Starting phenix.real_space_refine on Sat Jul 4 03:19:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zr6_14884/07_2026/7zr6_14884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr6_14884/07_2026/7zr6_14884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zr6_14884/07_2026/7zr6_14884.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zr6_14884/07_2026/7zr6_14884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zr6_14884/07_2026/7zr6_14884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr6_14884/07_2026/7zr6_14884.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr6_14884/07_2026/7zr6_14884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr6_14884/07_2026/7zr6_14884.cif" } resolution = 4.2 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= 0.002 sd= 0.029 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 7 5.49 5 S 91 5.16 5 C 11196 2.51 5 N 3012 2.21 5 O 3394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17700 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5132 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "B" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5112 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 1 Chain: "C" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2337 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 4, 'TRANS': 272} Chain: "K" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1503 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "P" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3554 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.39, per 1000 atoms: 0.19 Number of scatterers: 17700 At special positions: 0 Unit cell: (127.28, 140.18, 195.22, 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 91 16.00 P 7 15.00 O 3394 8.00 N 3012 7.00 C 11196 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 501.4 milliseconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 16 sheets defined 49.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 37 through 46 removed outlier: 4.026A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 61 removed outlier: 3.654A pdb=" N LEU A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 removed outlier: 4.198A pdb=" N ILE A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.218A pdb=" N ALA A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.587A pdb=" N SER A 135 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 removed outlier: 3.680A pdb=" N VAL A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.695A pdb=" N ILE A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 removed outlier: 4.179A pdb=" N TYR A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 420 Processing helix chain 'A' and resid 424 through 444 removed outlier: 4.422A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.740A pdb=" N TYR A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 496 removed outlier: 3.891A pdb=" N VAL A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.544A pdb=" N GLY A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 523 removed outlier: 4.416A pdb=" N GLN A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.855A pdb=" N LYS A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 571 removed outlier: 4.266A pdb=" N LYS A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 616 through 621 removed outlier: 4.202A pdb=" N MET A 621 " --> pdb=" O GLY A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 3.777A pdb=" N GLU A 636 " --> pdb=" O HIS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 4.000A pdb=" N ASP A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.589A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.584A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.804A pdb=" N LEU B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.092A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.689A pdb=" N VAL B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.723A pdb=" N ILE B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR B 297 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.758A pdb=" N TYR B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 399 through 419 removed outlier: 4.194A pdb=" N ARG B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 441 removed outlier: 3.740A pdb=" N LYS B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 490 through 496 removed outlier: 3.656A pdb=" N ASN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 removed outlier: 4.438A pdb=" N VAL B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 525 removed outlier: 3.728A pdb=" N GLU B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 4.167A pdb=" N LYS B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 removed outlier: 3.532A pdb=" N CYS B 564 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS B 568 " --> pdb=" O CYS B 564 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 removed outlier: 3.500A pdb=" N ARG B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.906A pdb=" N MET B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET B 621 " --> pdb=" O MET B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 621' Processing helix chain 'B' and resid 632 through 645 removed outlier: 4.051A pdb=" N GLU B 636 " --> pdb=" O HIS B 632 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 639 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 removed outlier: 3.662A pdb=" N LYS B 652 " --> pdb=" O ASP B 648 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.940A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET B 683 " --> pdb=" O ARG B 679 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 684 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 685 " --> pdb=" O TYR B 681 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 74 Processing helix chain 'C' and resid 77 through 111 removed outlier: 3.957A pdb=" N LYS C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 Processing helix chain 'C' and resid 142 through 163 removed outlier: 3.603A pdb=" N GLN C 146 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS C 148 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR C 150 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 155 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 202 through 227 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.734A pdb=" N THR C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 278 Processing helix chain 'K' and resid 537 through 543 removed outlier: 3.683A pdb=" N LEU K 541 " --> pdb=" O LEU K 537 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS K 542 " --> pdb=" O TYR K 538 " (cutoff:3.500A) Processing helix chain 'K' and resid 549 through 569 removed outlier: 4.201A pdb=" N LEU K 553 " --> pdb=" O GLU K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 580 No H-bonds generated for 'chain 'K' and resid 578 through 580' Processing helix chain 'K' and resid 634 through 652 removed outlier: 3.979A pdb=" N ASP K 638 " --> pdb=" O SER K 634 " (cutoff:3.500A) Processing helix chain 'K' and resid 661 through 671 Processing helix chain 'K' and resid 686 through 697 removed outlier: 4.189A pdb=" N LEU K 697 " --> pdb=" O MET K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 719 removed outlier: 4.071A pdb=" N ILE K 710 " --> pdb=" O LEU K 706 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 removed outlier: 3.863A pdb=" N LEU P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 58 Processing helix chain 'P' and resid 61 through 75 removed outlier: 3.882A pdb=" N TYR P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 92 removed outlier: 3.616A pdb=" N ALA P 81 " --> pdb=" O CYS P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 110 Processing helix chain 'P' and resid 111 through 126 removed outlier: 4.344A pdb=" N ALA P 115 " --> pdb=" O LYS P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 149 Processing helix chain 'P' and resid 187 through 200 Processing helix chain 'P' and resid 205 through 222 removed outlier: 3.737A pdb=" N ALA P 209 " --> pdb=" O HIS P 205 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS P 222 " --> pdb=" O GLU P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 257 Processing helix chain 'P' and resid 278 through 293 removed outlier: 3.606A pdb=" N VAL P 282 " --> pdb=" O PHE P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 306 through 313 removed outlier: 3.965A pdb=" N ILE P 312 " --> pdb=" O ASN P 308 " (cutoff:3.500A) Processing helix chain 'P' and resid 314 through 323 Processing helix chain 'P' and resid 324 through 336 Processing helix chain 'P' and resid 362 through 368 removed outlier: 4.378A pdb=" N ILE P 366 " --> pdb=" O THR P 362 " (cutoff:3.500A) Processing helix chain 'P' and resid 379 through 387 removed outlier: 4.147A pdb=" N LEU P 385 " --> pdb=" O MET P 381 " (cutoff:3.500A) Processing helix chain 'P' and resid 407 through 418 removed outlier: 3.642A pdb=" N THR P 411 " --> pdb=" O GLY P 407 " (cutoff:3.500A) Processing helix chain 'P' and resid 450 through 454 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.729A pdb=" N GLU A 13 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 159 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 143 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 159 removed outlier: 3.749A pdb=" N THR A 83 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 3.760A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 331 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 323 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 329 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 378 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS A 354 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER A 383 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A 356 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 355 " --> pdb=" O MET A 363 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET A 363 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 511 through 513 removed outlier: 7.113A pdb=" N TYR A 484 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N MET A 513 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 486 " --> pdb=" O MET A 513 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 578 through 579 removed outlier: 3.511A pdb=" N ILE A 628 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 592 " --> pdb=" O HIS A 625 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.806A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 333 through 336 removed outlier: 7.021A pdb=" N LEU B 333 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL B 318 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 335 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 318 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 128 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.826A pdb=" N SER B 322 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY C 123 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 324 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 468 removed outlier: 4.707A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 511 " --> pdb=" O TYR B 484 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 575 through 580 removed outlier: 7.365A pdb=" N LEU B 626 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 578 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 628 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE B 580 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 582 through 584 Processing sheet with id=AB4, first strand: chain 'P' and resid 266 through 268 removed outlier: 5.976A pdb=" N GLN P 465 " --> pdb=" O ARG P 470 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ARG P 470 " --> pdb=" O GLN P 465 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'P' and resid 396 through 397 removed outlier: 3.839A pdb=" N SER P 396 " --> pdb=" O GLN P 405 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 424 through 425 removed outlier: 6.110A pdb=" N ARG P 425 " --> pdb=" O VAL P 445 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2118 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: 2.02 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5625 1.34 - 1.46: 2741 1.46 - 1.58: 9493 1.58 - 1.70: 14 1.70 - 1.82: 151 Bond restraints: 18024 Sorted by residual: bond pdb=" O1P SEP C 13 " pdb=" P SEP C 13 " ideal model delta sigma weight residual 1.610 1.656 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" CA ARG C 36 " pdb=" CB ARG C 36 " ideal model delta sigma weight residual 1.528 1.555 -0.027 1.59e-02 3.96e+03 2.83e+00 bond pdb=" CB VAL A 144 " pdb=" CG2 VAL A 144 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 bond pdb=" CA LEU B 401 " pdb=" C LEU B 401 " ideal model delta sigma weight residual 1.522 1.501 0.022 1.38e-02 5.25e+03 2.46e+00 bond pdb=" C GLU A 368 " pdb=" N LEU A 369 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.40e-02 5.10e+03 1.90e+00 ... (remaining 18019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 23525 2.01 - 4.02: 604 4.02 - 6.03: 88 6.03 - 8.04: 19 8.04 - 10.05: 9 Bond angle restraints: 24245 Sorted by residual: angle pdb=" C ASP K 587 " pdb=" CA ASP K 587 " pdb=" CB ASP K 587 " ideal model delta sigma weight residual 117.23 109.21 8.02 1.36e+00 5.41e-01 3.48e+01 angle pdb=" C GLN B 118 " pdb=" CA GLN B 118 " pdb=" CB GLN B 118 " ideal model delta sigma weight residual 115.79 108.77 7.02 1.19e+00 7.06e-01 3.48e+01 angle pdb=" CG ARG C 36 " pdb=" CD ARG C 36 " pdb=" NE ARG C 36 " ideal model delta sigma weight residual 112.00 122.05 -10.05 2.20e+00 2.07e-01 2.09e+01 angle pdb=" C PHE P 190 " pdb=" N MET P 191 " pdb=" CA MET P 191 " ideal model delta sigma weight residual 121.14 113.39 7.75 1.75e+00 3.27e-01 1.96e+01 angle pdb=" CA ASP K 587 " pdb=" C ASP K 587 " pdb=" N LEU K 588 " ideal model delta sigma weight residual 119.98 116.26 3.72 8.50e-01 1.38e+00 1.92e+01 ... (remaining 24240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9913 17.93 - 35.87: 972 35.87 - 53.80: 143 53.80 - 71.74: 16 71.74 - 89.67: 22 Dihedral angle restraints: 11066 sinusoidal: 4692 harmonic: 6374 Sorted by residual: dihedral pdb=" CA ARG C 167 " pdb=" C ARG C 167 " pdb=" N TRP C 168 " pdb=" CA TRP C 168 " ideal model delta harmonic sigma weight residual 180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LYS K 522 " pdb=" C LYS K 522 " pdb=" N PRO K 523 " pdb=" CA PRO K 523 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR B 309 " pdb=" C THR B 309 " pdb=" N ASN B 310 " pdb=" CA ASN B 310 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 11063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2020 0.051 - 0.101: 509 0.101 - 0.152: 99 0.152 - 0.202: 4 0.202 - 0.253: 4 Chirality restraints: 2636 Sorted by residual: chirality pdb=" CA PRO K 523 " pdb=" N PRO K 523 " pdb=" C PRO K 523 " pdb=" CB PRO K 523 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE B 605 " pdb=" CA ILE B 605 " pdb=" CG1 ILE B 605 " pdb=" CG2 ILE B 605 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU K 588 " pdb=" CB LEU K 588 " pdb=" CD1 LEU K 588 " pdb=" CD2 LEU K 588 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2633 not shown) Planarity restraints: 3109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 36 " -0.232 9.50e-02 1.11e+02 1.06e-01 1.11e+01 pdb=" NE ARG C 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 36 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG C 36 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 36 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 587 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 588 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 588 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 588 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE K 707 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO K 708 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO K 708 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 708 " 0.030 5.00e-02 4.00e+02 ... (remaining 3106 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 407 2.66 - 3.22: 18207 3.22 - 3.78: 26979 3.78 - 4.34: 35014 4.34 - 4.90: 53635 Nonbonded interactions: 134242 Sorted by model distance: nonbonded pdb=" O LEU A 27 " pdb=" OG1 THR A 31 " model vdw 2.106 3.040 nonbonded pdb=" O LEU B 102 " pdb=" OH TYR B 134 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASN A 101 " pdb=" O3' ATP A 801 " model vdw 2.162 3.040 nonbonded pdb=" OD1 ASN B 425 " pdb=" OG1 THR C 131 " model vdw 2.173 3.040 nonbonded pdb=" OG SER B 434 " pdb=" NZ LYS B 438 " model vdw 2.181 3.120 ... (remaining 134237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 220 or resid 273 through 801)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 12.650 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18027 Z= 0.162 Angle : 0.792 10.050 24245 Z= 0.435 Chirality : 0.046 0.253 2636 Planarity : 0.005 0.106 3109 Dihedral : 14.375 89.672 6938 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.69 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.90 (0.17), residues: 2147 helix: -0.34 (0.16), residues: 942 sheet: -0.16 (0.39), residues: 200 loop : -2.45 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG C 36 TYR 0.016 0.002 TYR P 51 PHE 0.026 0.002 PHE P 287 TRP 0.025 0.003 TRP B 598 HIS 0.005 0.001 HIS P 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (18024) covalent geometry : angle 0.79228 / 0.44 (24245) hydrogen bonds : bond 0.14884 / 9.92 ( 736) hydrogen bonds : angle 6.34323 / 4.37 ( 2118) Misc. bond : bond 0.00377 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.8208 (tp) cc_final: 0.7945 (tp) REVERT: A 76 ILE cc_start: 0.7722 (mt) cc_final: 0.7435 (mm) REVERT: A 95 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7508 (mmmt) REVERT: A 286 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8181 (ttmt) REVERT: A 288 ILE cc_start: 0.8033 (tt) cc_final: 0.7704 (tt) REVERT: A 289 TRP cc_start: 0.6593 (p90) cc_final: 0.6237 (p90) REVERT: A 337 ARG cc_start: 0.7054 (mtt-85) cc_final: 0.6511 (mtt-85) REVERT: A 392 ARG cc_start: 0.7512 (mmt90) cc_final: 0.7125 (mmt-90) REVERT: A 394 MET cc_start: 0.6674 (ppp) cc_final: 0.6346 (ppp) REVERT: A 421 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 431 GLU cc_start: 0.7358 (tp30) cc_final: 0.7143 (tm-30) REVERT: A 550 LYS cc_start: 0.8118 (pttp) cc_final: 0.7889 (ptmm) REVERT: A 557 LYS cc_start: 0.7989 (pttp) cc_final: 0.7676 (pttp) REVERT: A 621 MET cc_start: 0.5867 (mmp) cc_final: 0.5346 (mmm) REVERT: A 639 ARG cc_start: 0.7319 (ttp80) cc_final: 0.7067 (ttp80) REVERT: A 640 GLN cc_start: 0.8267 (pp30) cc_final: 0.7985 (pp30) REVERT: A 645 ASP cc_start: 0.7105 (t0) cc_final: 0.6549 (t0) REVERT: A 672 ASP cc_start: 0.7719 (p0) cc_final: 0.7420 (p0) REVERT: A 680 ILE cc_start: 0.8688 (mp) cc_final: 0.8277 (mp) REVERT: A 684 ILE cc_start: 0.8226 (pt) cc_final: 0.7931 (pt) REVERT: B 18 GLN cc_start: 0.7194 (mp10) cc_final: 0.6939 (mp10) REVERT: B 58 SER cc_start: 0.5676 (t) cc_final: 0.5281 (p) REVERT: B 153 GLU cc_start: 0.8094 (mp0) cc_final: 0.7738 (mp0) REVERT: B 200 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6857 (tm-30) REVERT: B 361 PHE cc_start: 0.8130 (t80) cc_final: 0.7652 (t80) REVERT: B 364 ASP cc_start: 0.7164 (p0) cc_final: 0.6795 (p0) REVERT: B 423 LYS cc_start: 0.8286 (mppt) cc_final: 0.8017 (mmtm) REVERT: B 428 LYS cc_start: 0.7135 (mmmt) cc_final: 0.6919 (mmmt) REVERT: B 450 ARG cc_start: 0.6802 (ttt-90) cc_final: 0.6585 (ttt180) REVERT: B 471 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7120 (tm-30) REVERT: B 475 ARG cc_start: 0.7329 (pmt170) cc_final: 0.6219 (pmt170) REVERT: B 553 MET cc_start: 0.5409 (tmm) cc_final: 0.5170 (tmm) REVERT: B 613 ASP cc_start: 0.5747 (p0) cc_final: 0.5451 (p0) REVERT: B 648 ASP cc_start: 0.7698 (p0) cc_final: 0.7441 (p0) REVERT: B 652 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8650 (mttp) REVERT: C 39 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7620 (ttp80) REVERT: C 49 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8451 (tm-30) REVERT: C 217 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8498 (mm-40) REVERT: C 253 ASN cc_start: 0.6550 (m110) cc_final: 0.6345 (m110) REVERT: K 646 LEU cc_start: 0.5116 (tp) cc_final: 0.4844 (tt) REVERT: P 39 PHE cc_start: 0.5000 (t80) cc_final: 0.4730 (t80) REVERT: P 80 TYR cc_start: 0.7791 (m-80) cc_final: 0.7506 (m-80) REVERT: P 293 TYR cc_start: 0.5344 (m-80) cc_final: 0.5132 (m-80) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.1521 time to fit residues: 93.1790 Evaluate side-chains 382 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.0020 chunk 77 optimal weight: 2.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN C 34 GLN C 188 ASN K 585 HIS P 342 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.200015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.171021 restraints weight = 35244.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.167424 restraints weight = 56583.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.168845 restraints weight = 52549.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.169636 restraints weight = 33769.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.169663 restraints weight = 31609.831| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 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 0.043 18027 Z= 0.155 Angle : 0.671 8.753 24245 Z= 0.355 Chirality : 0.046 0.232 2636 Planarity : 0.006 0.123 3109 Dihedral : 6.646 167.140 2368 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.87 % Favored : 91.90 % Rotamer: Outliers : 0.36 % Allowed : 6.18 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.73 (0.18), residues: 2147 helix: -0.02 (0.16), residues: 965 sheet: -0.74 (0.35), residues: 231 loop : -2.49 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 36 TYR 0.023 0.002 TYR A 373 PHE 0.028 0.002 PHE A 32 TRP 0.019 0.002 TRP K 531 HIS 0.004 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (18024) covalent geometry : angle 0.67121 / 0.35 (24245) hydrogen bonds : bond 0.04421 / 2.88 ( 736) hydrogen bonds : angle 4.94303 / 3.45 ( 2118) Misc. bond : bond 0.00309 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 410 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.6641 (ptmm) cc_final: 0.6282 (ptmt) REVERT: A 74 ASP cc_start: 0.6700 (m-30) cc_final: 0.6387 (m-30) REVERT: A 75 ILE cc_start: 0.8623 (tp) cc_final: 0.8307 (tp) REVERT: A 170 ASP cc_start: 0.7540 (p0) cc_final: 0.7294 (p0) REVERT: A 177 ARG cc_start: 0.7275 (ptt-90) cc_final: 0.6991 (ptt90) REVERT: A 274 GLU cc_start: 0.6926 (mp0) cc_final: 0.6558 (mp0) REVERT: A 288 ILE cc_start: 0.8413 (tt) cc_final: 0.8096 (tt) REVERT: A 289 TRP cc_start: 0.6977 (p90) cc_final: 0.6450 (p90) REVERT: A 380 VAL cc_start: 0.8480 (t) cc_final: 0.8070 (m) REVERT: A 392 ARG cc_start: 0.7018 (mmt90) cc_final: 0.6788 (mmt-90) REVERT: A 428 LYS cc_start: 0.8138 (ptmm) cc_final: 0.7537 (ttpp) REVERT: A 431 GLU cc_start: 0.6506 (tp30) cc_final: 0.6143 (tp30) REVERT: A 435 LYS cc_start: 0.8253 (mttt) cc_final: 0.7962 (mttm) REVERT: A 493 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6943 (pp30) REVERT: A 519 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 550 LYS cc_start: 0.8060 (pttp) cc_final: 0.7839 (ptmm) REVERT: A 557 LYS cc_start: 0.7740 (pttp) cc_final: 0.7414 (pttp) REVERT: A 577 LYS cc_start: 0.7568 (mtmm) cc_final: 0.7323 (mtmm) REVERT: A 639 ARG cc_start: 0.6924 (ttp80) cc_final: 0.6512 (ttp80) REVERT: A 640 GLN cc_start: 0.7951 (pp30) cc_final: 0.7326 (pp30) REVERT: A 680 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8060 (tt) REVERT: A 684 ILE cc_start: 0.8411 (pt) cc_final: 0.7828 (pt) REVERT: B 69 LYS cc_start: 0.8160 (mptt) cc_final: 0.7918 (mptt) REVERT: B 72 LYS cc_start: 0.7683 (pttt) cc_final: 0.7483 (pttt) REVERT: B 125 MET cc_start: 0.6937 (tpp) cc_final: 0.6687 (ttm) REVERT: B 133 PHE cc_start: 0.7074 (t80) cc_final: 0.6805 (t80) REVERT: B 139 VAL cc_start: 0.8485 (t) cc_final: 0.8259 (m) REVERT: B 145 VAL cc_start: 0.7683 (t) cc_final: 0.7289 (p) REVERT: B 157 TRP cc_start: 0.8005 (t60) cc_final: 0.7224 (t60) REVERT: B 204 LYS cc_start: 0.8492 (tmtt) cc_final: 0.8091 (tmtt) REVERT: B 297 THR cc_start: 0.7102 (p) cc_final: 0.6737 (p) REVERT: B 342 ASP cc_start: 0.6964 (p0) cc_final: 0.6245 (p0) REVERT: B 385 ASP cc_start: 0.7228 (p0) cc_final: 0.7004 (p0) REVERT: B 395 LEU cc_start: 0.8127 (tt) cc_final: 0.7851 (tt) REVERT: B 428 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7270 (mmmt) REVERT: B 553 MET cc_start: 0.5456 (tmm) cc_final: 0.5130 (tmm) REVERT: B 567 MET cc_start: 0.7231 (ppp) cc_final: 0.6807 (ppp) REVERT: B 613 ASP cc_start: 0.6587 (p0) cc_final: 0.6314 (p0) REVERT: B 637 THR cc_start: 0.8240 (p) cc_final: 0.7925 (p) REVERT: B 674 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7388 (tm-30) REVERT: C 48 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: C 106 ARG cc_start: 0.7845 (tmt-80) cc_final: 0.7561 (tpt90) REVERT: C 107 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7184 (mtmm) REVERT: C 179 VAL cc_start: 0.4015 (m) cc_final: 0.3569 (m) REVERT: C 231 ARG cc_start: 0.4173 (ttp80) cc_final: 0.3935 (mmm160) REVERT: C 253 ASN cc_start: 0.6741 (m110) cc_final: 0.6088 (m110) REVERT: K 584 LEU cc_start: 0.4792 (mp) cc_final: 0.4342 (tt) REVERT: K 689 MET cc_start: 0.6829 (mmp) cc_final: 0.6606 (mmp) REVERT: P 46 ASN cc_start: 0.6562 (t0) cc_final: 0.6112 (m-40) REVERT: P 134 MET cc_start: 0.6041 (ppp) cc_final: 0.5598 (ppp) REVERT: P 320 LYS cc_start: 0.8303 (tppt) cc_final: 0.8080 (tppt) REVERT: P 331 PHE cc_start: 0.7405 (m-80) cc_final: 0.7126 (m-80) outliers start: 7 outliers final: 0 residues processed: 412 average time/residue: 0.1545 time to fit residues: 91.0646 Evaluate side-chains 365 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 362 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 32 optimal weight: 0.2980 chunk 140 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 169 optimal weight: 0.0020 chunk 93 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 HIS A 524 GLN A 609 GLN B 407 ASN B 496 ASN C 34 GLN P 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.203767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.176121 restraints weight = 35527.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.173481 restraints weight = 60530.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.175919 restraints weight = 47407.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.175847 restraints weight = 29225.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.176313 restraints weight = 27937.116| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18027 Z= 0.118 Angle : 0.619 8.190 24245 Z= 0.324 Chirality : 0.043 0.235 2636 Planarity : 0.004 0.102 3109 Dihedral : 5.345 89.084 2368 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.57 % Favored : 93.20 % Rotamer: Outliers : 0.26 % Allowed : 3.50 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.57 (0.18), residues: 2147 helix: 0.12 (0.17), residues: 976 sheet: -0.91 (0.34), residues: 238 loop : -2.38 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 392 TYR 0.024 0.001 TYR C 189 PHE 0.018 0.001 PHE C 237 TRP 0.040 0.002 TRP C 98 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (18024) covalent geometry : angle 0.61881 / 0.32 (24245) hydrogen bonds : bond 0.03838 / 2.50 ( 736) hydrogen bonds : angle 4.63310 / 3.24 ( 2118) Misc. bond : bond 0.00186 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 399 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ILE cc_start: 0.7795 (mm) cc_final: 0.7467 (mt) REVERT: A 144 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8215 (m) REVERT: A 170 ASP cc_start: 0.7446 (p0) cc_final: 0.7172 (p0) REVERT: A 177 ARG cc_start: 0.7175 (ptt-90) cc_final: 0.6939 (ptt90) REVERT: A 289 TRP cc_start: 0.6817 (p90) cc_final: 0.6255 (p90) REVERT: A 380 VAL cc_start: 0.8425 (t) cc_final: 0.7938 (m) REVERT: A 394 MET cc_start: 0.6986 (ppp) cc_final: 0.6722 (ppp) REVERT: A 453 GLU cc_start: 0.6473 (mp0) cc_final: 0.6271 (mp0) REVERT: A 550 LYS cc_start: 0.8023 (pttp) cc_final: 0.7815 (ptmm) REVERT: A 557 LYS cc_start: 0.7751 (pttp) cc_final: 0.7513 (pttp) REVERT: A 609 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7536 (pp30) REVERT: A 636 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 639 ARG cc_start: 0.6918 (ttp80) cc_final: 0.6569 (ttp80) REVERT: A 640 GLN cc_start: 0.7981 (pp30) cc_final: 0.7681 (pp30) REVERT: A 648 ASP cc_start: 0.7351 (t0) cc_final: 0.7076 (t70) REVERT: A 680 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8416 (mt) REVERT: A 684 ILE cc_start: 0.8416 (pt) cc_final: 0.7855 (pt) REVERT: B 56 TYR cc_start: 0.6735 (t80) cc_final: 0.6494 (t80) REVERT: B 69 LYS cc_start: 0.8156 (mptt) cc_final: 0.7876 (mptt) REVERT: B 71 LEU cc_start: 0.8192 (tt) cc_final: 0.7850 (mp) REVERT: B 72 LYS cc_start: 0.7612 (pttt) cc_final: 0.7305 (pttt) REVERT: B 204 LYS cc_start: 0.8516 (tmtt) cc_final: 0.8113 (tmtt) REVERT: B 342 ASP cc_start: 0.6966 (p0) cc_final: 0.6309 (p0) REVERT: B 385 ASP cc_start: 0.7243 (p0) cc_final: 0.7034 (p0) REVERT: B 550 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7428 (mmtp) REVERT: B 567 MET cc_start: 0.7110 (ppp) cc_final: 0.6696 (ppp) REVERT: B 684 ILE cc_start: 0.8753 (mt) cc_final: 0.8525 (mm) REVERT: C 42 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 48 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: C 107 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7029 (mtmm) REVERT: C 108 LYS cc_start: 0.6812 (pttp) cc_final: 0.6238 (ttpp) REVERT: C 217 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8593 (mm-40) REVERT: C 253 ASN cc_start: 0.6768 (m110) cc_final: 0.5424 (m110) REVERT: P 134 MET cc_start: 0.5879 (ppp) cc_final: 0.5452 (ppp) REVERT: P 320 LYS cc_start: 0.8355 (tppt) cc_final: 0.8087 (tppt) REVERT: P 331 PHE cc_start: 0.7391 (m-80) cc_final: 0.7105 (m-80) REVERT: P 381 MET cc_start: 0.4631 (ttp) cc_final: 0.4126 (ttp) outliers start: 5 outliers final: 0 residues processed: 401 average time/residue: 0.1529 time to fit residues: 87.7156 Evaluate side-chains 367 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 363 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 153 optimal weight: 0.0030 chunk 139 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 chunk 127 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN B 407 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN P 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.207071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.184536 restraints weight = 37182.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.182514 restraints weight = 69392.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.184033 restraints weight = 58630.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.183951 restraints weight = 36161.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.184369 restraints weight = 36201.409| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18027 Z= 0.115 Angle : 0.614 8.330 24245 Z= 0.320 Chirality : 0.043 0.234 2636 Planarity : 0.005 0.129 3109 Dihedral : 5.218 88.961 2368 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.99 % Favored : 92.78 % Rotamer: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.43 (0.18), residues: 2147 helix: 0.23 (0.17), residues: 971 sheet: -0.63 (0.35), residues: 222 loop : -2.33 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 36 TYR 0.022 0.001 TYR A 137 PHE 0.026 0.001 PHE P 39 TRP 0.020 0.001 TRP C 98 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (18024) covalent geometry : angle 0.61402 / 0.32 (24245) hydrogen bonds : bond 0.03702 / 2.41 ( 736) hydrogen bonds : angle 4.50714 / 3.16 ( 2118) Misc. bond : bond 0.00402 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 392 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7565 (p0) cc_final: 0.7231 (p0) REVERT: A 289 TRP cc_start: 0.6763 (p90) cc_final: 0.6126 (p90) REVERT: A 380 VAL cc_start: 0.8338 (t) cc_final: 0.7839 (m) REVERT: A 394 MET cc_start: 0.6985 (ppp) cc_final: 0.6665 (ppp) REVERT: A 519 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6985 (mm-30) REVERT: A 557 LYS cc_start: 0.7770 (pttp) cc_final: 0.7460 (pttp) REVERT: A 577 LYS cc_start: 0.7431 (mtmm) cc_final: 0.7101 (mtmm) REVERT: A 606 MET cc_start: 0.7645 (tpt) cc_final: 0.7408 (tpp) REVERT: A 611 LEU cc_start: 0.7366 (mp) cc_final: 0.6983 (mp) REVERT: A 617 MET cc_start: 0.6122 (ppp) cc_final: 0.5904 (ppp) REVERT: A 636 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 639 ARG cc_start: 0.6937 (ttp80) cc_final: 0.6693 (ttp80) REVERT: A 640 GLN cc_start: 0.7962 (pp30) cc_final: 0.7625 (pp30) REVERT: A 674 GLN cc_start: 0.6884 (pm20) cc_final: 0.6641 (pm20) REVERT: A 680 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 684 ILE cc_start: 0.8387 (pt) cc_final: 0.7921 (pt) REVERT: B 69 LYS cc_start: 0.8145 (mptt) cc_final: 0.7753 (mptt) REVERT: B 71 LEU cc_start: 0.8237 (tt) cc_final: 0.7179 (mp) REVERT: B 102 LEU cc_start: 0.7114 (tt) cc_final: 0.6596 (tt) REVERT: B 157 TRP cc_start: 0.8089 (t60) cc_final: 0.7261 (t60) REVERT: B 203 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7449 (ttmm) REVERT: B 204 LYS cc_start: 0.8426 (tmtt) cc_final: 0.7967 (tmtt) REVERT: B 277 ILE cc_start: 0.6389 (mp) cc_final: 0.6136 (mt) REVERT: B 342 ASP cc_start: 0.7027 (p0) cc_final: 0.6379 (p0) REVERT: B 489 GLU cc_start: 0.6260 (mm-30) cc_final: 0.6006 (mm-30) REVERT: B 550 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7574 (mmtp) REVERT: B 552 LYS cc_start: 0.7721 (pttm) cc_final: 0.7498 (pttm) REVERT: B 567 MET cc_start: 0.7033 (ppp) cc_final: 0.6720 (ppp) REVERT: B 674 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7451 (tm-30) REVERT: B 684 ILE cc_start: 0.8711 (mt) cc_final: 0.8498 (mm) REVERT: C 46 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7119 (mm-30) REVERT: C 107 LYS cc_start: 0.7916 (mtmm) cc_final: 0.6783 (mtmm) REVERT: C 108 LYS cc_start: 0.7023 (pttp) cc_final: 0.6532 (ttpp) REVERT: C 253 ASN cc_start: 0.6841 (m110) cc_final: 0.6347 (m110) REVERT: P 46 ASN cc_start: 0.6375 (t0) cc_final: 0.5902 (m-40) REVERT: P 134 MET cc_start: 0.5562 (ppp) cc_final: 0.5241 (ppp) REVERT: P 320 LYS cc_start: 0.8384 (tppt) cc_final: 0.8109 (tppt) REVERT: P 331 PHE cc_start: 0.7273 (m-80) cc_final: 0.7040 (m-80) REVERT: P 381 MET cc_start: 0.4682 (ttp) cc_final: 0.4210 (ttp) outliers start: 2 outliers final: 0 residues processed: 393 average time/residue: 0.1570 time to fit residues: 88.7068 Evaluate side-chains 355 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 95 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 150 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 192 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN A 609 GLN ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 425 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 188 ASN ** P 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.200840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.178192 restraints weight = 36523.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175476 restraints weight = 68247.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175942 restraints weight = 59310.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.174790 restraints weight = 40005.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175409 restraints weight = 42127.217| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18027 Z= 0.207 Angle : 0.732 10.394 24245 Z= 0.387 Chirality : 0.048 0.249 2636 Planarity : 0.006 0.115 3109 Dihedral : 5.736 71.522 2368 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.90 % Favored : 90.87 % Rotamer: Outliers : 0.15 % Allowed : 3.45 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.72 (0.17), residues: 2147 helix: -0.02 (0.16), residues: 975 sheet: -0.70 (0.35), residues: 231 loop : -2.50 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 36 TYR 0.035 0.002 TYR A 373 PHE 0.046 0.002 PHE A 32 TRP 0.026 0.002 TRP C 7 HIS 0.006 0.002 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (18024) covalent geometry : angle 0.73220 / 0.39 (24245) hydrogen bonds : bond 0.05133 / 3.29 ( 736) hydrogen bonds : angle 4.95035 / 3.42 ( 2118) Misc. bond : bond 0.00377 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 398 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.8506 (tp) cc_final: 0.8200 (tp) REVERT: A 76 ILE cc_start: 0.7397 (mm) cc_final: 0.7143 (mm) REVERT: A 170 ASP cc_start: 0.7681 (p0) cc_final: 0.7369 (p0) REVERT: A 289 TRP cc_start: 0.6881 (p90) cc_final: 0.6259 (p90) REVERT: A 292 ASN cc_start: 0.7780 (t0) cc_final: 0.7506 (t0) REVERT: A 309 THR cc_start: 0.7827 (p) cc_final: 0.7045 (p) REVERT: A 375 ASN cc_start: 0.7292 (t0) cc_final: 0.7077 (t0) REVERT: A 378 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.6741 (mmm-85) REVERT: A 380 VAL cc_start: 0.8246 (t) cc_final: 0.7751 (m) REVERT: A 394 MET cc_start: 0.6913 (ppp) cc_final: 0.6658 (ppp) REVERT: A 395 LEU cc_start: 0.7305 (mt) cc_final: 0.6203 (mt) REVERT: A 402 LYS cc_start: 0.8098 (pttm) cc_final: 0.7764 (mptt) REVERT: A 407 ASN cc_start: 0.8355 (m110) cc_final: 0.8011 (m-40) REVERT: A 453 GLU cc_start: 0.6741 (mp0) cc_final: 0.6496 (mp0) REVERT: A 466 MET cc_start: 0.7697 (tpt) cc_final: 0.7093 (tpt) REVERT: A 489 GLU cc_start: 0.6493 (mp0) cc_final: 0.6075 (mp0) REVERT: A 505 LYS cc_start: 0.7362 (pptt) cc_final: 0.7082 (pptt) REVERT: A 547 GLU cc_start: 0.8314 (mp0) cc_final: 0.8092 (mp0) REVERT: A 557 LYS cc_start: 0.8168 (pttp) cc_final: 0.7672 (pttp) REVERT: A 577 LYS cc_start: 0.7614 (mtmm) cc_final: 0.7324 (mtmm) REVERT: A 611 LEU cc_start: 0.7461 (mp) cc_final: 0.7226 (mt) REVERT: A 636 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 639 ARG cc_start: 0.7101 (ttp80) cc_final: 0.6886 (ttp80) REVERT: A 640 GLN cc_start: 0.8027 (pp30) cc_final: 0.7676 (pp30) REVERT: A 645 ASP cc_start: 0.7226 (t0) cc_final: 0.7006 (t0) REVERT: A 648 ASP cc_start: 0.7237 (t0) cc_final: 0.6627 (t70) REVERT: A 684 ILE cc_start: 0.8361 (pt) cc_final: 0.8038 (pt) REVERT: B 21 ILE cc_start: 0.8211 (tp) cc_final: 0.7974 (tt) REVERT: B 69 LYS cc_start: 0.8272 (mptt) cc_final: 0.7933 (mptt) REVERT: B 71 LEU cc_start: 0.8214 (tt) cc_final: 0.7910 (tt) REVERT: B 83 THR cc_start: 0.8477 (t) cc_final: 0.8250 (m) REVERT: B 98 LEU cc_start: 0.8858 (tt) cc_final: 0.8616 (tt) REVERT: B 145 VAL cc_start: 0.7995 (t) cc_final: 0.7753 (p) REVERT: B 154 GLN cc_start: 0.7419 (tp40) cc_final: 0.7017 (tp40) REVERT: B 204 LYS cc_start: 0.8399 (tmtt) cc_final: 0.8002 (tmtt) REVERT: B 215 LEU cc_start: 0.7758 (tt) cc_final: 0.7342 (mt) REVERT: B 567 MET cc_start: 0.7196 (ppp) cc_final: 0.6660 (ppp) REVERT: B 637 THR cc_start: 0.8362 (p) cc_final: 0.8160 (p) REVERT: C 42 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7201 (tm-30) REVERT: C 46 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7080 (mm-30) REVERT: C 106 ARG cc_start: 0.7982 (tmt-80) cc_final: 0.6635 (tmt-80) REVERT: C 253 ASN cc_start: 0.7006 (m110) cc_final: 0.6609 (m110) REVERT: K 537 LEU cc_start: 0.7060 (tp) cc_final: 0.6636 (tp) REVERT: K 668 MET cc_start: 0.3326 (tmm) cc_final: 0.1428 (ptm) REVERT: P 46 ASN cc_start: 0.6412 (t0) cc_final: 0.6057 (m-40) REVERT: P 320 LYS cc_start: 0.8414 (tppt) cc_final: 0.8093 (tppt) REVERT: P 331 PHE cc_start: 0.7398 (m-80) cc_final: 0.7123 (m-80) REVERT: P 381 MET cc_start: 0.5040 (ttp) cc_final: 0.4526 (ttp) outliers start: 3 outliers final: 0 residues processed: 400 average time/residue: 0.1400 time to fit residues: 81.3226 Evaluate side-chains 366 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN A 609 GLN ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 130 ASN ** K 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.201371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179187 restraints weight = 36457.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.176658 restraints weight = 62092.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.177401 restraints weight = 55286.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.176974 restraints weight = 35660.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.177467 restraints weight = 34120.050| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18027 Z= 0.185 Angle : 0.702 11.761 24245 Z= 0.367 Chirality : 0.046 0.188 2636 Planarity : 0.006 0.184 3109 Dihedral : 5.717 78.112 2368 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.66 % Favored : 91.10 % Rotamer: Outliers : 0.21 % Allowed : 2.88 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.69 (0.17), residues: 2147 helix: 0.01 (0.16), residues: 968 sheet: -0.73 (0.35), residues: 225 loop : -2.46 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 36 TYR 0.024 0.002 TYR B 305 PHE 0.034 0.002 PHE A 32 TRP 0.055 0.002 TRP C 98 HIS 0.005 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (18024) covalent geometry : angle 0.70170 / 0.37 (24245) hydrogen bonds : bond 0.04570 / 2.92 ( 736) hydrogen bonds : angle 4.84541 / 3.36 ( 2118) Misc. bond : bond 0.00451 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 388 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7622 (p0) cc_final: 0.7304 (p0) REVERT: A 289 TRP cc_start: 0.6932 (p90) cc_final: 0.6134 (p90) REVERT: A 292 ASN cc_start: 0.7787 (t0) cc_final: 0.7529 (t0) REVERT: A 299 GLU cc_start: 0.7126 (pp20) cc_final: 0.6878 (pp20) REVERT: A 309 THR cc_start: 0.7882 (p) cc_final: 0.7675 (p) REVERT: A 380 VAL cc_start: 0.8183 (t) cc_final: 0.7770 (m) REVERT: A 395 LEU cc_start: 0.7286 (mt) cc_final: 0.6167 (mt) REVERT: A 402 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7769 (ptpp) REVERT: A 407 ASN cc_start: 0.8375 (m110) cc_final: 0.8078 (m-40) REVERT: A 453 GLU cc_start: 0.6790 (mp0) cc_final: 0.6522 (mp0) REVERT: A 489 GLU cc_start: 0.6408 (mp0) cc_final: 0.5988 (mp0) REVERT: A 505 LYS cc_start: 0.7408 (pptt) cc_final: 0.7124 (pptt) REVERT: A 557 LYS cc_start: 0.8194 (pttp) cc_final: 0.7658 (pttp) REVERT: A 577 LYS cc_start: 0.7660 (mtmm) cc_final: 0.7323 (mtmm) REVERT: A 636 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 639 ARG cc_start: 0.7077 (ttp80) cc_final: 0.6868 (ttp80) REVERT: A 640 GLN cc_start: 0.8011 (pp30) cc_final: 0.7653 (pp30) REVERT: A 648 ASP cc_start: 0.7183 (t0) cc_final: 0.6336 (t0) REVERT: A 682 ARG cc_start: 0.7613 (ptm-80) cc_final: 0.7259 (ttp-110) REVERT: A 684 ILE cc_start: 0.8311 (pt) cc_final: 0.7740 (pt) REVERT: B 25 MET cc_start: 0.7232 (tpp) cc_final: 0.7016 (tpp) REVERT: B 69 LYS cc_start: 0.8272 (mptt) cc_final: 0.7970 (mptt) REVERT: B 70 GLU cc_start: 0.7588 (pp20) cc_final: 0.7199 (pp20) REVERT: B 71 LEU cc_start: 0.8134 (tt) cc_final: 0.7630 (tt) REVERT: B 102 LEU cc_start: 0.7428 (tt) cc_final: 0.6977 (tt) REVERT: B 145 VAL cc_start: 0.7887 (t) cc_final: 0.7667 (p) REVERT: B 154 GLN cc_start: 0.7254 (tp40) cc_final: 0.6777 (tp40) REVERT: B 157 TRP cc_start: 0.8239 (t60) cc_final: 0.7123 (t60) REVERT: B 204 LYS cc_start: 0.8465 (tmtt) cc_final: 0.8038 (tmtt) REVERT: B 441 ILE cc_start: 0.8712 (tp) cc_final: 0.8331 (tt) REVERT: B 471 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6675 (tm-30) REVERT: B 475 ARG cc_start: 0.7718 (pmt170) cc_final: 0.6286 (pmt170) REVERT: B 539 GLU cc_start: 0.7131 (tp30) cc_final: 0.6778 (tp30) REVERT: B 552 LYS cc_start: 0.7683 (pttm) cc_final: 0.7480 (pttm) REVERT: B 567 MET cc_start: 0.7279 (ppp) cc_final: 0.6773 (ppp) REVERT: B 571 LEU cc_start: 0.7504 (tp) cc_final: 0.7256 (tp) REVERT: B 599 THR cc_start: 0.7993 (t) cc_final: 0.7603 (p) REVERT: C 32 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7372 (ttm170) REVERT: C 42 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7168 (tm-30) REVERT: C 46 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7086 (mm-30) REVERT: C 48 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: C 105 MET cc_start: 0.5911 (ppp) cc_final: 0.5692 (ppp) REVERT: C 106 ARG cc_start: 0.7910 (tmt-80) cc_final: 0.7508 (tmt-80) REVERT: C 107 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7380 (mttm) REVERT: C 253 ASN cc_start: 0.7012 (m110) cc_final: 0.6715 (m110) REVERT: K 537 LEU cc_start: 0.7090 (tp) cc_final: 0.6728 (tp) REVERT: K 668 MET cc_start: 0.3248 (tmm) cc_final: 0.1324 (ptm) REVERT: P 46 ASN cc_start: 0.6267 (t0) cc_final: 0.6014 (m110) REVERT: P 320 LYS cc_start: 0.8420 (tppt) cc_final: 0.8098 (tppt) REVERT: P 331 PHE cc_start: 0.7320 (m-80) cc_final: 0.7059 (m-80) outliers start: 4 outliers final: 1 residues processed: 389 average time/residue: 0.1474 time to fit residues: 82.7510 Evaluate side-chains 369 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 145 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 461 GLN B 407 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 130 ASN K 559 GLN K 709 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.204010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.180375 restraints weight = 36699.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.178480 restraints weight = 59828.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178677 restraints weight = 54743.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.178159 restraints weight = 36728.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178776 restraints weight = 33723.193| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18027 Z= 0.133 Angle : 0.667 10.722 24245 Z= 0.345 Chirality : 0.044 0.173 2636 Planarity : 0.005 0.140 3109 Dihedral : 5.438 81.486 2368 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.20 % Favored : 91.62 % Rotamer: Outliers : 0.15 % Allowed : 1.75 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.58 (0.17), residues: 2147 helix: 0.11 (0.16), residues: 963 sheet: -0.73 (0.36), residues: 221 loop : -2.38 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 36 TYR 0.020 0.001 TYR A 373 PHE 0.022 0.002 PHE A 32 TRP 0.042 0.002 TRP C 98 HIS 0.006 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (18024) covalent geometry : angle 0.66699 / 0.35 (24245) hydrogen bonds : bond 0.04045 / 2.62 ( 736) hydrogen bonds : angle 4.67053 / 3.25 ( 2118) Misc. bond : bond 0.00548 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 389 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7566 (p0) cc_final: 0.7224 (p0) REVERT: A 292 ASN cc_start: 0.7728 (t0) cc_final: 0.7471 (t0) REVERT: A 309 THR cc_start: 0.7935 (p) cc_final: 0.7727 (p) REVERT: A 363 MET cc_start: 0.8153 (ptm) cc_final: 0.7763 (ptm) REVERT: A 378 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.7127 (mmm-85) REVERT: A 380 VAL cc_start: 0.8067 (t) cc_final: 0.7587 (m) REVERT: A 394 MET cc_start: 0.6922 (ppp) cc_final: 0.6682 (ppp) REVERT: A 402 LYS cc_start: 0.7782 (ptpp) cc_final: 0.7530 (ptpp) REVERT: A 407 ASN cc_start: 0.8383 (m110) cc_final: 0.8064 (m-40) REVERT: A 428 LYS cc_start: 0.8051 (pttp) cc_final: 0.7064 (ttpp) REVERT: A 431 GLU cc_start: 0.6808 (pp20) cc_final: 0.6598 (pp20) REVERT: A 453 GLU cc_start: 0.6824 (mp0) cc_final: 0.6455 (mp0) REVERT: A 466 MET cc_start: 0.7815 (tpt) cc_final: 0.7222 (tpt) REVERT: A 489 GLU cc_start: 0.6322 (mp0) cc_final: 0.5788 (mp0) REVERT: A 519 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 523 GLN cc_start: 0.7887 (pm20) cc_final: 0.7560 (pm20) REVERT: A 557 LYS cc_start: 0.8284 (pttp) cc_final: 0.7698 (pttp) REVERT: A 577 LYS cc_start: 0.7514 (mtmm) cc_final: 0.7149 (mtmm) REVERT: A 617 MET cc_start: 0.6305 (ppp) cc_final: 0.6068 (ppp) REVERT: A 636 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 639 ARG cc_start: 0.7058 (ttp80) cc_final: 0.6827 (ttp80) REVERT: A 640 GLN cc_start: 0.7991 (pp30) cc_final: 0.7630 (pp30) REVERT: A 648 ASP cc_start: 0.6779 (t0) cc_final: 0.6319 (t0) REVERT: A 684 ILE cc_start: 0.8267 (pt) cc_final: 0.7737 (pt) REVERT: B 25 MET cc_start: 0.7234 (tpp) cc_final: 0.6963 (tpp) REVERT: B 69 LYS cc_start: 0.8264 (mptt) cc_final: 0.7950 (mptt) REVERT: B 70 GLU cc_start: 0.7440 (pp20) cc_final: 0.7109 (pp20) REVERT: B 71 LEU cc_start: 0.8083 (tt) cc_final: 0.7621 (tt) REVERT: B 143 VAL cc_start: 0.7130 (m) cc_final: 0.6926 (m) REVERT: B 145 VAL cc_start: 0.7888 (t) cc_final: 0.7586 (p) REVERT: B 154 GLN cc_start: 0.7277 (tp40) cc_final: 0.6873 (tp40) REVERT: B 157 TRP cc_start: 0.8141 (t60) cc_final: 0.7092 (t60) REVERT: B 204 LYS cc_start: 0.8423 (tmtt) cc_final: 0.8012 (tmtt) REVERT: B 435 LYS cc_start: 0.7565 (mmmt) cc_final: 0.7213 (mmmt) REVERT: B 441 ILE cc_start: 0.8701 (tp) cc_final: 0.8215 (tt) REVERT: B 471 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6603 (tm-30) REVERT: B 475 ARG cc_start: 0.7676 (pmt170) cc_final: 0.6218 (pmt170) REVERT: B 489 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5954 (mm-30) REVERT: B 539 GLU cc_start: 0.6981 (tp30) cc_final: 0.6747 (tp30) REVERT: B 552 LYS cc_start: 0.7698 (pttm) cc_final: 0.7486 (pttm) REVERT: B 567 MET cc_start: 0.7227 (ppp) cc_final: 0.6703 (ppp) REVERT: B 571 LEU cc_start: 0.7661 (tp) cc_final: 0.7281 (tt) REVERT: C 49 GLU cc_start: 0.8240 (pp20) cc_final: 0.7984 (pp20) REVERT: C 105 MET cc_start: 0.5933 (ppp) cc_final: 0.5620 (ppp) REVERT: C 112 MET cc_start: 0.7801 (mmp) cc_final: 0.7524 (mmm) REVERT: C 253 ASN cc_start: 0.7041 (m110) cc_final: 0.6782 (m110) REVERT: K 537 LEU cc_start: 0.6867 (tp) cc_final: 0.6502 (tp) REVERT: K 668 MET cc_start: 0.3260 (tmm) cc_final: 0.1484 (ptm) REVERT: P 46 ASN cc_start: 0.6242 (t0) cc_final: 0.6038 (m-40) REVERT: P 320 LYS cc_start: 0.8421 (tppt) cc_final: 0.8096 (tppt) REVERT: P 331 PHE cc_start: 0.7421 (m-80) cc_final: 0.7108 (m-80) REVERT: P 381 MET cc_start: 0.5153 (ttp) cc_final: 0.4492 (ttp) outliers start: 3 outliers final: 1 residues processed: 391 average time/residue: 0.1491 time to fit residues: 84.2180 Evaluate side-chains 366 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 7 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 208 optimal weight: 0.0470 chunk 132 optimal weight: 7.9990 chunk 48 optimal weight: 0.1980 chunk 79 optimal weight: 0.4980 chunk 172 optimal weight: 6.9990 chunk 47 optimal weight: 0.0060 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 183 optimal weight: 0.9980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 461 GLN A 609 GLN B 407 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 130 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.205759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.182243 restraints weight = 36564.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.179379 restraints weight = 66368.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.180494 restraints weight = 55435.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179611 restraints weight = 37673.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.180323 restraints weight = 32297.937| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 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 : 0.003 0.040 18027 Z= 0.117 Angle : 0.652 10.843 24245 Z= 0.335 Chirality : 0.043 0.166 2636 Planarity : 0.005 0.117 3109 Dihedral : 5.258 84.844 2368 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.41 % Favored : 92.41 % Rotamer: Outliers : 0.15 % Allowed : 1.24 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.46 (0.18), residues: 2147 helix: 0.21 (0.17), residues: 970 sheet: -0.67 (0.35), residues: 217 loop : -2.33 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 36 TYR 0.023 0.001 TYR A 137 PHE 0.021 0.001 PHE B 659 TRP 0.034 0.002 TRP C 98 HIS 0.006 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (18024) covalent geometry : angle 0.65171 / 0.33 (24245) hydrogen bonds : bond 0.03678 / 2.40 ( 736) hydrogen bonds : angle 4.54896 / 3.16 ( 2118) Misc. bond : bond 0.00325 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 382 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7808 (t0) cc_final: 0.7579 (t70) REVERT: A 170 ASP cc_start: 0.7269 (p0) cc_final: 0.6972 (t70) REVERT: A 292 ASN cc_start: 0.7751 (t0) cc_final: 0.7452 (t0) REVERT: A 309 THR cc_start: 0.7948 (p) cc_final: 0.7701 (p) REVERT: A 378 ARG cc_start: 0.7440 (mmm-85) cc_final: 0.7199 (mmm-85) REVERT: A 380 VAL cc_start: 0.8172 (t) cc_final: 0.7726 (m) REVERT: A 394 MET cc_start: 0.6993 (ppp) cc_final: 0.6742 (ppp) REVERT: A 428 LYS cc_start: 0.7999 (pttp) cc_final: 0.6874 (ttpp) REVERT: A 431 GLU cc_start: 0.6757 (pp20) cc_final: 0.6543 (pp20) REVERT: A 453 GLU cc_start: 0.6731 (mp0) cc_final: 0.6399 (mp0) REVERT: A 489 GLU cc_start: 0.6213 (mp0) cc_final: 0.5771 (mp0) REVERT: A 547 GLU cc_start: 0.8249 (mp0) cc_final: 0.8045 (mp0) REVERT: A 557 LYS cc_start: 0.8282 (pttp) cc_final: 0.7686 (pttp) REVERT: A 577 LYS cc_start: 0.7455 (mtmm) cc_final: 0.7129 (mtmm) REVERT: A 611 LEU cc_start: 0.7446 (mm) cc_final: 0.7238 (mt) REVERT: A 617 MET cc_start: 0.6351 (ppp) cc_final: 0.6094 (ppp) REVERT: A 636 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 639 ARG cc_start: 0.7048 (ttp80) cc_final: 0.6793 (ttp80) REVERT: A 640 GLN cc_start: 0.7962 (pp30) cc_final: 0.7596 (pp30) REVERT: A 648 ASP cc_start: 0.6660 (t0) cc_final: 0.6210 (t0) REVERT: A 684 ILE cc_start: 0.8214 (pt) cc_final: 0.7697 (pt) REVERT: B 25 MET cc_start: 0.7173 (tpp) cc_final: 0.6920 (tpp) REVERT: B 69 LYS cc_start: 0.8257 (mptt) cc_final: 0.7914 (mptt) REVERT: B 70 GLU cc_start: 0.7360 (pp20) cc_final: 0.7032 (pp20) REVERT: B 71 LEU cc_start: 0.7977 (tt) cc_final: 0.7553 (tt) REVERT: B 154 GLN cc_start: 0.7174 (tp40) cc_final: 0.6774 (tp40) REVERT: B 157 TRP cc_start: 0.8044 (t60) cc_final: 0.7119 (t60) REVERT: B 168 ARG cc_start: 0.6891 (ptm-80) cc_final: 0.6635 (ptm-80) REVERT: B 170 ASP cc_start: 0.6992 (p0) cc_final: 0.6707 (t70) REVERT: B 204 LYS cc_start: 0.8372 (tmtt) cc_final: 0.7924 (tmtt) REVERT: B 435 LYS cc_start: 0.7678 (mmmt) cc_final: 0.7345 (mmmt) REVERT: B 441 ILE cc_start: 0.8682 (tp) cc_final: 0.8319 (tt) REVERT: B 448 ARG cc_start: 0.6804 (ttm170) cc_final: 0.6504 (ttm170) REVERT: B 471 GLU cc_start: 0.6894 (tm-30) cc_final: 0.6611 (tm-30) REVERT: B 475 ARG cc_start: 0.7644 (pmt170) cc_final: 0.6166 (pmt170) REVERT: B 489 GLU cc_start: 0.6236 (mm-30) cc_final: 0.6009 (mm-30) REVERT: B 550 LYS cc_start: 0.7554 (mmtp) cc_final: 0.7075 (mmtp) REVERT: B 552 LYS cc_start: 0.7702 (pttm) cc_final: 0.7470 (pttm) REVERT: B 567 MET cc_start: 0.7243 (ppp) cc_final: 0.6802 (ppp) REVERT: B 571 LEU cc_start: 0.7509 (tp) cc_final: 0.7108 (tt) REVERT: C 107 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7595 (mtmm) REVERT: C 112 MET cc_start: 0.7792 (mmp) cc_final: 0.7553 (mmm) REVERT: C 253 ASN cc_start: 0.7038 (m110) cc_final: 0.6521 (m110) REVERT: K 537 LEU cc_start: 0.6847 (tp) cc_final: 0.6556 (tp) REVERT: K 668 MET cc_start: 0.3157 (tmm) cc_final: 0.1492 (ptm) REVERT: P 320 LYS cc_start: 0.8365 (tppt) cc_final: 0.8050 (tppt) REVERT: P 331 PHE cc_start: 0.7405 (m-80) cc_final: 0.7100 (m-80) REVERT: P 381 MET cc_start: 0.5194 (ttp) cc_final: 0.4557 (ttp) outliers start: 3 outliers final: 1 residues processed: 383 average time/residue: 0.1576 time to fit residues: 87.1373 Evaluate side-chains 372 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 371 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 104 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 197 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 461 GLN ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 130 ASN ** P 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.203162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.178662 restraints weight = 36566.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176394 restraints weight = 66970.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.177656 restraints weight = 56119.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.177785 restraints weight = 36433.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.178028 restraints weight = 35675.858| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18027 Z= 0.157 Angle : 0.694 11.813 24245 Z= 0.359 Chirality : 0.045 0.183 2636 Planarity : 0.005 0.126 3109 Dihedral : 5.363 80.968 2368 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.52 % Favored : 91.29 % Rotamer: Outliers : 0.10 % Allowed : 0.93 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.46 (0.18), residues: 2147 helix: 0.22 (0.17), residues: 963 sheet: -0.64 (0.36), residues: 215 loop : -2.33 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 392 TYR 0.033 0.002 TYR B 301 PHE 0.031 0.002 PHE A 32 TRP 0.030 0.002 TRP C 98 HIS 0.007 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (18024) covalent geometry : angle 0.69352 / 0.36 (24245) hydrogen bonds : bond 0.04282 / 2.76 ( 736) hydrogen bonds : angle 4.69934 / 3.26 ( 2118) Misc. bond : bond 0.00351 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 388 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7867 (t0) cc_final: 0.7578 (t0) REVERT: A 168 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7935 (tmm-80) REVERT: A 170 ASP cc_start: 0.7375 (p0) cc_final: 0.7065 (p0) REVERT: A 289 TRP cc_start: 0.6810 (p90) cc_final: 0.6350 (p90) REVERT: A 309 THR cc_start: 0.7863 (p) cc_final: 0.7353 (p) REVERT: A 363 MET cc_start: 0.7864 (ptm) cc_final: 0.7597 (ptm) REVERT: A 378 ARG cc_start: 0.7408 (mmm-85) cc_final: 0.6717 (mmm-85) REVERT: A 380 VAL cc_start: 0.8211 (t) cc_final: 0.7867 (m) REVERT: A 382 ASP cc_start: 0.7681 (t0) cc_final: 0.7190 (m-30) REVERT: A 383 SER cc_start: 0.8116 (t) cc_final: 0.7876 (t) REVERT: A 395 LEU cc_start: 0.7092 (mt) cc_final: 0.6083 (mt) REVERT: A 402 LYS cc_start: 0.7756 (ptpp) cc_final: 0.7517 (ptpp) REVERT: A 428 LYS cc_start: 0.8110 (pttp) cc_final: 0.7060 (ttpp) REVERT: A 436 ASN cc_start: 0.7575 (t0) cc_final: 0.7229 (t0) REVERT: A 453 GLU cc_start: 0.6847 (mp0) cc_final: 0.6490 (mp0) REVERT: A 519 GLU cc_start: 0.7215 (mm-30) cc_final: 0.7013 (mm-30) REVERT: A 557 LYS cc_start: 0.8255 (pttp) cc_final: 0.7642 (pttp) REVERT: A 577 LYS cc_start: 0.7459 (mtmm) cc_final: 0.7165 (mtmm) REVERT: A 611 LEU cc_start: 0.7651 (mm) cc_final: 0.7388 (mt) REVERT: A 639 ARG cc_start: 0.7010 (ttp80) cc_final: 0.6739 (ttp80) REVERT: A 640 GLN cc_start: 0.7781 (pp30) cc_final: 0.7511 (pp30) REVERT: A 648 ASP cc_start: 0.6662 (t0) cc_final: 0.6308 (t0) REVERT: A 682 ARG cc_start: 0.7417 (ptm-80) cc_final: 0.7064 (ttp-110) REVERT: A 684 ILE cc_start: 0.8199 (pt) cc_final: 0.7549 (pt) REVERT: B 69 LYS cc_start: 0.8259 (mptt) cc_final: 0.7920 (mptt) REVERT: B 70 GLU cc_start: 0.7464 (pp20) cc_final: 0.7187 (pp20) REVERT: B 71 LEU cc_start: 0.8060 (tt) cc_final: 0.7665 (tt) REVERT: B 93 MET cc_start: 0.6762 (mmm) cc_final: 0.6345 (mmm) REVERT: B 95 LYS cc_start: 0.8096 (ptmm) cc_final: 0.7681 (ptmm) REVERT: B 98 LEU cc_start: 0.8814 (tt) cc_final: 0.8483 (tt) REVERT: B 125 MET cc_start: 0.6969 (tpp) cc_final: 0.6605 (tpp) REVERT: B 143 VAL cc_start: 0.7094 (m) cc_final: 0.6881 (m) REVERT: B 154 GLN cc_start: 0.7022 (tp40) cc_final: 0.6668 (tp40) REVERT: B 203 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7793 (ttmm) REVERT: B 204 LYS cc_start: 0.8441 (tmtt) cc_final: 0.8031 (tmtt) REVERT: B 435 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7424 (mmmm) REVERT: B 441 ILE cc_start: 0.8672 (tp) cc_final: 0.8264 (tt) REVERT: B 471 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6578 (tm-30) REVERT: B 475 ARG cc_start: 0.7673 (pmt170) cc_final: 0.6187 (pmt170) REVERT: B 489 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5984 (mm-30) REVERT: B 539 GLU cc_start: 0.6961 (tp30) cc_final: 0.6688 (tp30) REVERT: B 550 LYS cc_start: 0.7574 (mmtp) cc_final: 0.7274 (mmtp) REVERT: B 567 MET cc_start: 0.7209 (ppp) cc_final: 0.6753 (ppp) REVERT: B 571 LEU cc_start: 0.7728 (tp) cc_final: 0.7341 (tt) REVERT: C 25 THR cc_start: 0.7656 (m) cc_final: 0.7442 (m) REVERT: C 42 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 107 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7286 (mtmm) REVERT: C 257 GLU cc_start: 0.7732 (tt0) cc_final: 0.7479 (tt0) REVERT: K 537 LEU cc_start: 0.6818 (tp) cc_final: 0.6503 (tp) REVERT: P 320 LYS cc_start: 0.8467 (tppt) cc_final: 0.8153 (tppt) REVERT: P 331 PHE cc_start: 0.7251 (m-80) cc_final: 0.7032 (m-80) REVERT: P 381 MET cc_start: 0.5153 (ttp) cc_final: 0.4520 (ttp) outliers start: 2 outliers final: 0 residues processed: 389 average time/residue: 0.1510 time to fit residues: 84.7598 Evaluate side-chains 361 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 461 GLN A 609 GLN ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 130 ASN C 253 ASN ** P 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.202926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.178946 restraints weight = 36556.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.175138 restraints weight = 65979.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.176785 restraints weight = 58409.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176797 restraints weight = 34864.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.177198 restraints weight = 32909.323| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18027 Z= 0.161 Angle : 0.714 11.956 24245 Z= 0.370 Chirality : 0.046 0.184 2636 Planarity : 0.005 0.130 3109 Dihedral : 5.499 80.671 2368 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.43 % Favored : 91.38 % Rotamer: Outliers : 0.15 % Allowed : 0.57 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.56 (0.18), residues: 2147 helix: 0.11 (0.16), residues: 970 sheet: -0.65 (0.36), residues: 215 loop : -2.39 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 36 TYR 0.036 0.002 TYR B 301 PHE 0.030 0.002 PHE A 32 TRP 0.027 0.002 TRP C 98 HIS 0.007 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (18024) covalent geometry : angle 0.71364 / 0.37 (24245) hydrogen bonds : bond 0.04366 / 2.83 ( 736) hydrogen bonds : angle 4.78143 / 3.32 ( 2118) Misc. bond : bond 0.00339 / 0.16 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 380 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7902 (t0) cc_final: 0.7619 (t0) REVERT: A 168 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8043 (tmm-80) REVERT: A 289 TRP cc_start: 0.6804 (p90) cc_final: 0.6314 (p90) REVERT: A 299 GLU cc_start: 0.7141 (pp20) cc_final: 0.6848 (pp20) REVERT: A 309 THR cc_start: 0.7953 (p) cc_final: 0.7454 (p) REVERT: A 363 MET cc_start: 0.7903 (ptm) cc_final: 0.7694 (ptp) REVERT: A 378 ARG cc_start: 0.7447 (mmm-85) cc_final: 0.6786 (mmm-85) REVERT: A 380 VAL cc_start: 0.8209 (t) cc_final: 0.7845 (m) REVERT: A 382 ASP cc_start: 0.7641 (t0) cc_final: 0.7171 (m-30) REVERT: A 394 MET cc_start: 0.6996 (ppp) cc_final: 0.6718 (ppp) REVERT: A 395 LEU cc_start: 0.7184 (mt) cc_final: 0.6244 (mt) REVERT: A 402 LYS cc_start: 0.7819 (ptpp) cc_final: 0.7581 (ptpp) REVERT: A 428 LYS cc_start: 0.8087 (pttp) cc_final: 0.7139 (ttpp) REVERT: A 431 GLU cc_start: 0.6782 (pp20) cc_final: 0.6545 (pp20) REVERT: A 453 GLU cc_start: 0.6846 (mp0) cc_final: 0.6467 (mp0) REVERT: A 557 LYS cc_start: 0.8359 (pttp) cc_final: 0.7778 (pttp) REVERT: A 577 LYS cc_start: 0.7494 (mtmm) cc_final: 0.7152 (mtmm) REVERT: A 620 MET cc_start: 0.7526 (tpt) cc_final: 0.7157 (tpp) REVERT: A 636 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 639 ARG cc_start: 0.7138 (ttp80) cc_final: 0.6916 (ttp80) REVERT: A 640 GLN cc_start: 0.7997 (pp30) cc_final: 0.7647 (pp30) REVERT: A 648 ASP cc_start: 0.6731 (t0) cc_final: 0.6362 (t0) REVERT: A 682 ARG cc_start: 0.7609 (ptm-80) cc_final: 0.7234 (ttp-110) REVERT: A 684 ILE cc_start: 0.8226 (pt) cc_final: 0.7617 (pt) REVERT: B 69 LYS cc_start: 0.8238 (mptt) cc_final: 0.7880 (mptt) REVERT: B 70 GLU cc_start: 0.7576 (pp20) cc_final: 0.7290 (pp20) REVERT: B 71 LEU cc_start: 0.8083 (tt) cc_final: 0.7724 (tt) REVERT: B 93 MET cc_start: 0.6704 (mmm) cc_final: 0.6362 (mmm) REVERT: B 95 LYS cc_start: 0.8233 (ptmm) cc_final: 0.7651 (ptmm) REVERT: B 98 LEU cc_start: 0.8880 (tt) cc_final: 0.8600 (tt) REVERT: B 145 VAL cc_start: 0.7927 (p) cc_final: 0.7592 (t) REVERT: B 154 GLN cc_start: 0.7171 (tp40) cc_final: 0.6775 (tp40) REVERT: B 157 TRP cc_start: 0.8046 (t60) cc_final: 0.7230 (t60) REVERT: B 203 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7819 (ttmm) REVERT: B 204 LYS cc_start: 0.8310 (tmtt) cc_final: 0.7887 (tmtt) REVERT: B 277 ILE cc_start: 0.6747 (mp) cc_final: 0.6530 (mt) REVERT: B 435 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7488 (mmmm) REVERT: B 441 ILE cc_start: 0.8855 (tp) cc_final: 0.8205 (tt) REVERT: B 475 ARG cc_start: 0.7761 (pmt170) cc_final: 0.6471 (pmt170) REVERT: B 489 GLU cc_start: 0.6262 (mm-30) cc_final: 0.6030 (mm-30) REVERT: B 493 GLN cc_start: 0.6109 (tm-30) cc_final: 0.5903 (tm-30) REVERT: B 550 LYS cc_start: 0.7683 (mmtp) cc_final: 0.7305 (mmtp) REVERT: B 552 LYS cc_start: 0.7718 (pttm) cc_final: 0.7504 (pttm) REVERT: B 567 MET cc_start: 0.7232 (ppp) cc_final: 0.6679 (ppp) REVERT: B 683 MET cc_start: 0.8381 (mmt) cc_final: 0.8048 (mmt) REVERT: C 48 GLU cc_start: 0.7579 (pm20) cc_final: 0.7167 (pm20) REVERT: C 108 LYS cc_start: 0.7447 (ptmm) cc_final: 0.7175 (mtmm) REVERT: C 253 ASN cc_start: 0.6483 (m-40) cc_final: 0.6147 (m-40) REVERT: C 257 GLU cc_start: 0.7974 (tt0) cc_final: 0.7740 (tt0) REVERT: K 537 LEU cc_start: 0.7156 (tp) cc_final: 0.6878 (tp) REVERT: P 320 LYS cc_start: 0.8410 (tppt) cc_final: 0.8084 (tppt) REVERT: P 331 PHE cc_start: 0.7395 (m-80) cc_final: 0.7121 (m-80) REVERT: P 381 MET cc_start: 0.5303 (ttp) cc_final: 0.4636 (ttp) outliers start: 3 outliers final: 1 residues processed: 381 average time/residue: 0.1603 time to fit residues: 87.5212 Evaluate side-chains 371 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 115 optimal weight: 0.2980 chunk 40 optimal weight: 0.2980 chunk 182 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 436 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.204806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179712 restraints weight = 36701.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.177427 restraints weight = 71758.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178833 restraints weight = 55596.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.179003 restraints weight = 38857.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.179069 restraints weight = 33063.243| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18027 Z= 0.130 Angle : 0.684 11.703 24245 Z= 0.352 Chirality : 0.044 0.195 2636 Planarity : 0.005 0.119 3109 Dihedral : 5.354 83.234 2368 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.78 % Favored : 92.04 % Rotamer: Outliers : 0.05 % Allowed : 0.26 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.47 (0.18), residues: 2147 helix: 0.21 (0.17), residues: 970 sheet: -0.64 (0.36), residues: 215 loop : -2.36 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 36 TYR 0.021 0.001 TYR B 134 PHE 0.021 0.001 PHE B 659 TRP 0.025 0.002 TRP C 98 HIS 0.008 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (18024) covalent geometry : angle 0.68399 / 0.35 (24245) hydrogen bonds : bond 0.03933 / 2.54 ( 736) hydrogen bonds : angle 4.64024 / 3.22 ( 2118) Misc. bond : bond 0.00335 / 0.16 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.20 seconds wall clock time: 53 minutes 49.22 seconds (3229.22 seconds total)