Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 14:04:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/04_2023/7zr6_14884_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/04_2023/7zr6_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/04_2023/7zr6_14884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/04_2023/7zr6_14884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/04_2023/7zr6_14884_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/04_2023/7zr6_14884_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A GLU 37": "OE1" <-> "OE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 653": "OD1" <-> "OD2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "K ASP 555": "OD1" <-> "OD2" Residue "K TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 182": "OE1" <-> "OE2" Residue "P GLU 193": "OE1" <-> "OE2" Residue "P GLU 262": "OE1" <-> "OE2" Residue "P TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 333": "OE1" <-> "OE2" Residue "P PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/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: 8.96, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.09 Conformation dependent library (CDL) restraints added in 2.8 seconds 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... running ksdssp... Secondary structure from input PDB file: 80 helices and 16 sheets defined 43.6% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 36 through 60 removed outlier: 4.912A pdb=" N SER A 48 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 49 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 57 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 58 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 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 109 through 116 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 401 through 420 Processing helix chain 'A' and resid 425 through 443 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 448 through 454 removed outlier: 4.755A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.527A pdb=" N ARG A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 547 through 559 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 562 through 570 Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 617 through 620 Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.513A pdb=" N SER A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 39 through 60 removed outlier: 3.584A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 308 removed outlier: 4.159A pdb=" N PHE B 304 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 400 through 420 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) removed outlier: 4.111A pdb=" N ALA B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 440 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 491 through 495 Processing helix chain 'B' and resid 499 through 503 removed outlier: 3.649A pdb=" N ARG B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 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 548 through 559 removed outlier: 3.989A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 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 600 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 620 removed outlier: 4.319A pdb=" N MET B 620 " --> pdb=" O MET B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 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 649 through 666 removed outlier: 3.742A pdb=" N SER B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 688 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 25 through 73 Processing helix chain 'C' and resid 78 through 110 removed outlier: 3.957A pdb=" N LYS C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 119 No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 143 through 164 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) removed outlier: 4.069A pdb=" N MET C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 185 through 200 removed outlier: 5.103A pdb=" N VAL C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 226 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 235 through 242 Processing helix chain 'C' and resid 246 through 277 Processing helix chain 'K' and resid 538 through 542 removed outlier: 3.648A pdb=" N HIS K 542 " --> pdb=" O HIS K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 550 through 570 removed outlier: 4.073A pdb=" N LYS K 570 " --> pdb=" O TYR K 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 579 through 581 No H-bonds generated for 'chain 'K' and resid 579 through 581' Processing helix chain 'K' and resid 635 through 651 Processing helix chain 'K' and resid 662 through 670 Processing helix chain 'K' and resid 687 through 696 Processing helix chain 'K' and resid 707 through 720 Processing helix chain 'P' and resid 22 through 40 Processing helix chain 'P' and resid 44 through 57 Processing helix chain 'P' and resid 62 through 74 Processing helix chain 'P' and resid 78 through 91 Processing helix chain 'P' and resid 96 through 109 Processing helix chain 'P' and resid 112 through 125 Processing helix chain 'P' and resid 130 through 149 Processing helix chain 'P' and resid 188 through 200 Processing helix chain 'P' and resid 206 through 221 Processing helix chain 'P' and resid 247 through 256 Processing helix chain 'P' and resid 279 through 292 Processing helix chain 'P' and resid 307 through 312 removed outlier: 3.965A pdb=" N ILE P 312 " --> pdb=" O ASN P 308 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 322 Processing helix chain 'P' and resid 325 through 337 removed outlier: 4.262A pdb=" N TRP P 337 " --> pdb=" O GLU P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 367 Processing helix chain 'P' and resid 380 through 386 removed outlier: 4.147A pdb=" N LEU P 385 " --> pdb=" O MET P 381 " (cutoff:3.500A) Processing helix chain 'P' and resid 408 through 417 Processing helix chain 'P' and resid 451 through 453 No H-bonds generated for 'chain 'P' and resid 451 through 453' Processing sheet with id= A, first strand: chain 'A' and resid 73 through 75 Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.749A pdb=" N THR A 83 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing sheet with id= C, 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) Processing sheet with id= D, first strand: chain 'A' and resid 456 through 458 Processing sheet with id= E, first strand: chain 'A' and resid 533 through 535 removed outlier: 5.695A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 511 " --> pdb=" O ILE A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 589 through 593 removed outlier: 3.751A pdb=" N VAL A 592 " --> pdb=" O HIS A 625 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 73 through 75 Processing sheet with id= H, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= I, first strand: chain 'B' and resid 180 through 184 removed outlier: 3.870A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 143 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 159 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 533 through 535 removed outlier: 5.938A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 511 " --> pdb=" O TYR B 484 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 589 through 592 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= L, first strand: chain 'B' and resid 315 through 319 removed outlier: 6.637A pdb=" N ILE B 335 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL B 318 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 333 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 582 through 584 Processing sheet with id= N, first strand: chain 'P' and resid 264 through 268 removed outlier: 7.638A pdb=" N LYS P 236 " --> pdb=" O PRO P 265 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ILE P 267 " --> pdb=" O LYS P 236 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR P 238 " --> pdb=" O ILE P 267 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'P' and resid 342 through 344 Processing sheet with id= P, first strand: chain 'P' and resid 423 through 425 653 hydrogen bonds defined for protein. 1830 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: 5.01 Time building geometry restraints manager: 8.55 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: 97.56 - 106.02: 309 106.02 - 114.48: 10539 114.48 - 122.93: 12063 122.93 - 131.39: 1308 131.39 - 139.84: 26 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: 421 2.66 - 3.22: 18245 3.22 - 3.78: 27056 3.78 - 4.34: 35168 4.34 - 4.90: 53684 Nonbonded interactions: 134574 Sorted by model distance: nonbonded pdb=" O LEU A 27 " pdb=" OG1 THR A 31 " model vdw 2.106 2.440 nonbonded pdb=" O LEU B 102 " pdb=" OH TYR B 134 " model vdw 2.151 2.440 nonbonded pdb=" OD1 ASN A 101 " pdb=" O3' ATP A 801 " model vdw 2.162 2.440 nonbonded pdb=" OD1 ASN B 425 " pdb=" OG1 THR C 131 " model vdw 2.173 2.440 nonbonded pdb=" O ASN C 178 " pdb=" N VAL C 182 " model vdw 2.180 2.520 ... (remaining 134569 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 220 or resid 273 through 692 or resid 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.860 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 46.030 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 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 18024 Z= 0.215 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 : 16.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.69 % Favored : 92.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 2.037 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 outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.3685 time to fit residues: 222.7176 Evaluate side-chains 374 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 195 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN B 425 ASN C 34 GLN C 188 ASN K 540 HIS K 585 HIS P 196 GLN P 246 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 18024 Z= 0.185 Angle : 0.621 8.170 24245 Z= 0.327 Chirality : 0.044 0.237 2636 Planarity : 0.005 0.099 3109 Dihedral : 6.523 170.469 2368 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.01 % Favored : 91.80 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.18), residues: 2147 helix: 0.10 (0.17), residues: 921 sheet: -0.67 (0.35), residues: 233 loop : -2.38 (0.18), residues: 993 *********************** 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 413 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 407 time to evaluate : 2.058 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 outliers start: 6 outliers final: 2 residues processed: 409 average time/residue: 0.3683 time to fit residues: 212.7157 Evaluate side-chains 366 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 364 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1894 time to fit residues: 3.4490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 211 optimal weight: 20.0000 chunk 174 optimal weight: 0.7980 chunk 193 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN C 34 GLN C 188 ASN ** K 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 18024 Z= 0.222 Angle : 0.629 8.393 24245 Z= 0.331 Chirality : 0.044 0.276 2636 Planarity : 0.004 0.089 3109 Dihedral : 5.429 75.682 2368 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.43 % Favored : 91.34 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 2147 helix: 0.08 (0.17), residues: 930 sheet: -0.83 (0.35), residues: 238 loop : -2.41 (0.18), residues: 979 *********************** 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 403 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 401 time to evaluate : 1.998 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 outliers start: 2 outliers final: 1 residues processed: 401 average time/residue: 0.3723 time to fit residues: 210.9712 Evaluate side-chains 360 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 359 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1948 time to fit residues: 3.2759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 93 optimal weight: 0.0070 chunk 131 optimal weight: 20.0000 chunk 196 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 34 GLN ** P 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 18024 Z= 0.221 Angle : 0.631 8.510 24245 Z= 0.332 Chirality : 0.044 0.213 2636 Planarity : 0.005 0.128 3109 Dihedral : 5.433 75.638 2368 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.71 % Favored : 91.10 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.18), residues: 2147 helix: 0.08 (0.17), residues: 934 sheet: -0.92 (0.35), residues: 247 loop : -2.36 (0.19), residues: 966 *********************** 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 401 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 400 time to evaluate : 2.138 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 outliers start: 1 outliers final: 1 residues processed: 400 average time/residue: 0.3716 time to fit residues: 210.7211 Evaluate side-chains 374 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2076 time to fit residues: 3.3246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 186 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** K 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 628 GLN P 46 ASN P 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 18024 Z= 0.172 Angle : 0.607 9.055 24245 Z= 0.312 Chirality : 0.043 0.201 2636 Planarity : 0.005 0.087 3109 Dihedral : 5.334 78.648 2368 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.69 % Favored : 92.13 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2147 helix: 0.27 (0.17), residues: 923 sheet: -0.81 (0.35), residues: 236 loop : -2.32 (0.18), residues: 988 *********************** 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 376 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 373 time to evaluate : 2.206 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 outliers start: 3 outliers final: 0 residues processed: 375 average time/residue: 0.3699 time to fit residues: 197.3883 Evaluate side-chains 351 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 0.6980 chunk 187 optimal weight: 0.0040 chunk 41 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 0.3980 chunk 172 optimal weight: 8.9990 chunk 96 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 68 optimal weight: 0.0010 chunk 109 optimal weight: 0.6980 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN A 640 GLN B 315 HIS ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 18024 Z= 0.146 Angle : 0.600 8.148 24245 Z= 0.309 Chirality : 0.042 0.204 2636 Planarity : 0.005 0.125 3109 Dihedral : 5.125 82.489 2368 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.22 % Favored : 92.59 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2147 helix: 0.35 (0.17), residues: 925 sheet: -0.87 (0.35), residues: 234 loop : -2.28 (0.18), residues: 988 *********************** 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 373 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 371 time to evaluate : 2.195 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 outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.3614 time to fit residues: 191.5737 Evaluate side-chains 352 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 0.7980 chunk 23 optimal weight: 0.0170 chunk 118 optimal weight: 0.0010 chunk 151 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 175 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 HIS ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 18024 Z= 0.149 Angle : 0.590 7.539 24245 Z= 0.304 Chirality : 0.042 0.178 2636 Planarity : 0.004 0.105 3109 Dihedral : 5.019 83.129 2368 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.36 % Favored : 92.45 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.18), residues: 2147 helix: 0.41 (0.17), residues: 924 sheet: -0.81 (0.35), residues: 231 loop : -2.27 (0.18), residues: 992 *********************** 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 373 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 2.079 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 outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.3707 time to fit residues: 196.3666 Evaluate side-chains 350 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 162 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 HIS A 447 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 146 GLN K 540 HIS ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 18024 Z= 0.267 Angle : 0.680 12.171 24245 Z= 0.353 Chirality : 0.046 0.193 2636 Planarity : 0.005 0.105 3109 Dihedral : 5.491 78.778 2368 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.36 % Favored : 90.50 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.18), residues: 2147 helix: 0.15 (0.17), residues: 919 sheet: -0.85 (0.35), residues: 239 loop : -2.37 (0.18), residues: 989 *********************** 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 380 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 2.204 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 outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.3718 time to fit residues: 200.2773 Evaluate side-chains 341 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 151 optimal weight: 5.9990 chunk 59 optimal weight: 0.0670 chunk 174 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** K 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 18024 Z= 0.168 Angle : 0.649 11.742 24245 Z= 0.333 Chirality : 0.043 0.194 2636 Planarity : 0.006 0.188 3109 Dihedral : 5.272 77.306 2368 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2147 helix: 0.28 (0.17), residues: 923 sheet: -0.65 (0.35), residues: 230 loop : -2.38 (0.18), residues: 994 *********************** 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 366 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 365 time to evaluate : 1.921 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 outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.3655 time to fit residues: 190.3073 Evaluate side-chains 334 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 2.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 0.0870 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 214 optimal weight: 0.0050 chunk 197 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 442 HIS ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** K 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 18024 Z= 0.241 Angle : 0.686 12.213 24245 Z= 0.357 Chirality : 0.046 0.196 2636 Planarity : 0.005 0.094 3109 Dihedral : 5.449 82.273 2368 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.27 % Favored : 90.59 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.18), residues: 2147 helix: 0.16 (0.17), residues: 917 sheet: -0.71 (0.36), residues: 229 loop : -2.41 (0.18), residues: 1001 ********************** 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 363 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 362 time to evaluate : 2.227 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 outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.3812 time to fit residues: 196.4010 Evaluate side-chains 339 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** K 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.203636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.181017 restraints weight = 36544.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.178101 restraints weight = 66870.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179520 restraints weight = 57781.244| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 18024 Z= 0.196 Angle : 0.668 11.604 24245 Z= 0.344 Chirality : 0.044 0.205 2636 Planarity : 0.005 0.136 3109 Dihedral : 5.307 82.559 2368 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.15 % Favored : 91.66 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.18), residues: 2147 helix: 0.21 (0.17), residues: 925 sheet: -0.79 (0.35), residues: 229 loop : -2.39 (0.18), residues: 993 =============================================================================== Job complete usr+sys time: 4504.62 seconds wall clock time: 82 minutes 21.17 seconds (4941.17 seconds total)