Starting phenix.real_space_refine on Thu Jun 19 15:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fn6_29306/06_2025/8fn6_29306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fn6_29306/06_2025/8fn6_29306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fn6_29306/06_2025/8fn6_29306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fn6_29306/06_2025/8fn6_29306.map" model { file = "/net/cci-nas-00/data/ceres_data/8fn6_29306/06_2025/8fn6_29306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fn6_29306/06_2025/8fn6_29306.cif" } resolution = 3.7 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= 0.001 sd= 0.059 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 49 5.49 5 S 124 5.16 5 C 13997 2.51 5 N 3921 2.21 5 O 4330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22421 Number of models: 1 Model: "" Number of chains: 8 Chain: "g" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 960 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 22} Link IDs: {'rna2p': 5, 'rna3p': 40} Chain breaks: 1 Chain: "1" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2768 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain: "2" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3421 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3705 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain: "4" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5790 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 20, 'TRANS': 720} Chain breaks: 1 Chain: "5" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2163 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 15, 'TRANS': 260} Chain: "6" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3583 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 11, 'TRANS': 440} Chain: "g" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.96, per 1000 atoms: 0.58 Number of scatterers: 22421 At special positions: 0 Unit cell: (115.5, 139.7, 213.4, 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 124 16.00 P 49 15.00 O 4330 8.00 N 3921 7.00 C 13997 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 2.7 seconds 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5206 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 10 sheets defined 59.8% alpha, 4.9% beta 18 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 7.06 Creating SS restraints... Processing helix chain '1' and resid 195 through 217 removed outlier: 4.142A pdb=" N ILE 1 199 " --> pdb=" O LYS 1 195 " (cutoff:3.500A) Processing helix chain '1' and resid 245 through 253 Processing helix chain '1' and resid 269 through 274 removed outlier: 3.502A pdb=" N GLN 1 274 " --> pdb=" O LEU 1 270 " (cutoff:3.500A) Processing helix chain '1' and resid 277 through 282 Processing helix chain '1' and resid 349 through 356 Processing helix chain '1' and resid 440 through 459 removed outlier: 4.104A pdb=" N VAL 1 444 " --> pdb=" O ASP 1 440 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY 1 445 " --> pdb=" O VAL 1 441 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG 1 454 " --> pdb=" O GLU 1 450 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU 1 455 " --> pdb=" O LEU 1 451 " (cutoff:3.500A) Processing helix chain '1' and resid 461 through 466 removed outlier: 4.003A pdb=" N GLU 1 466 " --> pdb=" O ASP 1 462 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 60 Processing helix chain '2' and resid 67 through 78 Processing helix chain '2' and resid 89 through 104 removed outlier: 3.607A pdb=" N LEU 2 93 " --> pdb=" O LYS 2 89 " (cutoff:3.500A) Processing helix chain '2' and resid 134 through 138 removed outlier: 4.183A pdb=" N TYR 2 138 " --> pdb=" O GLU 2 134 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 134 through 138' Processing helix chain '2' and resid 192 through 196 removed outlier: 4.534A pdb=" N LYS 2 195 " --> pdb=" O ASP 2 192 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 236 removed outlier: 3.535A pdb=" N ALA 2 216 " --> pdb=" O ALA 2 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP 2 227 " --> pdb=" O MET 2 223 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 259 removed outlier: 3.711A pdb=" N ALA 2 255 " --> pdb=" O ARG 2 252 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS 2 256 " --> pdb=" O SER 2 253 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN 2 257 " --> pdb=" O VAL 2 254 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 275 removed outlier: 3.534A pdb=" N VAL 2 267 " --> pdb=" O PRO 2 263 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 299 removed outlier: 4.540A pdb=" N ALA 2 290 " --> pdb=" O SER 2 286 " (cutoff:3.500A) Processing helix chain '2' and resid 365 through 373 removed outlier: 3.861A pdb=" N ALA 2 369 " --> pdb=" O LYS 2 365 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 384 removed outlier: 3.877A pdb=" N ASP 2 383 " --> pdb=" O SER 2 380 " (cutoff:3.500A) Processing helix chain '2' and resid 449 through 453 removed outlier: 3.851A pdb=" N ARG 2 453 " --> pdb=" O GLN 2 450 " (cutoff:3.500A) Processing helix chain '2' and resid 456 through 474 Processing helix chain '3' and resid 4 through 19 Processing helix chain '3' and resid 24 through 36 Processing helix chain '3' and resid 38 through 62 removed outlier: 3.645A pdb=" N LEU 3 42 " --> pdb=" O SER 3 38 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU 3 43 " --> pdb=" O PRO 3 39 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU 3 54 " --> pdb=" O GLU 3 50 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN 3 55 " --> pdb=" O LEU 3 51 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN 3 56 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG 3 57 " --> pdb=" O ALA 3 53 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 101 Processing helix chain '3' and resid 106 through 119 Processing helix chain '3' and resid 124 through 134 Processing helix chain '3' and resid 142 through 158 removed outlier: 3.602A pdb=" N ILE 3 146 " --> pdb=" O GLN 3 142 " (cutoff:3.500A) Proline residue: 3 152 - end of helix removed outlier: 3.703A pdb=" N ARG 3 155 " --> pdb=" O LEU 3 151 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU 3 156 " --> pdb=" O PRO 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 161 No H-bonds generated for 'chain '3' and resid 159 through 161' Processing helix chain '3' and resid 162 through 176 removed outlier: 4.404A pdb=" N HIS 3 168 " --> pdb=" O ARG 3 164 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE 3 176 " --> pdb=" O LEU 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 183 through 194 Processing helix chain '3' and resid 199 through 210 removed outlier: 3.866A pdb=" N LEU 3 210 " --> pdb=" O CYS 3 206 " (cutoff:3.500A) Processing helix chain '3' and resid 214 through 225 removed outlier: 3.809A pdb=" N ALA 3 218 " --> pdb=" O PHE 3 214 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL 3 225 " --> pdb=" O ILE 3 221 " (cutoff:3.500A) Processing helix chain '3' and resid 225 through 236 Processing helix chain '3' and resid 238 through 257 removed outlier: 3.536A pdb=" N VAL 3 242 " --> pdb=" O ASP 3 238 " (cutoff:3.500A) Processing helix chain '3' and resid 260 through 274 Processing helix chain '3' and resid 279 through 291 removed outlier: 3.668A pdb=" N PHE 3 290 " --> pdb=" O VAL 3 286 " (cutoff:3.500A) Processing helix chain '3' and resid 297 through 309 removed outlier: 3.826A pdb=" N ALA 3 309 " --> pdb=" O SER 3 305 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 316 Processing helix chain '3' and resid 321 through 335 Processing helix chain '3' and resid 340 through 353 removed outlier: 4.402A pdb=" N ASN 3 353 " --> pdb=" O ASN 3 349 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 371 removed outlier: 4.017A pdb=" N LEU 3 362 " --> pdb=" O LEU 3 358 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 376 No H-bonds generated for 'chain '3' and resid 374 through 376' Processing helix chain '3' and resid 377 through 385 Processing helix chain '3' and resid 387 through 396 removed outlier: 3.965A pdb=" N HIS 3 395 " --> pdb=" O ARG 3 391 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN 3 396 " --> pdb=" O ARG 3 392 " (cutoff:3.500A) Processing helix chain '3' and resid 399 through 413 Processing helix chain '3' and resid 418 through 435 Proline residue: 3 427 - end of helix Processing helix chain '3' and resid 440 through 457 Processing helix chain '3' and resid 462 through 480 Processing helix chain '4' and resid 337 through 346 Processing helix chain '4' and resid 351 through 360 removed outlier: 3.749A pdb=" N MET 4 355 " --> pdb=" O SER 4 351 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN 4 360 " --> pdb=" O PHE 4 356 " (cutoff:3.500A) Processing helix chain '4' and resid 367 through 381 removed outlier: 4.051A pdb=" N GLU 4 380 " --> pdb=" O CYS 4 376 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS 4 381 " --> pdb=" O LEU 4 377 " (cutoff:3.500A) Processing helix chain '4' and resid 385 through 395 Processing helix chain '4' and resid 400 through 414 Processing helix chain '4' and resid 439 through 451 Processing helix chain '4' and resid 467 through 487 removed outlier: 3.543A pdb=" N SER 4 471 " --> pdb=" O ASN 4 467 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY 4 487 " --> pdb=" O SER 4 483 " (cutoff:3.500A) Processing helix chain '4' and resid 490 through 501 Processing helix chain '4' and resid 508 through 522 removed outlier: 3.876A pdb=" N GLY 4 522 " --> pdb=" O ILE 4 518 " (cutoff:3.500A) Processing helix chain '4' and resid 525 through 540 Processing helix chain '4' and resid 543 through 565 removed outlier: 3.500A pdb=" N LEU 4 547 " --> pdb=" O TYR 4 543 " (cutoff:3.500A) Proline residue: 4 552 - end of helix removed outlier: 3.602A pdb=" N LEU 4 565 " --> pdb=" O VAL 4 561 " (cutoff:3.500A) Processing helix chain '4' and resid 572 through 590 removed outlier: 3.593A pdb=" N VAL 4 576 " --> pdb=" O ASN 4 572 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU 4 588 " --> pdb=" O THR 4 584 " (cutoff:3.500A) Processing helix chain '4' and resid 595 through 608 removed outlier: 3.616A pdb=" N LYS 4 607 " --> pdb=" O HIS 4 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN 4 608 " --> pdb=" O THR 4 604 " (cutoff:3.500A) Processing helix chain '4' and resid 615 through 626 removed outlier: 4.480A pdb=" N SER 4 619 " --> pdb=" O GLU 4 615 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG 4 626 " --> pdb=" O LEU 4 622 " (cutoff:3.500A) Processing helix chain '4' and resid 627 through 633 removed outlier: 6.441A pdb=" N THR 4 630 " --> pdb=" O THR 4 627 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER 4 631 " --> pdb=" O ARG 4 628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA 4 632 " --> pdb=" O ARG 4 629 " (cutoff:3.500A) Processing helix chain '4' and resid 643 through 647 removed outlier: 3.715A pdb=" N GLN 4 646 " --> pdb=" O ASN 4 643 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 4 647 " --> pdb=" O MET 4 644 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 643 through 647' Processing helix chain '4' and resid 648 through 660 removed outlier: 3.852A pdb=" N GLY 4 653 " --> pdb=" O ASP 4 649 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU 4 654 " --> pdb=" O ASP 4 650 " (cutoff:3.500A) Processing helix chain '4' and resid 662 through 666 removed outlier: 3.609A pdb=" N LEU 4 665 " --> pdb=" O THR 4 662 " (cutoff:3.500A) Processing helix chain '4' and resid 667 through 684 Processing helix chain '4' and resid 689 through 704 removed outlier: 3.687A pdb=" N VAL 4 693 " --> pdb=" O PRO 4 689 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN 4 703 " --> pdb=" O VAL 4 699 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY 4 704 " --> pdb=" O TRP 4 700 " (cutoff:3.500A) Processing helix chain '4' and resid 705 through 707 No H-bonds generated for 'chain '4' and resid 705 through 707' Processing helix chain '4' and resid 711 through 720 Processing helix chain '4' and resid 721 through 725 Processing helix chain '4' and resid 726 through 737 Processing helix chain '4' and resid 744 through 751 Processing helix chain '4' and resid 753 through 761 removed outlier: 3.890A pdb=" N LEU 4 758 " --> pdb=" O PRO 4 755 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU 4 759 " --> pdb=" O ARG 4 756 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 4 760 " --> pdb=" O ARG 4 757 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU 4 761 " --> pdb=" O LEU 4 758 " (cutoff:3.500A) Processing helix chain '4' and resid 762 through 773 Processing helix chain '4' and resid 775 through 781 removed outlier: 3.814A pdb=" N MET 4 779 " --> pdb=" O GLU 4 775 " (cutoff:3.500A) Processing helix chain '4' and resid 783 through 799 removed outlier: 4.024A pdb=" N LEU 4 787 " --> pdb=" O LEU 4 783 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL 4 788 " --> pdb=" O SER 4 784 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA 4 789 " --> pdb=" O HIS 4 785 " (cutoff:3.500A) Processing helix chain '4' and resid 805 through 818 Processing helix chain '4' and resid 824 through 833 removed outlier: 3.567A pdb=" N THR 4 832 " --> pdb=" O ASN 4 828 " (cutoff:3.500A) Processing helix chain '4' and resid 834 through 836 No H-bonds generated for 'chain '4' and resid 834 through 836' Processing helix chain '4' and resid 848 through 857 Processing helix chain '4' and resid 862 through 876 Processing helix chain '4' and resid 884 through 894 removed outlier: 3.746A pdb=" N ARG 4 890 " --> pdb=" O LEU 4 886 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY 4 891 " --> pdb=" O LEU 4 887 " (cutoff:3.500A) Processing helix chain '4' and resid 899 through 913 removed outlier: 3.803A pdb=" N TYR 4 903 " --> pdb=" O ASN 4 899 " (cutoff:3.500A) Processing helix chain '4' and resid 918 through 933 removed outlier: 3.599A pdb=" N PHE 4 929 " --> pdb=" O LEU 4 925 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU 4 932 " --> pdb=" O SER 4 928 " (cutoff:3.500A) Processing helix chain '4' and resid 936 through 950 removed outlier: 4.047A pdb=" N SER 4 945 " --> pdb=" O SER 4 941 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER 4 946 " --> pdb=" O ARG 4 942 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE 4 947 " --> pdb=" O MET 4 943 " (cutoff:3.500A) Processing helix chain '4' and resid 951 through 954 Processing helix chain '4' and resid 956 through 970 removed outlier: 4.088A pdb=" N ALA 4 960 " --> pdb=" O ASP 4 956 " (cutoff:3.500A) Processing helix chain '4' and resid 977 through 990 removed outlier: 4.247A pdb=" N ALA 4 981 " --> pdb=" O ASP 4 977 " (cutoff:3.500A) Processing helix chain '4' and resid 995 through 1010 Processing helix chain '4' and resid 1013 through 1030 removed outlier: 4.083A pdb=" N VAL 41017 " --> pdb=" O HIS 41013 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN 41030 " --> pdb=" O ARG 41026 " (cutoff:3.500A) Processing helix chain '4' and resid 1034 through 1049 Processing helix chain '4' and resid 1052 through 1059 removed outlier: 3.815A pdb=" N ASN 41058 " --> pdb=" O GLY 41054 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 41059 " --> pdb=" O ALA 41055 " (cutoff:3.500A) Processing helix chain '4' and resid 1059 through 1068 removed outlier: 3.681A pdb=" N SER 41065 " --> pdb=" O ALA 41061 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE 41066 " --> pdb=" O LEU 41062 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 41067 " --> pdb=" O GLY 41063 " (cutoff:3.500A) Processing helix chain '4' and resid 1074 through 1085 Processing helix chain '5' and resid 34 through 52 removed outlier: 3.580A pdb=" N LEU 5 38 " --> pdb=" O ASN 5 34 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL 5 39 " --> pdb=" O ARG 5 35 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG 5 43 " --> pdb=" O VAL 5 39 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP 5 44 " --> pdb=" O HIS 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 66 through 71 removed outlier: 3.684A pdb=" N ARG 5 71 " --> pdb=" O GLU 5 68 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 93 No H-bonds generated for 'chain '5' and resid 91 through 93' Processing helix chain '5' and resid 94 through 109 removed outlier: 3.601A pdb=" N GLU 5 100 " --> pdb=" O THR 5 96 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG 5 103 " --> pdb=" O MET 5 99 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA 5 108 " --> pdb=" O TYR 5 104 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 120 Processing helix chain '5' and resid 147 through 158 removed outlier: 3.760A pdb=" N HIS 5 151 " --> pdb=" O ASN 5 147 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 185 removed outlier: 4.082A pdb=" N TYR 5 184 " --> pdb=" O PRO 5 180 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE 5 185 " --> pdb=" O LEU 5 181 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 180 through 185' Processing helix chain '5' and resid 198 through 210 Processing helix chain '5' and resid 212 through 216 removed outlier: 4.006A pdb=" N GLU 5 216 " --> pdb=" O PRO 5 213 " (cutoff:3.500A) Processing helix chain '5' and resid 246 through 255 removed outlier: 4.385A pdb=" N MET 5 250 " --> pdb=" O TYR 5 246 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP 5 251 " --> pdb=" O GLU 5 247 " (cutoff:3.500A) Processing helix chain '5' and resid 265 through 272 Processing helix chain '5' and resid 274 through 279 removed outlier: 3.811A pdb=" N VAL 5 279 " --> pdb=" O MET 5 275 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 81 removed outlier: 3.811A pdb=" N GLY 6 81 " --> pdb=" O HIS 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 83 through 97 removed outlier: 4.049A pdb=" N ALA 6 87 " --> pdb=" O ASN 6 83 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA 6 96 " --> pdb=" O ARG 6 92 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR 6 97 " --> pdb=" O VAL 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 119 removed outlier: 3.512A pdb=" N VAL 6 109 " --> pdb=" O ASP 6 105 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 6 112 " --> pdb=" O SER 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 125 through 133 removed outlier: 3.614A pdb=" N ASP 6 133 " --> pdb=" O ARG 6 129 " (cutoff:3.500A) Processing helix chain '6' and resid 146 through 154 removed outlier: 3.509A pdb=" N VAL 6 150 " --> pdb=" O VAL 6 146 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 175 removed outlier: 3.636A pdb=" N VAL 6 165 " --> pdb=" O ASP 6 161 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE 6 166 " --> pdb=" O ALA 6 162 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU 6 167 " --> pdb=" O ARG 6 163 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG 6 175 " --> pdb=" O GLN 6 171 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 196 removed outlier: 3.946A pdb=" N LYS 6 194 " --> pdb=" O SER 6 190 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY 6 196 " --> pdb=" O PHE 6 192 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 215 Processing helix chain '6' and resid 222 through 235 removed outlier: 4.078A pdb=" N ILE 6 226 " --> pdb=" O ALA 6 222 " (cutoff:3.500A) Processing helix chain '6' and resid 238 through 252 Processing helix chain '6' and resid 257 through 270 Proline residue: 6 263 - end of helix Processing helix chain '6' and resid 278 through 287 removed outlier: 3.509A pdb=" N THR 6 284 " --> pdb=" O LYS 6 280 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 309 removed outlier: 3.593A pdb=" N GLY 6 309 " --> pdb=" O PHE 6 305 " (cutoff:3.500A) Processing helix chain '6' and resid 312 through 324 removed outlier: 3.775A pdb=" N VAL 6 324 " --> pdb=" O THR 6 320 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 328 removed outlier: 4.555A pdb=" N ASP 6 328 " --> pdb=" O GLU 6 325 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 325 through 328' Processing helix chain '6' and resid 334 through 346 removed outlier: 3.549A pdb=" N THR 6 338 " --> pdb=" O TYR 6 334 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE 6 342 " --> pdb=" O THR 6 338 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN 6 343 " --> pdb=" O LEU 6 339 " (cutoff:3.500A) Processing helix chain '6' and resid 349 through 359 removed outlier: 3.820A pdb=" N PHE 6 353 " --> pdb=" O ASN 6 349 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG 6 359 " --> pdb=" O ASN 6 355 " (cutoff:3.500A) Processing helix chain '6' and resid 368 through 381 removed outlier: 4.101A pdb=" N HIS 6 381 " --> pdb=" O THR 6 377 " (cutoff:3.500A) Processing helix chain '6' and resid 386 through 401 removed outlier: 3.814A pdb=" N ARG 6 392 " --> pdb=" O GLU 6 388 " (cutoff:3.500A) Processing helix chain '6' and resid 405 through 420 Processing helix chain '6' and resid 423 through 435 removed outlier: 4.257A pdb=" N VAL 6 435 " --> pdb=" O SER 6 431 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 457 Processing helix chain '6' and resid 460 through 474 Proline residue: 6 466 - end of helix Processing helix chain '6' and resid 474 through 479 Processing helix chain '6' and resid 484 through 496 Processing helix chain '6' and resid 500 through 509 Processing sheet with id=AA1, first strand: chain '1' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain '1' and resid 221 through 229 removed outlier: 3.604A pdb=" N LYS 1 229 " --> pdb=" O VAL 1 262 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL 1 262 " --> pdb=" O LYS 1 229 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 262 through 263 current: chain '1' and resid 304 through 309 removed outlier: 7.575A pdb=" N GLN 1 304 " --> pdb=" O SER 1 320 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER 1 320 " --> pdb=" O GLN 1 304 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N HIS 1 306 " --> pdb=" O VAL 1 318 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL 1 318 " --> pdb=" O HIS 1 306 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP 1 308 " --> pdb=" O LEU 1 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 315 through 320 current: chain '1' and resid 400 through 412 Processing sheet with id=AA3, first strand: chain '1' and resid 243 through 244 Processing sheet with id=AA4, first strand: chain '1' and resid 362 through 364 Processing sheet with id=AA5, first strand: chain '2' and resid 175 through 179 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 175 through 179 current: chain '2' and resid 277 through 280 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 277 through 280 current: chain '2' and resid 323 through 325 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 323 through 325 current: chain '2' and resid 353 through 360 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 353 through 360 current: chain '2' and resid 418 through 429 Processing sheet with id=AA6, first strand: chain '5' and resid 57 through 61 removed outlier: 6.969A pdb=" N ALA 5 13 " --> pdb=" O HIS 5 59 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET 5 61 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL 5 15 " --> pdb=" O MET 5 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 76 through 78 Processing sheet with id=AA8, first strand: chain '5' and resid 131 through 134 Processing sheet with id=AA9, first strand: chain '5' and resid 192 through 196 removed outlier: 6.210A pdb=" N LEU 5 193 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU 5 222 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR 5 195 " --> pdb=" O LEU 5 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '5' and resid 228 through 229 1019 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7318 1.34 - 1.46: 4084 1.46 - 1.58: 11244 1.58 - 1.70: 95 1.70 - 1.82: 191 Bond restraints: 22932 Sorted by residual: bond pdb=" C4 ATP g 201 " pdb=" C5 ATP g 201 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.43e+01 bond pdb=" C5 ATP g 201 " pdb=" C6 ATP g 201 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 bond pdb=" C8 ATP g 201 " pdb=" N7 ATP g 201 " ideal model delta sigma weight residual 1.310 1.355 -0.045 1.00e-02 1.00e+04 2.07e+01 bond pdb=" C5 ATP g 201 " pdb=" N7 ATP g 201 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" C4 ATP g 201 " pdb=" N9 ATP g 201 " ideal model delta sigma weight residual 1.374 1.332 0.042 1.00e-02 1.00e+04 1.80e+01 ... (remaining 22927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 31147 3.66 - 7.32: 123 7.32 - 10.98: 18 10.98 - 14.64: 1 14.64 - 18.30: 1 Bond angle restraints: 31290 Sorted by residual: angle pdb=" PB ATP g 201 " pdb=" O3B ATP g 201 " pdb=" PG ATP g 201 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP g 201 " pdb=" O3A ATP g 201 " pdb=" PB ATP g 201 " ideal model delta sigma weight residual 136.83 124.25 12.58 1.00e+00 1.00e+00 1.58e+02 angle pdb=" C5 ATP g 201 " pdb=" C4 ATP g 201 " pdb=" N3 ATP g 201 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" N3 ATP g 201 " pdb=" C4 ATP g 201 " pdb=" N9 ATP g 201 " ideal model delta sigma weight residual 127.04 135.03 -7.99 1.15e+00 7.59e-01 4.84e+01 angle pdb=" N1 ATP g 201 " pdb=" C2 ATP g 201 " pdb=" N3 ATP g 201 " ideal model delta sigma weight residual 128.69 123.63 5.06 1.00e+00 1.00e+00 2.56e+01 ... (remaining 31285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.43: 12745 25.43 - 50.85: 1076 50.85 - 76.28: 136 76.28 - 101.70: 27 101.70 - 127.13: 2 Dihedral angle restraints: 13986 sinusoidal: 5992 harmonic: 7994 Sorted by residual: dihedral pdb=" O4' A g 5 " pdb=" C1' A g 5 " pdb=" N9 A g 5 " pdb=" C4 A g 5 " ideal model delta sinusoidal sigma weight residual -106.00 -167.61 61.61 1 1.70e+01 3.46e-03 1.74e+01 dihedral pdb=" CA ASP 4 862 " pdb=" C ASP 4 862 " pdb=" N LYS 4 863 " pdb=" CA LYS 4 863 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLN 5 75 " pdb=" C GLN 5 75 " pdb=" N MET 5 76 " pdb=" CA MET 5 76 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 13983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3024 0.051 - 0.103: 523 0.103 - 0.154: 80 0.154 - 0.205: 6 0.205 - 0.256: 2 Chirality restraints: 3635 Sorted by residual: chirality pdb=" CB VAL 4 501 " pdb=" CA VAL 4 501 " pdb=" CG1 VAL 4 501 " pdb=" CG2 VAL 4 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL 1 372 " pdb=" CA VAL 1 372 " pdb=" CG1 VAL 1 372 " pdb=" CG2 VAL 1 372 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE 4 366 " pdb=" N ILE 4 366 " pdb=" C ILE 4 366 " pdb=" CB ILE 4 366 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 3632 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 492 " -0.020 2.00e-02 2.50e+03 2.13e-02 7.93e+00 pdb=" CG PHE 6 492 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 492 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 492 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 492 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 492 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE 6 492 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 6 489 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C GLU 6 489 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU 6 489 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU 6 490 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 4 361 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C GLU 4 361 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU 4 361 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN 4 362 " 0.012 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1706 2.74 - 3.28: 23417 3.28 - 3.82: 37118 3.82 - 4.36: 40715 4.36 - 4.90: 68598 Nonbonded interactions: 171554 Sorted by model distance: nonbonded pdb=" OG SER 4 525 " pdb=" OE1 GLU 4 528 " model vdw 2.196 3.040 nonbonded pdb=" O LEU 3 370 " pdb=" OG SER 3 374 " model vdw 2.200 3.040 nonbonded pdb=" O ARG 6 281 " pdb=" OG1 THR 6 284 " model vdw 2.235 3.040 nonbonded pdb=" O ARG 41056 " pdb=" OG SER 41060 " model vdw 2.240 3.040 nonbonded pdb=" OD2 ASP 2 124 " pdb=" NH2 ARG 6 235 " model vdw 2.249 3.120 ... (remaining 171549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 53.920 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 22933 Z= 0.164 Angle : 0.652 18.302 31290 Z= 0.362 Chirality : 0.040 0.256 3635 Planarity : 0.004 0.043 3880 Dihedral : 17.575 127.130 8780 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 0.60 % Allowed : 26.07 % Favored : 73.32 % 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: -0.22 (0.17), residues: 2711 helix: 0.91 (0.14), residues: 1502 sheet: 0.02 (0.36), residues: 217 loop : -1.84 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 2 443 HIS 0.005 0.001 HIS 6 475 PHE 0.048 0.001 PHE 6 492 TYR 0.015 0.001 TYR 4 341 ARG 0.008 0.000 ARG 3 415 Details of bonding type rmsd hydrogen bonds : bond 0.14385 ( 1055) hydrogen bonds : angle 5.54177 ( 3048) covalent geometry : bond 0.00281 (22932) covalent geometry : angle 0.65163 (31290) Misc. bond : bond 0.03971 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 248 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 103 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7429 (mmt90) REVERT: 5 167 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: 5 265 TRP cc_start: 0.7608 (t-100) cc_final: 0.6314 (m-90) outliers start: 14 outliers final: 5 residues processed: 259 average time/residue: 0.3609 time to fit residues: 147.9197 Evaluate side-chains 235 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 228 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 275 LEU Chi-restraints excluded: chain 4 residue 494 LEU Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 6 residue 402 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 140 HIS 3 168 HIS ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 922 GLN 4 950 ASN 41052 HIS 5 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.174866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.140444 restraints weight = 44456.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.140279 restraints weight = 59809.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.141887 restraints weight = 50887.937| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22933 Z= 0.178 Angle : 0.602 8.172 31290 Z= 0.310 Chirality : 0.040 0.171 3635 Planarity : 0.004 0.047 3880 Dihedral : 10.482 129.785 3671 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.74 % Allowed : 24.10 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2711 helix: 1.09 (0.14), residues: 1505 sheet: 0.01 (0.35), residues: 219 loop : -1.97 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 2 443 HIS 0.007 0.001 HIS 41013 PHE 0.022 0.002 PHE 4 473 TYR 0.020 0.002 TYR 5 184 ARG 0.009 0.000 ARG 6 322 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 1055) hydrogen bonds : angle 4.41898 ( 3048) covalent geometry : bond 0.00412 (22932) covalent geometry : angle 0.60237 (31290) Misc. bond : bond 0.00174 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 249 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 258 ASN cc_start: 0.7836 (t0) cc_final: 0.7485 (t0) REVERT: 2 300 MET cc_start: 0.5215 (mmp) cc_final: 0.4775 (mmm) REVERT: 3 170 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7130 (mt) REVERT: 3 183 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6510 (pp) REVERT: 4 564 MET cc_start: 0.8122 (tpp) cc_final: 0.7776 (tpp) REVERT: 4 652 ILE cc_start: 0.8365 (mm) cc_final: 0.8040 (mt) REVERT: 4 654 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: 5 103 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7550 (mmt90) REVERT: 5 167 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.5960 (m-80) REVERT: 5 265 TRP cc_start: 0.7834 (t-100) cc_final: 0.6528 (m-90) REVERT: 6 164 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6552 (tm-30) REVERT: 6 307 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6979 (t80) REVERT: 6 470 ARG cc_start: 0.8044 (tpt-90) cc_final: 0.7641 (tpt-90) outliers start: 87 outliers final: 48 residues processed: 319 average time/residue: 0.3189 time to fit residues: 164.8023 Evaluate side-chains 277 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 353 VAL Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 184 VAL Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 323 LEU Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 4 residue 447 CYS Chi-restraints excluded: chain 4 residue 536 ILE Chi-restraints excluded: chain 4 residue 546 LEU Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 980 VAL Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 114 LEU Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 238 ILE Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 400 ILE Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 449 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 155 optimal weight: 0.5980 chunk 222 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 156 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 242 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 8 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 113 GLN 3 277 GLN ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 75 GLN 6 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.177171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.143046 restraints weight = 44613.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.143300 restraints weight = 58929.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.144754 restraints weight = 47211.268| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22933 Z= 0.107 Angle : 0.546 9.656 31290 Z= 0.277 Chirality : 0.039 0.301 3635 Planarity : 0.004 0.057 3880 Dihedral : 10.217 127.085 3663 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.52 % Allowed : 24.91 % Favored : 71.56 % 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: 0.07 (0.17), residues: 2711 helix: 1.26 (0.14), residues: 1509 sheet: 0.04 (0.35), residues: 216 loop : -1.91 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 443 HIS 0.006 0.001 HIS 41013 PHE 0.025 0.001 PHE 6 492 TYR 0.022 0.001 TYR 4 341 ARG 0.005 0.000 ARG 2 151 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 1055) hydrogen bonds : angle 4.15500 ( 3048) covalent geometry : bond 0.00233 (22932) covalent geometry : angle 0.54621 (31290) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 249 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 455 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8590 (tt) REVERT: 2 258 ASN cc_start: 0.7765 (t0) cc_final: 0.7381 (t0) REVERT: 3 100 TYR cc_start: 0.7246 (t80) cc_final: 0.7015 (t80) REVERT: 3 128 MET cc_start: 0.8279 (ttm) cc_final: 0.8063 (ttm) REVERT: 3 170 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7028 (mt) REVERT: 4 564 MET cc_start: 0.7963 (tpp) cc_final: 0.7639 (tpp) REVERT: 4 652 ILE cc_start: 0.8274 (mm) cc_final: 0.7956 (mt) REVERT: 4 836 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.6517 (m-70) REVERT: 5 167 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.5643 (m-80) REVERT: 5 265 TRP cc_start: 0.7727 (t-100) cc_final: 0.6394 (m-90) REVERT: 6 164 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6388 (tm-30) REVERT: 6 307 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6607 (t80) REVERT: 6 403 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7578 (pm20) outliers start: 82 outliers final: 40 residues processed: 314 average time/residue: 0.2993 time to fit residues: 152.3605 Evaluate side-chains 273 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 364 LEU Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 1 residue 455 LEU Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 287 ASN Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 189 ILE Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 403 GLN Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 269 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 186 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 217 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 254 GLN ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.176572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.142043 restraints weight = 44829.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.141940 restraints weight = 57110.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.143171 restraints weight = 52310.008| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22933 Z= 0.116 Angle : 0.553 13.095 31290 Z= 0.278 Chirality : 0.039 0.259 3635 Planarity : 0.004 0.057 3880 Dihedral : 10.065 127.028 3659 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.95 % Allowed : 24.48 % Favored : 71.56 % 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: 0.10 (0.17), residues: 2711 helix: 1.31 (0.14), residues: 1502 sheet: -0.09 (0.35), residues: 205 loop : -1.87 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 2 443 HIS 0.005 0.001 HIS 41013 PHE 0.028 0.001 PHE 6 492 TYR 0.014 0.001 TYR 5 184 ARG 0.006 0.000 ARG 1 465 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 1055) hydrogen bonds : angle 4.05905 ( 3048) covalent geometry : bond 0.00262 (22932) covalent geometry : angle 0.55293 (31290) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 239 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 128 MET cc_start: 0.8309 (ttm) cc_final: 0.8087 (ttm) REVERT: 3 170 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7110 (mt) REVERT: 3 183 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6340 (pp) REVERT: 4 348 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: 4 448 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7709 (mt-10) REVERT: 4 564 MET cc_start: 0.7879 (tpp) cc_final: 0.7613 (tpp) REVERT: 4 652 ILE cc_start: 0.8281 (mm) cc_final: 0.8021 (mt) REVERT: 4 836 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6612 (m-70) REVERT: 5 167 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6139 (m-80) REVERT: 5 265 TRP cc_start: 0.7713 (t-100) cc_final: 0.6567 (t-100) REVERT: 6 164 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6386 (tm-30) REVERT: 6 307 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.6643 (t80) REVERT: 6 403 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7629 (pm20) outliers start: 92 outliers final: 50 residues processed: 319 average time/residue: 0.3049 time to fit residues: 159.5368 Evaluate side-chains 281 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 42 LEU Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 189 ILE Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 400 ILE Chi-restraints excluded: chain 6 residue 403 GLN Chi-restraints excluded: chain 6 residue 404 PHE Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9863 > 50: distance: 35 - 44: 11.274 distance: 45 - 46: 3.444 distance: 45 - 48: 3.646 distance: 46 - 47: 12.953 distance: 48 - 49: 13.268 distance: 49 - 50: 14.972 distance: 50 - 51: 20.741 distance: 52 - 53: 14.818 distance: 53 - 54: 13.016 distance: 53 - 56: 19.880 distance: 54 - 55: 31.356 distance: 54 - 60: 33.335 distance: 56 - 57: 17.016 distance: 57 - 58: 17.872 distance: 57 - 59: 18.275 distance: 60 - 61: 15.724 distance: 61 - 62: 25.998 distance: 61 - 64: 14.922 distance: 62 - 63: 22.143 distance: 62 - 68: 7.600 distance: 63 - 90: 23.910 distance: 64 - 65: 11.508 distance: 65 - 66: 8.178 distance: 65 - 67: 7.991 distance: 69 - 70: 9.873 distance: 69 - 72: 9.838 distance: 70 - 71: 4.107 distance: 70 - 73: 4.139 distance: 71 - 98: 4.895 distance: 73 - 74: 5.334 distance: 74 - 75: 8.141 distance: 74 - 77: 12.123 distance: 75 - 76: 7.358 distance: 75 - 84: 3.857 distance: 76 - 103: 9.194 distance: 77 - 78: 11.307 distance: 78 - 79: 3.686 distance: 78 - 80: 4.109 distance: 79 - 81: 11.931 distance: 80 - 82: 8.698 distance: 81 - 83: 5.290 distance: 82 - 83: 6.625 distance: 84 - 85: 4.114 distance: 85 - 86: 8.081 distance: 85 - 88: 11.381 distance: 86 - 87: 6.528 distance: 86 - 90: 6.848 distance: 87 - 109: 11.286 distance: 88 - 89: 18.806 distance: 90 - 91: 7.518 distance: 91 - 92: 5.107 distance: 91 - 94: 3.693 distance: 92 - 93: 3.565 distance: 93 - 120: 8.881 distance: 94 - 95: 16.744 distance: 95 - 96: 20.894 distance: 96 - 97: 30.493 distance: 98 - 99: 3.693 distance: 99 - 100: 5.372 distance: 99 - 102: 7.103 distance: 100 - 103: 7.850 distance: 101 - 129: 6.650 distance: 103 - 104: 10.715 distance: 104 - 105: 11.794 distance: 104 - 107: 12.274 distance: 105 - 106: 8.971 distance: 105 - 109: 6.322 distance: 106 - 138: 15.816 distance: 107 - 108: 10.872 distance: 109 - 110: 4.882 distance: 110 - 111: 5.607 distance: 110 - 113: 5.577 distance: 111 - 112: 4.131 distance: 113 - 114: 7.849 distance: 114 - 115: 13.276 distance: 114 - 116: 9.405 distance: 115 - 117: 14.731 distance: 116 - 118: 9.942 distance: 117 - 119: 7.383 distance: 118 - 119: 7.999