Starting phenix.real_space_refine on Thu Jun 27 08:26:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/06_2024/8xuo_38679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/06_2024/8xuo_38679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/06_2024/8xuo_38679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/06_2024/8xuo_38679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/06_2024/8xuo_38679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/06_2024/8xuo_38679_updated.pdb" } resolution = 2.84 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 58 5.16 5 C 7788 2.51 5 N 2102 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G GLU 271": "OE1" <-> "OE2" Residue "G GLU 334": "OE1" <-> "OE2" Residue "G GLU 433": "OE1" <-> "OE2" Residue "G GLU 572": "OE1" <-> "OE2" Residue "G GLU 582": "OE1" <-> "OE2" Residue "G GLU 608": "OE1" <-> "OE2" Residue "G GLU 634": "OE1" <-> "OE2" Residue "G GLU 767": "OE1" <-> "OE2" Residue "G GLU 770": "OE1" <-> "OE2" Residue "G GLU 776": "OE1" <-> "OE2" Residue "G GLU 799": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12254 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6064 Classifications: {'peptide': 752} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 715} Chain: "G" Number of atoms: 6064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6064 Classifications: {'peptide': 752} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 715} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.72, per 1000 atoms: 0.71 Number of scatterers: 12254 At special positions: 0 Unit cell: (106.25, 144.5, 96.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 16 15.00 O 2290 8.00 N 2102 7.00 C 7788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 2.1 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 12 sheets defined 37.4% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 159 through 168 removed outlier: 3.587A pdb=" N ARG A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.754A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 239 No H-bonds generated for 'chain 'A' and resid 236 through 239' Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.528A pdb=" N GLU A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.264A pdb=" N ILE A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'A' and resid 333 through 346 removed outlier: 4.118A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.542A pdb=" N SER A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 removed outlier: 4.043A pdb=" N ASN A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 3.710A pdb=" N ALA A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 413 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.987A pdb=" N THR A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 556 through 562 removed outlier: 3.859A pdb=" N ILE A 559 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Proline residue: A 560 - end of helix No H-bonds generated for 'chain 'A' and resid 556 through 562' Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 673 through 675 No H-bonds generated for 'chain 'A' and resid 673 through 675' Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 696 through 700 Processing helix chain 'A' and resid 705 through 712 removed outlier: 4.082A pdb=" N VAL A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.545A pdb=" N SER A 761 " --> pdb=" O LYS A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 813 removed outlier: 3.724A pdb=" N PHE A 813 " --> pdb=" O ALA A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 813' Processing helix chain 'A' and resid 832 through 836 Processing helix chain 'A' and resid 850 through 869 Processing helix chain 'G' and resid 159 through 168 Processing helix chain 'G' and resid 189 through 197 Processing helix chain 'G' and resid 200 through 205 Processing helix chain 'G' and resid 220 through 231 removed outlier: 3.775A pdb=" N PHE G 231 " --> pdb=" O ILE G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 257 Processing helix chain 'G' and resid 270 through 279 removed outlier: 3.990A pdb=" N ILE G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA G 279 " --> pdb=" O ARG G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 302 Processing helix chain 'G' and resid 314 through 326 Processing helix chain 'G' and resid 333 through 346 removed outlier: 4.458A pdb=" N LEU G 337 " --> pdb=" O PRO G 333 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER G 338 " --> pdb=" O GLU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 363 Processing helix chain 'G' and resid 367 through 380 Processing helix chain 'G' and resid 387 through 400 removed outlier: 3.634A pdb=" N ASN G 391 " --> pdb=" O PRO G 387 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG G 400 " --> pdb=" O MET G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 414 removed outlier: 3.675A pdb=" N ALA G 407 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER G 413 " --> pdb=" O PHE G 409 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 433 Processing helix chain 'G' and resid 444 through 457 Processing helix chain 'G' and resid 479 through 491 Processing helix chain 'G' and resid 510 through 515 removed outlier: 3.764A pdb=" N THR G 515 " --> pdb=" O ARG G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 531 removed outlier: 3.583A pdb=" N THR G 531 " --> pdb=" O ASP G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 562 Proline residue: G 557 - end of helix Proline residue: G 560 - end of helix No H-bonds generated for 'chain 'G' and resid 553 through 562' Processing helix chain 'G' and resid 581 through 585 Processing helix chain 'G' and resid 604 through 607 Processing helix chain 'G' and resid 673 through 675 No H-bonds generated for 'chain 'G' and resid 673 through 675' Processing helix chain 'G' and resid 678 through 683 Processing helix chain 'G' and resid 696 through 700 Processing helix chain 'G' and resid 707 through 712 removed outlier: 4.198A pdb=" N LYS G 712 " --> pdb=" O LEU G 708 " (cutoff:3.500A) Processing helix chain 'G' and resid 738 through 740 No H-bonds generated for 'chain 'G' and resid 738 through 740' Processing helix chain 'G' and resid 757 through 765 Processing helix chain 'G' and resid 810 through 813 removed outlier: 3.542A pdb=" N PHE G 813 " --> pdb=" O ALA G 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 810 through 813' Processing helix chain 'G' and resid 832 through 836 Processing helix chain 'G' and resid 850 through 869 Processing sheet with id= A, first strand: chain 'A' and resid 176 through 182 removed outlier: 7.173A pdb=" N ASN A 287 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N VAL A 179 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL A 289 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 181 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 291 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR A 260 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 290 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 262 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR A 292 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 264 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A 208 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N VAL A 263 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 210 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASP A 265 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 212 " --> pdb=" O ASP A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.200A pdb=" N SER A 540 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 568 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A 591 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 571 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA A 593 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER A 573 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N SER A 595 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN A 575 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR A 614 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N PHE A 594 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 616 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER A 596 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN A 618 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS A 638 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE A 617 " --> pdb=" O HIS A 638 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS A 640 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR A 619 " --> pdb=" O HIS A 640 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.005A pdb=" N SER A 644 " --> pdb=" O LEU A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 690 through 694 removed outlier: 6.639A pdb=" N LYS A 747 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU A 722 " --> pdb=" O LYS A 747 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 749 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASN A 724 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 751 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 771 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU A 750 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS A 773 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 795 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N MET A 774 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TRP A 797 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS A 818 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE A 798 " --> pdb=" O HIS A 818 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 820 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 842 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N LEU A 821 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET A 844 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS A 877 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU A 845 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER A 879 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 783 through 785 removed outlier: 6.243A pdb=" N SER A 805 " --> pdb=" O TRP A 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 461 through 465 removed outlier: 6.702A pdb=" N THR A 474 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 175 through 182 removed outlier: 3.901A pdb=" N GLU G 177 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR G 260 " --> pdb=" O PRO G 286 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR G 208 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL G 263 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE G 210 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASP G 265 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL G 212 " --> pdb=" O ASP G 265 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 518 through 520 removed outlier: 6.030A pdb=" N SER G 540 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL G 568 " --> pdb=" O PHE G 541 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR G 591 " --> pdb=" O LEU G 569 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL G 571 " --> pdb=" O TYR G 591 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA G 593 " --> pdb=" O VAL G 571 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER G 573 " --> pdb=" O ALA G 593 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER G 595 " --> pdb=" O SER G 573 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN G 575 " --> pdb=" O SER G 595 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR G 614 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE G 594 " --> pdb=" O THR G 614 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE G 616 " --> pdb=" O PHE G 594 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N SER G 596 " --> pdb=" O ILE G 616 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN G 618 " --> pdb=" O SER G 596 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS G 638 " --> pdb=" O ILE G 615 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE G 617 " --> pdb=" O HIS G 638 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS G 640 " --> pdb=" O ILE G 617 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR G 619 " --> pdb=" O HIS G 640 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'G' and resid 623 through 625 removed outlier: 6.240A pdb=" N SER G 644 " --> pdb=" O LEU G 624 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'G' and resid 689 through 694 removed outlier: 6.276A pdb=" N ASN G 719 " --> pdb=" O LEU G 690 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE G 692 " --> pdb=" O ASN G 719 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS G 721 " --> pdb=" O ILE G 692 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLY G 694 " --> pdb=" O LYS G 721 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE G 723 " --> pdb=" O GLY G 694 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS G 747 " --> pdb=" O LEU G 720 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N LEU G 722 " --> pdb=" O LYS G 747 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR G 749 " --> pdb=" O LEU G 722 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN G 724 " --> pdb=" O THR G 749 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU G 751 " --> pdb=" O ASN G 724 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL G 771 " --> pdb=" O LEU G 748 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N LEU G 750 " --> pdb=" O VAL G 771 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS G 773 " --> pdb=" O LEU G 750 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL G 795 " --> pdb=" O LEU G 772 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N MET G 774 " --> pdb=" O VAL G 795 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TRP G 797 " --> pdb=" O MET G 774 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS G 818 " --> pdb=" O LEU G 796 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE G 798 " --> pdb=" O HIS G 818 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL G 820 " --> pdb=" O ILE G 798 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL G 842 " --> pdb=" O LEU G 819 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N LEU G 821 " --> pdb=" O VAL G 842 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET G 844 " --> pdb=" O LEU G 821 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS G 877 " --> pdb=" O MET G 843 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LEU G 845 " --> pdb=" O LYS G 877 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER G 879 " --> pdb=" O LEU G 845 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 783 through 785 removed outlier: 6.494A pdb=" N SER G 805 " --> pdb=" O TRP G 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 461 through 465 removed outlier: 6.677A pdb=" N THR G 474 " --> pdb=" O MET G 464 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 858 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: 4.88 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2011 1.32 - 1.44: 3167 1.44 - 1.57: 7236 1.57 - 1.69: 18 1.69 - 1.82: 86 Bond restraints: 12518 Sorted by residual: bond pdb=" N VAL A 830 " pdb=" CA VAL A 830 " ideal model delta sigma weight residual 1.457 1.490 -0.033 9.00e-03 1.23e+04 1.36e+01 bond pdb=" N ILE A 431 " pdb=" CA ILE A 431 " ideal model delta sigma weight residual 1.461 1.503 -0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" N LEU A 429 " pdb=" CA LEU A 429 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" C ARG A 428 " pdb=" O ARG A 428 " ideal model delta sigma weight residual 1.237 1.196 0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" C PRO A 422 " pdb=" O PRO A 422 " ideal model delta sigma weight residual 1.233 1.193 0.040 1.23e-02 6.61e+03 1.08e+01 ... (remaining 12513 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.77: 176 103.77 - 111.86: 6131 111.86 - 119.95: 5068 119.95 - 128.04: 5439 128.04 - 136.14: 138 Bond angle restraints: 16952 Sorted by residual: angle pdb=" O TRP A 430 " pdb=" C TRP A 430 " pdb=" N ILE A 431 " ideal model delta sigma weight residual 122.09 116.21 5.88 1.08e+00 8.57e-01 2.96e+01 angle pdb=" N GLU A 433 " pdb=" CA GLU A 433 " pdb=" C GLU A 433 " ideal model delta sigma weight residual 111.28 105.43 5.85 1.09e+00 8.42e-01 2.88e+01 angle pdb=" N PRO G 648 " pdb=" CA PRO G 648 " pdb=" C PRO G 648 " ideal model delta sigma weight residual 111.14 103.39 7.75 1.56e+00 4.11e-01 2.47e+01 angle pdb=" CA TRP A 430 " pdb=" C TRP A 430 " pdb=" N ILE A 431 " ideal model delta sigma weight residual 117.17 122.73 -5.56 1.18e+00 7.18e-01 2.22e+01 angle pdb=" CA LEU A 426 " pdb=" C LEU A 426 " pdb=" O LEU A 426 " ideal model delta sigma weight residual 120.55 115.60 4.95 1.06e+00 8.90e-01 2.18e+01 ... (remaining 16947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 7326 35.53 - 71.07: 319 71.07 - 106.60: 36 106.60 - 142.14: 14 142.14 - 177.67: 5 Dihedral angle restraints: 7700 sinusoidal: 3292 harmonic: 4408 Sorted by residual: dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 117.67 -177.67 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 122.98 177.02 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP G 901 " pdb=" O3A ADP G 901 " pdb=" PB ADP G 901 " pdb=" PA ADP G 901 " ideal model delta sinusoidal sigma weight residual -60.00 84.01 -144.02 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 7697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 1885 1.004 - 2.007: 0 2.007 - 3.011: 0 3.011 - 4.014: 0 4.014 - 5.018: 7 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C2 IHP A 902 " pdb=" C1 IHP A 902 " pdb=" C3 IHP A 902 " pdb=" O12 IHP A 902 " both_signs ideal model delta sigma weight residual False -2.52 2.50 -5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C2 IHP G 902 " pdb=" C1 IHP G 902 " pdb=" C3 IHP G 902 " pdb=" O12 IHP G 902 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C5 IHP A 902 " pdb=" C4 IHP A 902 " pdb=" C6 IHP A 902 " pdb=" O15 IHP A 902 " both_signs ideal model delta sigma weight residual False -2.42 2.56 -4.98 2.00e-01 2.50e+01 6.20e+02 ... (remaining 1889 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 833 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ALA G 833 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA G 833 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU G 834 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 825 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ASP G 825 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP G 825 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN G 826 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 645 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C ALA G 645 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA G 645 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS G 646 " -0.017 2.00e-02 2.50e+03 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 120 2.56 - 3.14: 10225 3.14 - 3.73: 18914 3.73 - 4.31: 26111 4.31 - 4.90: 42980 Nonbonded interactions: 98350 Sorted by model distance: nonbonded pdb=" O LYS A 712 " pdb=" NZ LYS A 712 " model vdw 1.970 2.520 nonbonded pdb=" O LYS A 758 " pdb=" NZ LYS A 758 " model vdw 2.103 2.520 nonbonded pdb=" O LYS G 712 " pdb=" NZ LYS G 712 " model vdw 2.112 2.520 nonbonded pdb=" N GLU G 504 " pdb=" OE1 GLU G 504 " model vdw 2.176 2.520 nonbonded pdb=" N GLU G 785 " pdb=" OE1 GLU G 785 " model vdw 2.209 2.520 ... (remaining 98345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.910 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.940 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12518 Z= 0.277 Angle : 0.832 10.425 16952 Z= 0.464 Chirality : 0.301 5.018 1892 Planarity : 0.005 0.058 2134 Dihedral : 20.563 177.671 4828 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 2.71 % Allowed : 26.98 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1500 helix: 0.70 (0.22), residues: 520 sheet: 0.31 (0.36), residues: 216 loop : -0.31 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 754 HIS 0.006 0.001 HIS G 638 PHE 0.021 0.001 PHE G 779 TYR 0.016 0.001 TYR A 591 ARG 0.006 0.001 ARG G 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.7209 (ttt) cc_final: 0.6935 (ttp) REVERT: G 606 MET cc_start: 0.5930 (tpt) cc_final: 0.5705 (tpt) outliers start: 37 outliers final: 27 residues processed: 179 average time/residue: 0.8729 time to fit residues: 174.9325 Evaluate side-chains 146 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 591 TYR Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 635 ARG Chi-restraints excluded: chain G residue 697 SER Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 804 VAL 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: 1.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 380 HIS A 640 HIS A 642 ASN A 666 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 522 HIS G 537 HIS G 638 HIS G 640 HIS ** G 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12518 Z= 0.353 Angle : 0.856 15.054 16952 Z= 0.393 Chirality : 0.050 0.550 1892 Planarity : 0.005 0.050 2134 Dihedral : 11.945 170.370 1769 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.74 % Allowed : 23.61 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1500 helix: 0.81 (0.22), residues: 518 sheet: 0.44 (0.36), residues: 220 loop : -0.37 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 211 HIS 0.008 0.002 HIS G 638 PHE 0.015 0.002 PHE A 790 TYR 0.029 0.002 TYR G 591 ARG 0.007 0.001 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 140 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.4257 (OUTLIER) cc_final: 0.4036 (tm-30) REVERT: A 190 THR cc_start: 0.8993 (t) cc_final: 0.8782 (m) REVERT: A 219 ARG cc_start: 0.7050 (mtp-110) cc_final: 0.6593 (mtp-110) REVERT: A 610 TRP cc_start: 0.3328 (OUTLIER) cc_final: 0.2126 (m-90) REVERT: A 772 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (tt) REVERT: A 777 ASN cc_start: 0.7064 (m-40) cc_final: 0.6773 (t0) REVERT: A 800 ARG cc_start: 0.6486 (tpt-90) cc_final: 0.6021 (tpm170) REVERT: G 204 TYR cc_start: 0.5457 (OUTLIER) cc_final: 0.5219 (t80) REVERT: G 294 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8140 (ptm160) REVERT: G 579 PHE cc_start: 0.5790 (m-80) cc_final: 0.5321 (m-80) REVERT: G 581 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6560 (ptt180) REVERT: G 844 MET cc_start: 0.7178 (tmt) cc_final: 0.6693 (tmm) outliers start: 92 outliers final: 40 residues processed: 218 average time/residue: 1.0350 time to fit residues: 248.9332 Evaluate side-chains 155 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 204 TYR Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 581 ARG Chi-restraints excluded: chain G residue 591 TYR Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 622 ARG Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 817 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 666 GLN A 710 ASN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 HIS ** G 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 ASN G 768 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12518 Z= 0.362 Angle : 0.764 10.800 16952 Z= 0.369 Chirality : 0.049 0.420 1892 Planarity : 0.005 0.053 2134 Dihedral : 10.525 141.383 1748 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 7.77 % Allowed : 24.12 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1500 helix: 0.56 (0.23), residues: 510 sheet: 0.15 (0.35), residues: 244 loop : -0.62 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 757 HIS 0.005 0.001 HIS A 818 PHE 0.030 0.003 PHE A 579 TYR 0.030 0.002 TYR G 591 ARG 0.006 0.001 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 160 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.4328 (tm-30) REVERT: A 216 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7698 (tp-100) REVERT: A 219 ARG cc_start: 0.7055 (mtp-110) cc_final: 0.6647 (mtp-110) REVERT: A 239 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7279 (m90) REVERT: A 270 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: A 274 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: A 610 TRP cc_start: 0.3434 (OUTLIER) cc_final: 0.2135 (m-90) REVERT: A 772 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8666 (tt) REVERT: A 785 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6890 (mp0) REVERT: A 800 ARG cc_start: 0.6483 (tpt-90) cc_final: 0.6245 (mmm160) REVERT: A 841 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.5928 (mm110) REVERT: A 844 MET cc_start: 0.7240 (tmm) cc_final: 0.6887 (tmt) REVERT: G 246 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7411 (mt) REVERT: G 294 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8180 (ptm160) REVERT: G 370 TRP cc_start: 0.7037 (m100) cc_final: 0.6727 (m100) REVERT: G 579 PHE cc_start: 0.6021 (m-80) cc_final: 0.5783 (m-80) REVERT: G 718 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.5946 (mm-30) REVERT: G 732 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7629 (ptmt) REVERT: G 735 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8536 (tp) REVERT: G 815 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.6933 (mtt90) REVERT: G 844 MET cc_start: 0.7079 (tmt) cc_final: 0.6743 (tmm) outliers start: 106 outliers final: 35 residues processed: 247 average time/residue: 1.0766 time to fit residues: 290.8386 Evaluate side-chains 182 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 841 GLN Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 389 ASN Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 591 TYR Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 670 THR Chi-restraints excluded: chain G residue 680 VAL Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 804 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 287 ASN A 386 HIS A 666 GLN A 818 HIS ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12518 Z= 0.195 Angle : 0.612 8.494 16952 Z= 0.298 Chirality : 0.042 0.244 1892 Planarity : 0.004 0.045 2134 Dihedral : 9.709 142.403 1739 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.84 % Allowed : 27.13 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1500 helix: 0.89 (0.23), residues: 514 sheet: 0.32 (0.35), residues: 244 loop : -0.50 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 631 HIS 0.002 0.001 HIS G 818 PHE 0.024 0.001 PHE G 876 TYR 0.019 0.001 TYR G 591 ARG 0.009 0.001 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 150 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.6978 (mtp-110) cc_final: 0.6530 (mtp-110) REVERT: A 239 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7203 (m90) REVERT: A 511 ARG cc_start: 0.7157 (mtp-110) cc_final: 0.6901 (mtp85) REVERT: A 610 TRP cc_start: 0.3362 (OUTLIER) cc_final: 0.2060 (m-90) REVERT: A 772 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8692 (tt) REVERT: A 785 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7014 (mp0) REVERT: A 800 ARG cc_start: 0.6425 (tpt-90) cc_final: 0.6128 (mmm160) REVERT: A 815 ARG cc_start: 0.7268 (mtp85) cc_final: 0.6415 (mtm-85) REVERT: A 844 MET cc_start: 0.7297 (tmm) cc_final: 0.6956 (tmm) REVERT: G 239 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6937 (m90) REVERT: G 370 TRP cc_start: 0.7172 (m100) cc_final: 0.6860 (m100) REVERT: G 491 LYS cc_start: 0.7538 (tttt) cc_final: 0.7280 (tttm) REVERT: G 579 PHE cc_start: 0.5850 (m-80) cc_final: 0.5614 (m-80) REVERT: G 732 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7598 (ptmt) REVERT: G 815 ARG cc_start: 0.7564 (mmm-85) cc_final: 0.6641 (mtt90) REVERT: G 823 CYS cc_start: 0.6673 (t) cc_final: 0.6464 (t) outliers start: 66 outliers final: 26 residues processed: 201 average time/residue: 1.0657 time to fit residues: 235.0583 Evaluate side-chains 162 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 469 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 708 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 74 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12518 Z= 0.185 Angle : 0.589 7.575 16952 Z= 0.285 Chirality : 0.042 0.232 1892 Planarity : 0.004 0.043 2134 Dihedral : 9.308 142.414 1732 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.69 % Allowed : 27.42 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1500 helix: 1.04 (0.24), residues: 514 sheet: 0.45 (0.36), residues: 242 loop : -0.44 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 631 HIS 0.002 0.001 HIS G 818 PHE 0.026 0.001 PHE G 876 TYR 0.017 0.001 TYR G 591 ARG 0.009 0.001 ARG G 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 142 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: A 239 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7180 (m90) REVERT: A 610 TRP cc_start: 0.3408 (OUTLIER) cc_final: 0.2109 (m-90) REVERT: A 757 TRP cc_start: 0.5842 (m100) cc_final: 0.5622 (m100) REVERT: A 785 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7105 (mp0) REVERT: A 800 ARG cc_start: 0.6470 (tpt-90) cc_final: 0.6212 (mmm160) REVERT: A 815 ARG cc_start: 0.7337 (mtp85) cc_final: 0.6549 (mtm-85) REVERT: A 844 MET cc_start: 0.7328 (tmm) cc_final: 0.7015 (tmt) REVERT: G 239 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7047 (m90) REVERT: G 294 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8110 (ptm160) REVERT: G 370 TRP cc_start: 0.7177 (m100) cc_final: 0.6764 (t-100) REVERT: G 579 PHE cc_start: 0.5789 (m-80) cc_final: 0.5556 (m-80) REVERT: G 732 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7542 (ptmt) REVERT: G 815 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.6528 (mtt90) REVERT: G 823 CYS cc_start: 0.6697 (t) cc_final: 0.6461 (t) REVERT: G 844 MET cc_start: 0.7051 (tmt) cc_final: 0.6548 (tmm) outliers start: 64 outliers final: 27 residues processed: 189 average time/residue: 1.0435 time to fit residues: 218.3870 Evaluate side-chains 159 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 817 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 0.0000 chunk 76 optimal weight: 0.0170 chunk 139 optimal weight: 8.9990 overall best weight: 0.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12518 Z= 0.168 Angle : 0.584 7.884 16952 Z= 0.282 Chirality : 0.042 0.225 1892 Planarity : 0.004 0.067 2134 Dihedral : 9.015 142.212 1732 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.11 % Allowed : 28.67 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.22), residues: 1500 helix: 1.25 (0.24), residues: 502 sheet: 0.43 (0.35), residues: 254 loop : -0.40 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 370 HIS 0.002 0.000 HIS G 818 PHE 0.028 0.001 PHE G 876 TYR 0.012 0.001 TYR G 591 ARG 0.012 0.001 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 142 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: A 239 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7122 (m90) REVERT: A 610 TRP cc_start: 0.3339 (OUTLIER) cc_final: 0.2048 (m-90) REVERT: A 639 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7179 (tt) REVERT: A 757 TRP cc_start: 0.5891 (m100) cc_final: 0.5651 (m100) REVERT: A 777 ASN cc_start: 0.7542 (m-40) cc_final: 0.7267 (t0) REVERT: A 785 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7156 (mp0) REVERT: A 815 ARG cc_start: 0.7310 (mtp85) cc_final: 0.6580 (mtm-85) REVERT: A 844 MET cc_start: 0.7413 (tmm) cc_final: 0.7028 (tmt) REVERT: G 294 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8139 (ptm160) REVERT: G 370 TRP cc_start: 0.7168 (m100) cc_final: 0.6777 (t-100) REVERT: G 579 PHE cc_start: 0.5664 (m-80) cc_final: 0.5463 (m-80) REVERT: G 732 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7482 (ptmt) REVERT: G 815 ARG cc_start: 0.7211 (mmm-85) cc_final: 0.6295 (mtt90) REVERT: G 823 CYS cc_start: 0.6669 (t) cc_final: 0.6430 (t) REVERT: G 844 MET cc_start: 0.6984 (tmt) cc_final: 0.6552 (tmm) outliers start: 56 outliers final: 23 residues processed: 184 average time/residue: 1.0458 time to fit residues: 211.9741 Evaluate side-chains 157 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12518 Z= 0.240 Angle : 0.636 7.743 16952 Z= 0.309 Chirality : 0.043 0.204 1892 Planarity : 0.004 0.056 2134 Dihedral : 9.082 142.981 1731 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.18 % Allowed : 29.55 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1500 helix: 1.04 (0.24), residues: 514 sheet: 0.29 (0.36), residues: 246 loop : -0.48 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 370 HIS 0.004 0.001 HIS G 818 PHE 0.026 0.002 PHE G 876 TYR 0.025 0.002 TYR G 591 ARG 0.012 0.001 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 138 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: A 239 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7235 (m90) REVERT: A 610 TRP cc_start: 0.3469 (OUTLIER) cc_final: 0.2130 (m-90) REVERT: A 639 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7305 (tt) REVERT: A 765 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7704 (mt0) REVERT: A 768 HIS cc_start: 0.7657 (m170) cc_final: 0.7321 (m90) REVERT: A 777 ASN cc_start: 0.7565 (m-40) cc_final: 0.7175 (t0) REVERT: A 785 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7236 (mp0) REVERT: A 800 ARG cc_start: 0.6822 (mmm160) cc_final: 0.6077 (tpm170) REVERT: A 815 ARG cc_start: 0.7480 (mtp85) cc_final: 0.6829 (mtm-85) REVERT: A 844 MET cc_start: 0.7358 (tmm) cc_final: 0.6953 (tmm) REVERT: G 239 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7179 (m90) REVERT: G 294 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8199 (ptm160) REVERT: G 370 TRP cc_start: 0.7277 (m100) cc_final: 0.6994 (m100) REVERT: G 581 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6761 (ppt170) REVERT: G 815 ARG cc_start: 0.7328 (mmm-85) cc_final: 0.6635 (mtt90) REVERT: G 844 MET cc_start: 0.6959 (tmt) cc_final: 0.6428 (tmm) outliers start: 57 outliers final: 29 residues processed: 182 average time/residue: 1.0635 time to fit residues: 212.7193 Evaluate side-chains 162 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 581 ARG Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 0.1980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN ** G 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12518 Z= 0.171 Angle : 0.597 8.596 16952 Z= 0.288 Chirality : 0.041 0.210 1892 Planarity : 0.004 0.056 2134 Dihedral : 8.840 141.284 1730 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.96 % Allowed : 29.47 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1500 helix: 1.11 (0.24), residues: 518 sheet: 0.28 (0.36), residues: 250 loop : -0.34 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 631 HIS 0.002 0.000 HIS A 818 PHE 0.029 0.001 PHE G 876 TYR 0.011 0.001 TYR G 591 ARG 0.015 0.001 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7233 (m90) REVERT: A 450 ASP cc_start: 0.7457 (t0) cc_final: 0.7024 (m-30) REVERT: A 610 TRP cc_start: 0.3444 (OUTLIER) cc_final: 0.2143 (m-90) REVERT: A 639 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7203 (tt) REVERT: A 765 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7746 (mt0) REVERT: A 768 HIS cc_start: 0.7570 (m170) cc_final: 0.7266 (m90) REVERT: A 777 ASN cc_start: 0.7581 (m-40) cc_final: 0.7156 (t0) REVERT: A 785 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7252 (mp0) REVERT: A 800 ARG cc_start: 0.6746 (mmm160) cc_final: 0.5942 (tpm170) REVERT: A 815 ARG cc_start: 0.7458 (mtp85) cc_final: 0.6820 (mtm-85) REVERT: A 844 MET cc_start: 0.7073 (tmm) cc_final: 0.6782 (tmt) REVERT: G 239 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7120 (m90) REVERT: G 294 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8139 (ptm160) REVERT: G 370 TRP cc_start: 0.7268 (m100) cc_final: 0.7006 (m100) REVERT: G 815 ARG cc_start: 0.7188 (mmm-85) cc_final: 0.6493 (mtt90) REVERT: G 823 CYS cc_start: 0.6652 (t) cc_final: 0.6384 (t) REVERT: G 844 MET cc_start: 0.6950 (tmt) cc_final: 0.6486 (tmm) outliers start: 54 outliers final: 28 residues processed: 172 average time/residue: 1.0784 time to fit residues: 203.9333 Evaluate side-chains 160 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 573 SER Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 708 LEU 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: 4.9990 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS ** G 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 873 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12518 Z= 0.391 Angle : 0.776 11.476 16952 Z= 0.380 Chirality : 0.047 0.218 1892 Planarity : 0.006 0.060 2134 Dihedral : 9.506 143.882 1730 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.74 % Allowed : 29.69 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1500 helix: 0.61 (0.23), residues: 514 sheet: -0.25 (0.33), residues: 268 loop : -0.55 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 211 HIS 0.005 0.001 HIS G 818 PHE 0.026 0.002 PHE G 876 TYR 0.046 0.003 TYR G 591 ARG 0.015 0.001 ARG G 622 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 138 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.6956 (mtp-110) cc_final: 0.6501 (mtp-110) REVERT: A 239 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.7395 (m90) REVERT: A 274 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: A 610 TRP cc_start: 0.3645 (OUTLIER) cc_final: 0.2237 (m-90) REVERT: A 639 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7477 (tt) REVERT: A 765 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7975 (mt0) REVERT: A 768 HIS cc_start: 0.7955 (m170) cc_final: 0.7504 (m90) REVERT: A 815 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7214 (mtm-85) REVERT: G 239 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7272 (m90) REVERT: G 294 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8200 (ptm160) REVERT: G 370 TRP cc_start: 0.7388 (m100) cc_final: 0.7065 (m100) REVERT: G 815 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.6769 (mtt90) REVERT: G 823 CYS cc_start: 0.7341 (t) cc_final: 0.6842 (t) REVERT: G 844 MET cc_start: 0.6934 (tmt) cc_final: 0.6575 (tmm) outliers start: 51 outliers final: 29 residues processed: 178 average time/residue: 1.0834 time to fit residues: 212.1276 Evaluate side-chains 157 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 644 SER Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 873 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12518 Z= 0.226 Angle : 0.662 9.983 16952 Z= 0.321 Chirality : 0.043 0.218 1892 Planarity : 0.005 0.058 2134 Dihedral : 9.203 139.787 1730 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.08 % Allowed : 30.94 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1500 helix: 0.84 (0.23), residues: 526 sheet: -0.12 (0.34), residues: 262 loop : -0.55 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 370 HIS 0.002 0.001 HIS A 638 PHE 0.028 0.002 PHE G 876 TYR 0.019 0.001 TYR G 591 ARG 0.017 0.001 ARG A 746 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7327 (m90) REVERT: A 610 TRP cc_start: 0.3551 (OUTLIER) cc_final: 0.2136 (m-90) REVERT: A 765 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7954 (mt0) REVERT: A 768 HIS cc_start: 0.7925 (m170) cc_final: 0.7526 (m90) REVERT: A 777 ASN cc_start: 0.7607 (m-40) cc_final: 0.7084 (t0) REVERT: A 800 ARG cc_start: 0.6696 (mmm160) cc_final: 0.5833 (tpm170) REVERT: A 815 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7214 (mtm-85) REVERT: A 817 LYS cc_start: 0.7334 (ttpt) cc_final: 0.6856 (mtpm) REVERT: A 844 MET cc_start: 0.6982 (tmm) cc_final: 0.6755 (tmt) REVERT: G 239 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.7162 (m90) REVERT: G 294 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8154 (ptm160) REVERT: G 370 TRP cc_start: 0.7404 (m100) cc_final: 0.7140 (m100) REVERT: G 815 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6981 (mtp85) REVERT: G 844 MET cc_start: 0.6866 (tmt) cc_final: 0.6252 (tmm) outliers start: 42 outliers final: 26 residues processed: 164 average time/residue: 1.0876 time to fit residues: 196.1751 Evaluate side-chains 151 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 644 SER Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 708 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 122 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 GLN G 846 GLN G 858 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.221553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.181131 restraints weight = 15860.484| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.44 r_work: 0.4023 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12518 Z= 0.187 Angle : 0.633 8.729 16952 Z= 0.309 Chirality : 0.042 0.210 1892 Planarity : 0.005 0.056 2134 Dihedral : 8.978 137.953 1730 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.35 % Allowed : 31.60 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1500 helix: 0.85 (0.23), residues: 530 sheet: 0.01 (0.34), residues: 262 loop : -0.50 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 370 HIS 0.002 0.001 HIS G 818 PHE 0.031 0.001 PHE A 779 TYR 0.013 0.001 TYR G 591 ARG 0.014 0.001 ARG A 746 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4357.44 seconds wall clock time: 77 minutes 29.45 seconds (4649.45 seconds total)