start: 0.8338 (mmm) cc_final: 0.7729 (mmm) outliers start: 64 outliers final: 45 residues processed: 179 average time/residue: 0.2692 time to fit residues: 69.2570 Evaluate side-chains 179 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 199 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.3980 chunk 43 optimal weight: 0.0670 chunk 28 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12781 Z= 0.184 Angle : 0.583 10.282 17430 Z= 0.269 Chirality : 0.048 0.394 1851 Planarity : 0.004 0.057 2228 Dihedral : 14.259 115.617 1936 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 4.46 % Allowed : 21.56 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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 (0.22), residues: 1505 helix: 1.02 (0.28), residues: 377 sheet: -1.03 (0.30), residues: 301 loop : -1.68 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 772 HIS 0.004 0.001 HIS C 151 PHE 0.010 0.001 PHE B 98 TYR 0.018 0.001 TYR A 827 ARG 0.006 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 128 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: C 155 MET cc_start: 0.6644 (mmt) cc_final: 0.6283 (mmt) REVERT: C 240 ASP cc_start: 0.7633 (t0) cc_final: 0.7247 (t0) REVERT: E 194 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6953 (tp30) REVERT: E 211 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.5493 (mmm) REVERT: E 222 TYR cc_start: 0.6968 (m-80) cc_final: 0.6435 (m-80) REVERT: E 239 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7465 (tt) REVERT: E 326 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: A 148 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8158 (tpt90) REVERT: A 342 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6482 (ttmt) REVERT: A 358 LYS cc_start: 0.8114 (ptpp) cc_final: 0.7892 (mmtt) REVERT: A 535 ASP cc_start: 0.7989 (p0) cc_final: 0.7648 (p0) REVERT: A 649 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7976 (ttt-90) REVERT: A 687 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8150 (mpm) REVERT: A 868 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8220 (mtm) REVERT: A 919 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: A 936 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: A 942 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7769 (mtpp) REVERT: B 89 MET cc_start: 0.8315 (mmm) cc_final: 0.7665 (mmm) REVERT: B 121 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6473 (pm20) outliers start: 58 outliers final: 40 residues processed: 173 average time/residue: 0.2623 time to fit residues: 65.7851 Evaluate side-chains 176 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 125 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 194 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 121 optimal weight: 0.3980 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 0.0770 chunk 142 optimal weight: 3.9990 chunk 86 optimal weight: 0.0070 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12781 Z= 0.164 Angle : 0.572 10.103 17430 Z= 0.263 Chirality : 0.047 0.464 1851 Planarity : 0.004 0.058 2228 Dihedral : 13.304 112.953 1932 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 4.08 % Allowed : 21.86 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.15 (0.22), residues: 1505 helix: 1.10 (0.28), residues: 377 sheet: -0.89 (0.31), residues: 293 loop : -1.65 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 772 HIS 0.004 0.001 HIS C 151 PHE 0.014 0.001 PHE B 98 TYR 0.013 0.001 TYR A 827 ARG 0.009 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 126 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: C 155 MET cc_start: 0.6626 (mmt) cc_final: 0.6272 (mmt) REVERT: C 240 ASP cc_start: 0.7624 (t0) cc_final: 0.7263 (t0) REVERT: E 194 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6929 (tp30) REVERT: E 211 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5374 (mmm) REVERT: E 222 TYR cc_start: 0.6917 (m-80) cc_final: 0.6514 (m-80) REVERT: E 239 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7440 (tt) REVERT: E 326 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: A 342 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6571 (ttmt) REVERT: A 358 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7881 (mmtt) REVERT: A 535 ASP cc_start: 0.7952 (p0) cc_final: 0.7664 (p0) REVERT: A 649 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.7965 (ttt-90) REVERT: A 687 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8114 (mpm) REVERT: A 868 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8199 (mtm) REVERT: A 919 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: A 936 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: A 942 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7834 (mtpp) REVERT: B 89 MET cc_start: 0.8326 (mmm) cc_final: 0.7669 (mmm) REVERT: B 121 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6450 (pm20) outliers start: 53 outliers final: 37 residues processed: 168 average time/residue: 0.2670 time to fit residues: 66.9915 Evaluate side-chains 169 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 122 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 0.0980 chunk 126 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12781 Z= 0.203 Angle : 0.581 10.298 17430 Z= 0.269 Chirality : 0.047 0.466 1851 Planarity : 0.004 0.058 2228 Dihedral : 12.976 110.250 1930 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 3.93 % Allowed : 22.17 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.20 (0.22), residues: 1505 helix: 1.00 (0.28), residues: 377 sheet: -0.94 (0.30), residues: 304 loop : -1.64 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 772 HIS 0.003 0.001 HIS A 407 PHE 0.013 0.001 PHE B 98 TYR 0.020 0.001 TYR A 827 ARG 0.008 0.000 ARG A 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3010 Ramachandran restraints generated. 1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 126 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: C 155 MET cc_start: 0.6623 (mmt) cc_final: 0.6253 (mmt) REVERT: C 240 ASP cc_start: 0.7585 (t0) cc_final: 0.7230 (t0) REVERT: E 194 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6950 (tp30) REVERT: E 211 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.5410 (mmm) REVERT: E 222 TYR cc_start: 0.6908 (m-80) cc_final: 0.6500 (m-80) REVERT: E 239 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7400 (tt) REVERT: E 326 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: A 148 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8166 (tpt90) REVERT: A 342 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6593 (ttmt) REVERT: A 358 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7887 (mmtt) REVERT: A 649 ARG cc_start: 0.8266 (mtp-110) cc_final: 0.7987 (ttt-90) REVERT: A 687 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8167 (mpm) REVERT: A 868 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8268 (mtm) REVERT: A 919 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: A 936 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: A 942 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7824 (mtpp) REVERT: B 89 MET cc_start: 0.8331 (mmm) cc_final: 0.7678 (mmm) REVERT: B 121 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6581 (pm20) outliers start: 51 outliers final: 38 residues processed: 165 average time/residue: 0.2856 time to fit residues: 66.8615 Evaluate side-chains 172 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 123 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain E residue 149 TRP Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LYS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 194 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 0.0370 chunk 21 optimal weight: 20.0000 chunk 104 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.182157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.123885 restraints weight = 15156.016| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.24 r_work: 0.3529 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12781 Z= 0.210 Angle : 0.578 10.242 17430 Z= 0.269 Chirality : 0.046 0.464 1851 Planarity : 0.004 0.058 2228 Dihedral : 12.653 108.594 1929 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 3.85 % Allowed : 22.17 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.21 (0.22), residues: 1505 helix: 0.98 (0.28), residues: 378 sheet: -0.93 (0.30), residues: 304 loop : -1.65 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 772 HIS 0.003 0.001 HIS A 407 PHE 0.011 0.001 PHE B 98 TYR 0.015 0.001 TYR A 827 ARG 0.008 0.000 ARG A 653 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.80 seconds wall clock time: 56 minutes 4.44 seconds (3364.44 seconds total)