Starting phenix.real_space_refine on Wed Feb 4 17:14:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ay0_43979/02_2026/9ay0_43979.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ay0_43979/02_2026/9ay0_43979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ay0_43979/02_2026/9ay0_43979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ay0_43979/02_2026/9ay0_43979.map" model { file = "/net/cci-nas-00/data/ceres_data/9ay0_43979/02_2026/9ay0_43979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ay0_43979/02_2026/9ay0_43979.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.016 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 3 5.49 5 S 54 5.16 5 C 7445 2.51 5 N 1927 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11527 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1444, 11487 Classifications: {'peptide': 1444} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1401} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'TPO:plan-1': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'GDS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.71, per 1000 atoms: 0.24 Number of scatterers: 11527 At special positions: 0 Unit cell: (93.024, 127.908, 158.004, 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 54 16.00 P 3 15.00 O 2098 8.00 N 1927 7.00 C 7445 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=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 570.5 milliseconds 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 7 sheets defined 71.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 36 through 59 removed outlier: 3.536A pdb=" N SER A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.609A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 99 removed outlier: 3.634A pdb=" N GLU A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 100 through 128 removed outlier: 3.508A pdb=" N VAL A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 115 " --> pdb=" O MET A 111 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 161 removed outlier: 3.662A pdb=" N TRP A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 189 removed outlier: 3.726A pdb=" N ILE A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.725A pdb=" N ASP A 213 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 215 " --> pdb=" O TYR A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 210 through 215' Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 226 through 236 removed outlier: 3.919A pdb=" N MET A 230 " --> pdb=" O MET A 226 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 270 removed outlier: 3.843A pdb=" N GLN A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 removed outlier: 4.027A pdb=" N ALA A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 301 removed outlier: 3.849A pdb=" N LEU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 327 removed outlier: 3.508A pdb=" N LEU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 390 removed outlier: 3.812A pdb=" N PHE A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 401 through 411 removed outlier: 4.080A pdb=" N VAL A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 420 removed outlier: 3.599A pdb=" N LEU A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 445 Proline residue: A 430 - end of helix removed outlier: 3.657A pdb=" N ILE A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 493 removed outlier: 3.750A pdb=" N ILE A 453 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Proline residue: A 460 - end of helix removed outlier: 3.904A pdb=" N ARG A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 501 removed outlier: 3.626A pdb=" N LEU A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 517 removed outlier: 3.739A pdb=" N TYR A 506 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 555 removed outlier: 4.410A pdb=" N THR A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) Proline residue: A 540 - end of helix removed outlier: 3.829A pdb=" N SER A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 573 Proline residue: A 566 - end of helix removed outlier: 4.241A pdb=" N THR A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 602 removed outlier: 3.710A pdb=" N LEU A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Proline residue: A 582 - end of helix removed outlier: 3.940A pdb=" N LEU A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 removed outlier: 4.011A pdb=" N LEU A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 713 Processing helix chain 'A' and resid 718 through 728 Processing helix chain 'A' and resid 730 through 739 removed outlier: 3.815A pdb=" N ASP A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 769 removed outlier: 4.292A pdb=" N ALA A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 removed outlier: 3.643A pdb=" N VAL A 783 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 795 Processing helix chain 'A' and resid 813 through 820 Processing helix chain 'A' and resid 836 through 844 removed outlier: 3.503A pdb=" N ILE A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 928 removed outlier: 5.026A pdb=" N ARG A 926 " --> pdb=" O ASN A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 946 removed outlier: 4.420A pdb=" N TYR A 939 " --> pdb=" O LYS A 935 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 940 " --> pdb=" O TRP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 983 removed outlier: 3.640A pdb=" N VAL A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS A 952 " --> pdb=" O PRO A 948 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 957 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 958 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 969 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 981 " --> pdb=" O GLU A 977 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 982 " --> pdb=" O VAL A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1017 removed outlier: 3.832A pdb=" N ALA A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A 995 " --> pdb=" O TYR A 991 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A1005 " --> pdb=" O GLY A1001 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A1017 " --> pdb=" O LEU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1034 removed outlier: 3.660A pdb=" N ALA A1021 " --> pdb=" O CYS A1017 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS A1026 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A1027 " --> pdb=" O LYS A1023 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 4.114A pdb=" N PHE A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1055 removed outlier: 3.558A pdb=" N ILE A1049 " --> pdb=" O PRO A1045 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A1051 " --> pdb=" O GLY A1047 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A1053 " --> pdb=" O ILE A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1063 Processing helix chain 'A' and resid 1063 through 1087 removed outlier: 4.092A pdb=" N THR A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A1068 " --> pdb=" O LEU A1064 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN A1074 " --> pdb=" O GLN A1070 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1091 No H-bonds generated for 'chain 'A' and resid 1089 through 1091' Processing helix chain 'A' and resid 1092 through 1126 Proline residue: A1098 - end of helix removed outlier: 3.945A pdb=" N VAL A1101 " --> pdb=" O ILE A1097 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1109 " --> pdb=" O TYR A1105 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A1112 " --> pdb=" O GLN A1108 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A1113 " --> pdb=" O TYR A1109 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR A1124 " --> pdb=" O LEU A1120 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1137 removed outlier: 3.629A pdb=" N SER A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS A1131 " --> pdb=" O PRO A1127 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A1132 " --> pdb=" O ILE A1128 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1146 Processing helix chain 'A' and resid 1147 through 1200 removed outlier: 3.870A pdb=" N ASN A1155 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A1162 " --> pdb=" O ARG A1158 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A1165 " --> pdb=" O ASN A1161 " (cutoff:3.500A) Proline residue: A1168 - end of helix removed outlier: 3.829A pdb=" N ASN A1171 " --> pdb=" O TYR A1167 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A1179 " --> pdb=" O TRP A1175 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A1183 " --> pdb=" O ARG A1179 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A1195 " --> pdb=" O ALA A1191 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A1200 " --> pdb=" O VAL A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1217 removed outlier: 3.696A pdb=" N VAL A1209 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A1216 " --> pdb=" O SER A1212 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1217 " --> pdb=" O LEU A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1237 removed outlier: 4.198A pdb=" N VAL A1227 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A1231 " --> pdb=" O VAL A1227 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A1232 " --> pdb=" O ARG A1228 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A1236 " --> pdb=" O GLU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1248 removed outlier: 4.009A pdb=" N GLU A1241 " --> pdb=" O ILE A1237 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A1246 " --> pdb=" O ARG A1242 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1261 removed outlier: 3.971A pdb=" N ARG A1261 " --> pdb=" O GLU A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1320 removed outlier: 3.898A pdb=" N LEU A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1347 Processing helix chain 'A' and resid 1363 through 1368 Processing helix chain 'A' and resid 1374 through 1385 removed outlier: 3.658A pdb=" N ILE A1378 " --> pdb=" O THR A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1395 removed outlier: 3.743A pdb=" N VAL A1391 " --> pdb=" O LEU A1387 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A1392 " --> pdb=" O LYS A1388 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A1393 " --> pdb=" O GLU A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1400 Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.865A pdb=" N GLY A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1426 removed outlier: 3.688A pdb=" N VAL A1426 " --> pdb=" O ARG A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1439 Processing helix chain 'A' and resid 1441 through 1455 removed outlier: 4.793A pdb=" N VAL A1447 " --> pdb=" O GLU A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1459 Processing helix chain 'A' and resid 1467 through 1472 removed outlier: 3.866A pdb=" N MET A1472 " --> pdb=" O ASN A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1497 Processing helix chain 'A' and resid 1500 through 1509 Processing helix chain 'A' and resid 1510 through 1515 Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 615 removed outlier: 3.596A pdb=" N PHE A 681 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 633 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY A 685 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP A 631 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA A 687 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLY A 629 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 689 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASN A 627 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A 626 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP A 630 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 649 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 632 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 647 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE A 634 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 694 through 696 removed outlier: 6.424A pdb=" N ALA A 694 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASP A 777 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL A 696 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR A 774 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA A 810 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU A 776 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR A 659 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 822 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 824 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 662 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 826 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 833 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP A 827 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.506A pdb=" N GLY A 705 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1289 through 1292 removed outlier: 5.770A pdb=" N LYS A1290 " --> pdb=" O THR A1279 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR A1279 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1272 " --> pdb=" O ILE A1296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1289 through 1292 removed outlier: 5.770A pdb=" N LYS A1290 " --> pdb=" O THR A1279 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR A1279 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR A1277 " --> pdb=" O GLU A1327 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A1327 " --> pdb=" O TYR A1277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1351 through 1352 removed outlier: 3.853A pdb=" N ARG A1476 " --> pdb=" O LYS A1301 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A1305 " --> pdb=" O ILE A1478 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A1477 " --> pdb=" O PHE A1488 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A1488 " --> pdb=" O ILE A1477 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A1479 " --> pdb=" O ALA A1486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 3.727A pdb=" N GLY A1361 " --> pdb=" O LEU A1403 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 4475 1.38 - 1.54: 7154 1.54 - 1.71: 48 1.71 - 1.87: 87 1.87 - 2.04: 1 Bond restraints: 11765 Sorted by residual: bond pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.717 1.619 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O3P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.528 1.612 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O2P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" CG1 GDS A1601 " pdb=" CD1 GDS A1601 " ideal model delta sigma weight residual 1.519 1.471 0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" O1P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.525 1.480 0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 11760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15243 2.07 - 4.15: 633 4.15 - 6.22: 50 6.22 - 8.30: 18 8.30 - 10.37: 7 Bond angle restraints: 15951 Sorted by residual: angle pdb=" N GLY A 932 " pdb=" CA GLY A 932 " pdb=" C GLY A 932 " ideal model delta sigma weight residual 113.18 104.12 9.06 2.37e+00 1.78e-01 1.46e+01 angle pdb=" N PHE A 565 " pdb=" CA PHE A 565 " pdb=" C PHE A 565 " ideal model delta sigma weight residual 109.81 118.01 -8.20 2.21e+00 2.05e-01 1.38e+01 angle pdb=" N VAL A 539 " pdb=" CA VAL A 539 " pdb=" C VAL A 539 " ideal model delta sigma weight residual 108.88 116.67 -7.79 2.16e+00 2.14e-01 1.30e+01 angle pdb=" N LEU A 189 " pdb=" CA LEU A 189 " pdb=" C LEU A 189 " ideal model delta sigma weight residual 109.81 117.46 -7.65 2.21e+00 2.05e-01 1.20e+01 angle pdb=" CA5 GDS A1601 " pdb=" CB5 GDS A1601 " pdb=" SG5 GDS A1601 " ideal model delta sigma weight residual 115.79 105.42 10.37 3.00e+00 1.11e-01 1.20e+01 ... (remaining 15946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.04: 6856 30.04 - 60.09: 167 60.09 - 90.13: 18 90.13 - 120.17: 1 120.17 - 150.21: 2 Dihedral angle restraints: 7044 sinusoidal: 2817 harmonic: 4227 Sorted by residual: dihedral pdb=" CB5 GDS A1601 " pdb=" C5 GDS A1601 " pdb=" CA5 GDS A1601 " pdb=" N4 GDS A1601 " ideal model delta sinusoidal sigma weight residual 106.65 -43.56 150.21 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" N4 GDS A1601 " pdb=" C5 GDS A1601 " pdb=" CA5 GDS A1601 " pdb=" N5 GDS A1601 " ideal model delta sinusoidal sigma weight residual 133.37 -85.67 -140.96 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" CA LYS A 270 " pdb=" C LYS A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta harmonic sigma weight residual 180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 7041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1540 0.075 - 0.149: 282 0.149 - 0.224: 27 0.224 - 0.298: 1 0.298 - 0.373: 1 Chirality restraints: 1851 Sorted by residual: chirality pdb=" CA5 GDS A1601 " pdb=" C5 GDS A1601 " pdb=" CB5 GDS A1601 " pdb=" N5 GDS A1601 " both_signs ideal model delta sigma weight residual False 2.63 2.25 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA PHE A 565 " pdb=" N PHE A 565 " pdb=" C PHE A 565 " pdb=" CB PHE A 565 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA PRO A1127 " pdb=" N PRO A1127 " pdb=" C PRO A1127 " pdb=" CB PRO A1127 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1848 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1140 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ALA A1140 " 0.052 2.00e-02 2.50e+03 pdb=" O ALA A1140 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A1141 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1178 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.15e+00 pdb=" C TYR A1178 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR A1178 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A1179 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 429 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 430 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " 0.035 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3866 2.88 - 3.38: 10764 3.38 - 3.89: 16547 3.89 - 4.39: 18109 4.39 - 4.90: 32642 Nonbonded interactions: 81928 Sorted by model distance: nonbonded pdb=" O ALA A 625 " pdb=" ND1 HIS A 690 " model vdw 2.369 3.120 nonbonded pdb=" N ASP A 562 " pdb=" OD1 ASP A 562 " model vdw 2.396 3.120 nonbonded pdb=" NH1 ARG A1364 " pdb=" OD1 ASP A1375 " model vdw 2.404 3.120 nonbonded pdb=" O PRO A 798 " pdb=" ND1 HIS A 803 " model vdw 2.422 3.120 nonbonded pdb=" OH TYR A 237 " pdb=" O GLU A 930 " model vdw 2.437 3.040 ... (remaining 81923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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: 6.280 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.008 0.098 11765 Z= 0.348 Angle : 0.958 10.375 15951 Z= 0.533 Chirality : 0.057 0.373 1851 Planarity : 0.008 0.087 1990 Dihedral : 13.677 150.213 4310 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.19), residues: 1429 helix: -1.74 (0.14), residues: 869 sheet: 1.27 (0.68), residues: 48 loop : -0.32 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A1280 TYR 0.030 0.003 TYR A 366 PHE 0.029 0.003 PHE A 534 TRP 0.026 0.003 TRP A 139 HIS 0.007 0.002 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00804 (11765) covalent geometry : angle 0.95796 (15951) hydrogen bonds : bond 0.18768 ( 567) hydrogen bonds : angle 5.77132 ( 1665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8372 (tttt) cc_final: 0.7905 (tppt) REVERT: A 657 ASN cc_start: 0.7832 (m-40) cc_final: 0.6820 (p0) REVERT: A 716 ARG cc_start: 0.5945 (mtt-85) cc_final: 0.5684 (mtm-85) REVERT: A 935 LYS cc_start: 0.7547 (mptt) cc_final: 0.6703 (mtmt) REVERT: A 1048 ARG cc_start: 0.7184 (mtm110) cc_final: 0.6887 (ttm110) REVERT: A 1055 ASN cc_start: 0.7198 (m-40) cc_final: 0.6919 (t0) REVERT: A 1248 ASP cc_start: 0.7918 (m-30) cc_final: 0.7578 (p0) REVERT: A 1350 SER cc_start: 0.6699 (m) cc_final: 0.6271 (p) REVERT: A 1424 MET cc_start: 0.8731 (tpp) cc_final: 0.8236 (mtt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1378 time to fit residues: 27.4759 Evaluate side-chains 84 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 202 GLN A 359 GLN A 387 GLN A 604 ASN A 648 ASN A 690 HIS A 794 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.203737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134592 restraints weight = 14350.830| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 4.00 r_work: 0.3524 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11765 Z= 0.149 Angle : 0.533 7.112 15951 Z= 0.298 Chirality : 0.040 0.149 1851 Planarity : 0.004 0.049 1990 Dihedral : 9.234 139.113 1606 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.95 % Allowed : 4.61 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1429 helix: -0.08 (0.17), residues: 871 sheet: 1.21 (0.59), residues: 67 loop : -0.01 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1467 TYR 0.017 0.001 TYR A 722 PHE 0.016 0.001 PHE A 431 TRP 0.017 0.001 TRP A 70 HIS 0.008 0.001 HIS A 790 Details of bonding type rmsd covalent geometry : bond 0.00308 (11765) covalent geometry : angle 0.53349 (15951) hydrogen bonds : bond 0.07421 ( 567) hydrogen bonds : angle 4.43427 ( 1665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: A 142 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: A 261 LYS cc_start: 0.8724 (tttt) cc_final: 0.8363 (tppt) REVERT: A 266 GLU cc_start: 0.8427 (tp30) cc_final: 0.8203 (tp30) REVERT: A 529 MET cc_start: 0.7928 (mtp) cc_final: 0.7703 (mtt) REVERT: A 579 MET cc_start: 0.8623 (ttm) cc_final: 0.8391 (ttt) REVERT: A 657 ASN cc_start: 0.7880 (m-40) cc_final: 0.6975 (p0) REVERT: A 676 MET cc_start: 0.8175 (mtm) cc_final: 0.7841 (mtt) REVERT: A 718 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7311 (m-30) REVERT: A 935 LYS cc_start: 0.7806 (mptt) cc_final: 0.7028 (mtmt) REVERT: A 1350 SER cc_start: 0.7353 (m) cc_final: 0.7060 (p) REVERT: A 1424 MET cc_start: 0.8768 (tpp) cc_final: 0.8286 (mtt) outliers start: 12 outliers final: 4 residues processed: 113 average time/residue: 0.0936 time to fit residues: 15.4244 Evaluate side-chains 89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1054 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 297 HIS A1372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.203291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137224 restraints weight = 14093.509| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.85 r_work: 0.3446 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11765 Z= 0.137 Angle : 0.501 7.189 15951 Z= 0.274 Chirality : 0.039 0.147 1851 Planarity : 0.004 0.052 1990 Dihedral : 8.768 133.954 1606 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.27 % Allowed : 6.12 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.21), residues: 1429 helix: 0.51 (0.17), residues: 874 sheet: 1.36 (0.60), residues: 67 loop : -0.15 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1476 TYR 0.013 0.001 TYR A 722 PHE 0.015 0.001 PHE A 431 TRP 0.011 0.001 TRP A 70 HIS 0.007 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00287 (11765) covalent geometry : angle 0.50149 (15951) hydrogen bonds : bond 0.06799 ( 567) hydrogen bonds : angle 4.07858 ( 1665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: A 261 LYS cc_start: 0.8655 (tttt) cc_final: 0.8276 (tppt) REVERT: A 266 GLU cc_start: 0.8235 (tp30) cc_final: 0.7998 (tp30) REVERT: A 529 MET cc_start: 0.7782 (mtp) cc_final: 0.7541 (mtt) REVERT: A 579 MET cc_start: 0.8487 (ttm) cc_final: 0.8278 (ttt) REVERT: A 657 ASN cc_start: 0.7834 (m-40) cc_final: 0.6943 (p0) REVERT: A 676 MET cc_start: 0.8247 (mtt) cc_final: 0.8045 (mtt) REVERT: A 718 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: A 727 LYS cc_start: 0.8407 (mttt) cc_final: 0.7726 (pttm) REVERT: A 935 LYS cc_start: 0.7791 (mptt) cc_final: 0.7340 (mmtm) REVERT: A 1048 ARG cc_start: 0.7590 (mtm110) cc_final: 0.7317 (ttm110) REVERT: A 1350 SER cc_start: 0.7561 (m) cc_final: 0.7184 (p) REVERT: A 1424 MET cc_start: 0.8813 (tpp) cc_final: 0.8300 (mtp) outliers start: 16 outliers final: 5 residues processed: 108 average time/residue: 0.1188 time to fit residues: 17.9881 Evaluate side-chains 90 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1164 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN A 648 ASN A 786 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.196053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.129358 restraints weight = 14244.782| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.94 r_work: 0.3353 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11765 Z= 0.191 Angle : 0.562 7.577 15951 Z= 0.305 Chirality : 0.042 0.172 1851 Planarity : 0.004 0.054 1990 Dihedral : 8.615 132.437 1606 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.27 % Allowed : 7.70 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1429 helix: 0.50 (0.17), residues: 868 sheet: 1.20 (0.60), residues: 68 loop : -0.21 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 716 TYR 0.015 0.002 TYR A 366 PHE 0.019 0.002 PHE A 44 TRP 0.012 0.001 TRP A 122 HIS 0.007 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00449 (11765) covalent geometry : angle 0.56185 (15951) hydrogen bonds : bond 0.08399 ( 567) hydrogen bonds : angle 4.31512 ( 1665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.357 Fit side-chains REVERT: A 99 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: A 199 HIS cc_start: 0.2811 (OUTLIER) cc_final: 0.2067 (m-70) REVERT: A 261 LYS cc_start: 0.8768 (tttt) cc_final: 0.8440 (tppt) REVERT: A 529 MET cc_start: 0.7915 (mtp) cc_final: 0.7678 (mtt) REVERT: A 716 ARG cc_start: 0.6682 (mtt90) cc_final: 0.6387 (mtm-85) REVERT: A 718 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: A 723 GLU cc_start: 0.8357 (mp0) cc_final: 0.8031 (pm20) REVERT: A 727 LYS cc_start: 0.8565 (mttt) cc_final: 0.7832 (pttm) REVERT: A 935 LYS cc_start: 0.8019 (mptt) cc_final: 0.6926 (tttm) REVERT: A 1048 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7395 (ttm110) REVERT: A 1350 SER cc_start: 0.8047 (m) cc_final: 0.7821 (p) REVERT: A 1424 MET cc_start: 0.8863 (tpp) cc_final: 0.8324 (mtp) outliers start: 16 outliers final: 10 residues processed: 113 average time/residue: 0.1107 time to fit residues: 17.7796 Evaluate side-chains 103 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 TRP Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1164 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.197463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129163 restraints weight = 14402.735| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.87 r_work: 0.3491 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11765 Z= 0.162 Angle : 0.513 8.415 15951 Z= 0.276 Chirality : 0.040 0.155 1851 Planarity : 0.004 0.056 1990 Dihedral : 8.179 126.968 1606 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.51 % Allowed : 8.26 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1429 helix: 0.67 (0.18), residues: 870 sheet: 1.12 (0.59), residues: 69 loop : -0.24 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 638 TYR 0.021 0.001 TYR A1105 PHE 0.016 0.001 PHE A 44 TRP 0.011 0.001 TRP A 122 HIS 0.006 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00377 (11765) covalent geometry : angle 0.51280 (15951) hydrogen bonds : bond 0.07167 ( 567) hydrogen bonds : angle 4.07219 ( 1665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.418 Fit side-chains REVERT: A 69 ASN cc_start: 0.7466 (t0) cc_final: 0.7196 (t0) REVERT: A 99 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: A 199 HIS cc_start: 0.2803 (OUTLIER) cc_final: 0.1834 (m-70) REVERT: A 261 LYS cc_start: 0.8806 (tttt) cc_final: 0.8501 (tppt) REVERT: A 489 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7647 (tt0) REVERT: A 529 MET cc_start: 0.7993 (mtp) cc_final: 0.7750 (mtt) REVERT: A 727 LYS cc_start: 0.8672 (mttt) cc_final: 0.7920 (pttm) REVERT: A 760 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7229 (mpp80) REVERT: A 935 LYS cc_start: 0.8042 (mptt) cc_final: 0.6989 (tttm) REVERT: A 1048 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7464 (ttm110) REVERT: A 1424 MET cc_start: 0.8868 (tpp) cc_final: 0.8390 (mtp) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 0.1033 time to fit residues: 17.6418 Evaluate side-chains 107 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 TRP Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1164 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN A1338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.199616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133317 restraints weight = 14468.292| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.69 r_work: 0.3502 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11765 Z= 0.120 Angle : 0.465 8.627 15951 Z= 0.250 Chirality : 0.038 0.141 1851 Planarity : 0.004 0.053 1990 Dihedral : 7.807 119.266 1606 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.19 % Allowed : 9.05 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1429 helix: 0.92 (0.18), residues: 867 sheet: 1.35 (0.60), residues: 67 loop : -0.28 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 760 TYR 0.022 0.001 TYR A1105 PHE 0.013 0.001 PHE A 44 TRP 0.009 0.001 TRP A 122 HIS 0.006 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00248 (11765) covalent geometry : angle 0.46465 (15951) hydrogen bonds : bond 0.06033 ( 567) hydrogen bonds : angle 3.84850 ( 1665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.462 Fit side-chains REVERT: A 69 ASN cc_start: 0.7217 (t0) cc_final: 0.6940 (t0) REVERT: A 76 MET cc_start: 0.9086 (mmt) cc_final: 0.8594 (mmt) REVERT: A 99 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: A 199 HIS cc_start: 0.2811 (OUTLIER) cc_final: 0.2160 (p-80) REVERT: A 261 LYS cc_start: 0.8735 (tttt) cc_final: 0.8449 (tppt) REVERT: A 394 ASN cc_start: 0.6578 (m-40) cc_final: 0.5984 (m110) REVERT: A 474 LYS cc_start: 0.8374 (tppp) cc_final: 0.7618 (tmmt) REVERT: A 529 MET cc_start: 0.7796 (mtp) cc_final: 0.7540 (mtt) REVERT: A 723 GLU cc_start: 0.8371 (mp0) cc_final: 0.8068 (pm20) REVERT: A 727 LYS cc_start: 0.8675 (mttt) cc_final: 0.7905 (pttm) REVERT: A 760 ARG cc_start: 0.7687 (mtt90) cc_final: 0.7368 (mpp80) REVERT: A 935 LYS cc_start: 0.7973 (mptt) cc_final: 0.6975 (tttm) REVERT: A 1048 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7381 (ttm110) REVERT: A 1424 MET cc_start: 0.8818 (tpp) cc_final: 0.8339 (mtp) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 0.1095 time to fit residues: 17.4562 Evaluate side-chains 110 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 636 TRP Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1340 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 140 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 627 ASN A1338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.201801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135632 restraints weight = 14108.978| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.78 r_work: 0.3470 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11765 Z= 0.106 Angle : 0.442 9.576 15951 Z= 0.236 Chirality : 0.038 0.151 1851 Planarity : 0.003 0.052 1990 Dihedral : 7.321 101.870 1606 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.71 % Allowed : 10.25 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1429 helix: 1.15 (0.18), residues: 876 sheet: 1.29 (0.60), residues: 69 loop : -0.23 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 760 TYR 0.023 0.001 TYR A1105 PHE 0.011 0.001 PHE A 44 TRP 0.008 0.001 TRP A 122 HIS 0.005 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00211 (11765) covalent geometry : angle 0.44212 (15951) hydrogen bonds : bond 0.05284 ( 567) hydrogen bonds : angle 3.64239 ( 1665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.475 Fit side-chains REVERT: A 69 ASN cc_start: 0.7318 (t0) cc_final: 0.7033 (t0) REVERT: A 99 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 261 LYS cc_start: 0.8678 (tttt) cc_final: 0.8324 (tppt) REVERT: A 474 LYS cc_start: 0.8255 (tppp) cc_final: 0.7498 (tmmt) REVERT: A 529 MET cc_start: 0.7684 (mtp) cc_final: 0.7426 (mtt) REVERT: A 657 ASN cc_start: 0.7807 (m-40) cc_final: 0.7564 (t0) REVERT: A 727 LYS cc_start: 0.8651 (mttt) cc_final: 0.7860 (pttm) REVERT: A 760 ARG cc_start: 0.7694 (mtt90) cc_final: 0.7383 (mpp80) REVERT: A 935 LYS cc_start: 0.7896 (mptt) cc_final: 0.6831 (tttm) REVERT: A 1338 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8031 (t0) REVERT: A 1424 MET cc_start: 0.8896 (tpp) cc_final: 0.8378 (mtp) outliers start: 9 outliers final: 6 residues processed: 112 average time/residue: 0.1149 time to fit residues: 18.4657 Evaluate side-chains 108 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1338 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 0.0020 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.203165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136025 restraints weight = 14099.649| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.73 r_work: 0.3471 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11765 Z= 0.102 Angle : 0.437 9.788 15951 Z= 0.233 Chirality : 0.038 0.146 1851 Planarity : 0.003 0.050 1990 Dihedral : 7.120 90.932 1606 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.11 % Allowed : 10.41 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.22), residues: 1429 helix: 1.26 (0.18), residues: 876 sheet: 1.37 (0.61), residues: 69 loop : -0.20 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 760 TYR 0.023 0.001 TYR A1105 PHE 0.009 0.001 PHE A 44 TRP 0.007 0.001 TRP A 122 HIS 0.005 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00196 (11765) covalent geometry : angle 0.43666 (15951) hydrogen bonds : bond 0.05058 ( 567) hydrogen bonds : angle 3.57985 ( 1665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.450 Fit side-chains REVERT: A 99 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 199 HIS cc_start: 0.3109 (OUTLIER) cc_final: 0.2517 (p-80) REVERT: A 261 LYS cc_start: 0.8688 (tttt) cc_final: 0.8335 (tppt) REVERT: A 474 LYS cc_start: 0.8248 (tppp) cc_final: 0.7512 (tmmt) REVERT: A 529 MET cc_start: 0.7676 (mtp) cc_final: 0.7398 (mtt) REVERT: A 647 LYS cc_start: 0.7491 (tmmt) cc_final: 0.7247 (tmmt) REVERT: A 657 ASN cc_start: 0.7994 (m-40) cc_final: 0.7669 (t0) REVERT: A 723 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: A 727 LYS cc_start: 0.8649 (mttt) cc_final: 0.7848 (pttm) REVERT: A 760 ARG cc_start: 0.7665 (mtt90) cc_final: 0.7342 (mpp80) REVERT: A 935 LYS cc_start: 0.7895 (mptt) cc_final: 0.6828 (tttm) REVERT: A 1424 MET cc_start: 0.8898 (tpp) cc_final: 0.8382 (mtp) outliers start: 14 outliers final: 7 residues processed: 115 average time/residue: 0.1065 time to fit residues: 17.8688 Evaluate side-chains 114 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1032 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.194915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128593 restraints weight = 14038.128| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.77 r_work: 0.3380 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11765 Z= 0.169 Angle : 0.521 10.030 15951 Z= 0.280 Chirality : 0.040 0.150 1851 Planarity : 0.004 0.055 1990 Dihedral : 7.174 91.728 1606 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.35 % Allowed : 10.33 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1429 helix: 0.98 (0.18), residues: 873 sheet: 1.66 (0.66), residues: 59 loop : -0.23 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 760 TYR 0.023 0.001 TYR A1105 PHE 0.016 0.001 PHE A 44 TRP 0.011 0.001 TRP A 122 HIS 0.008 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00398 (11765) covalent geometry : angle 0.52122 (15951) hydrogen bonds : bond 0.07413 ( 567) hydrogen bonds : angle 3.95461 ( 1665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.285 Fit side-chains REVERT: A 99 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: A 261 LYS cc_start: 0.8644 (tttt) cc_final: 0.8313 (tppt) REVERT: A 474 LYS cc_start: 0.8223 (tppp) cc_final: 0.7449 (tmmt) REVERT: A 529 MET cc_start: 0.7683 (mtp) cc_final: 0.7448 (mtt) REVERT: A 579 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8319 (ttt) REVERT: A 647 LYS cc_start: 0.7587 (tmmt) cc_final: 0.7355 (tmmt) REVERT: A 657 ASN cc_start: 0.8029 (m-40) cc_final: 0.7721 (t0) REVERT: A 723 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8174 (pm20) REVERT: A 727 LYS cc_start: 0.8713 (mttt) cc_final: 0.7867 (pttm) REVERT: A 760 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7383 (mpp80) REVERT: A 935 LYS cc_start: 0.7914 (mptt) cc_final: 0.6894 (tttm) REVERT: A 1048 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7314 (ttm110) REVERT: A 1424 MET cc_start: 0.8939 (tpp) cc_final: 0.8432 (mtp) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 0.1078 time to fit residues: 17.6955 Evaluate side-chains 114 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.199143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131574 restraints weight = 14194.634| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.88 r_work: 0.3419 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11765 Z= 0.124 Angle : 0.473 10.490 15951 Z= 0.253 Chirality : 0.038 0.148 1851 Planarity : 0.003 0.051 1990 Dihedral : 6.829 94.073 1606 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.11 % Allowed : 10.88 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1429 helix: 1.12 (0.18), residues: 873 sheet: 1.62 (0.67), residues: 59 loop : -0.28 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 760 TYR 0.024 0.001 TYR A1105 PHE 0.011 0.001 PHE A 954 TRP 0.009 0.001 TRP A 122 HIS 0.005 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00264 (11765) covalent geometry : angle 0.47288 (15951) hydrogen bonds : bond 0.05994 ( 567) hydrogen bonds : angle 3.73079 ( 1665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.319 Fit side-chains REVERT: A 76 MET cc_start: 0.8928 (mmt) cc_final: 0.8553 (mmt) REVERT: A 99 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: A 199 HIS cc_start: 0.3013 (OUTLIER) cc_final: 0.2486 (p-80) REVERT: A 261 LYS cc_start: 0.8664 (tttt) cc_final: 0.8324 (tppt) REVERT: A 474 LYS cc_start: 0.8280 (tppp) cc_final: 0.7408 (tmmt) REVERT: A 529 MET cc_start: 0.7642 (mtp) cc_final: 0.7384 (mtt) REVERT: A 636 TRP cc_start: 0.8471 (t-100) cc_final: 0.8212 (m100) REVERT: A 647 LYS cc_start: 0.7629 (tmmt) cc_final: 0.7387 (tmmt) REVERT: A 657 ASN cc_start: 0.8074 (m-40) cc_final: 0.7784 (t0) REVERT: A 723 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: A 727 LYS cc_start: 0.8726 (mttt) cc_final: 0.7857 (pttm) REVERT: A 760 ARG cc_start: 0.7724 (mtt90) cc_final: 0.7424 (mpp80) REVERT: A 935 LYS cc_start: 0.7892 (mptt) cc_final: 0.6886 (tttm) REVERT: A 1048 ARG cc_start: 0.7665 (mtm110) cc_final: 0.7326 (ttm110) REVERT: A 1424 MET cc_start: 0.8924 (tpp) cc_final: 0.8457 (mtp) outliers start: 14 outliers final: 8 residues processed: 115 average time/residue: 0.0992 time to fit residues: 16.5310 Evaluate side-chains 115 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1338 ASN A1469 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.192355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127323 restraints weight = 14268.022| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.78 r_work: 0.3323 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11765 Z= 0.199 Angle : 0.561 10.863 15951 Z= 0.299 Chirality : 0.042 0.159 1851 Planarity : 0.004 0.059 1990 Dihedral : 6.747 94.228 1606 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.43 % Allowed : 10.72 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.22), residues: 1429 helix: 0.78 (0.18), residues: 876 sheet: 1.54 (0.67), residues: 59 loop : -0.32 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 760 TYR 0.024 0.001 TYR A1105 PHE 0.019 0.002 PHE A 44 TRP 0.010 0.001 TRP A 122 HIS 0.006 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00485 (11765) covalent geometry : angle 0.56084 (15951) hydrogen bonds : bond 0.08163 ( 567) hydrogen bonds : angle 4.08859 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3459.73 seconds wall clock time: 59 minutes 42.46 seconds (3582.46 seconds total)