Starting phenix.real_space_refine on Mon Jul 22 10:09:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/07_2024/7zr6_14884.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/07_2024/7zr6_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_14884/07_2024/7zr6_14884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/07_2024/7zr6_14884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/07_2024/7zr6_14884.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr6_14884/07_2024/7zr6_14884.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 10.05, per 1000 atoms: 0.57 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: 7.44 Conformation dependent library (CDL) restraints added in 3.4 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... 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: 1.90 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: 5.61 Time building geometry restraints manager: 7.83 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: 9936 17.93 - 35.87: 990 35.87 - 53.80: 156 53.80 - 71.74: 21 71.74 - 89.67: 25 Dihedral angle restraints: 11128 sinusoidal: 4754 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 11125 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 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=" OG SER B 434 " pdb=" NZ LYS B 438 " model vdw 2.181 2.520 ... (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 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 48.110 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.000 ------------------------------------------------------------------------------- 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= 0.218 Angle : 0.792 10.050 24245 Z= 0.435 Chirality : 0.046 0.253 2636 Planarity : 0.005 0.106 3109 Dihedral : 14.743 89.672 7000 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 % 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 598 HIS 0.005 0.001 HIS P 205 PHE 0.026 0.002 PHE P 287 TYR 0.016 0.002 TYR P 51 ARG 0.037 0.001 ARG C 36 *********************** 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 : 1.822 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: 0.7826 (ttmm) cc_final: 0.7509 (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: 0.7988 (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: 0.8687 (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: 0.7136 (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: 0.3611 time to fit residues: 218.2406 Evaluate side-chains 382 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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: 2.9990 chunk 162 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS P 196 GLN P 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18024 Z= 0.205 Angle : 0.637 8.099 24245 Z= 0.336 Chirality : 0.044 0.236 2636 Planarity : 0.005 0.113 3109 Dihedral : 8.211 167.133 2430 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.10 % Favored : 91.66 % Rotamer: Outliers : 0.26 % Allowed : 5.92 % Favored : 93.82 % 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: -1.69 (0.18), residues: 2147 helix: 0.03 (0.17), residues: 970 sheet: -0.70 (0.35), residues: 233 loop : -2.50 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 531 HIS 0.004 0.001 HIS B 320 PHE 0.025 0.002 PHE A 32 TYR 0.021 0.002 TYR A 373 ARG 0.023 0.001 ARG B 392 *********************** 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 408 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 403 time to evaluate : 1.804 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 18 GLN cc_start: 0.6197 (mp10) cc_final: 0.5943 (mp10) REVERT: A 75 ILE cc_start: 0.8216 (tp) cc_final: 0.7902 (tp) REVERT: A 95 LYS cc_start: 0.7532 (ttmm) cc_final: 0.7213 (mtpp) REVERT: A 289 TRP cc_start: 0.6788 (p90) cc_final: 0.6437 (p90) REVERT: A 380 VAL cc_start: 0.7996 (t) cc_final: 0.7623 (m) REVERT: A 392 ARG cc_start: 0.7782 (mmt90) cc_final: 0.7215 (mmt-90) REVERT: A 424 GLU cc_start: 0.7211 (mp0) cc_final: 0.6928 (tm-30) REVERT: A 428 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7782 (ttpp) REVERT: A 431 GLU cc_start: 0.7323 (tp30) cc_final: 0.6962 (tp30) REVERT: A 550 LYS cc_start: 0.8145 (pttp) cc_final: 0.7908 (ptmm) REVERT: A 557 LYS cc_start: 0.7995 (pttp) cc_final: 0.7652 (pttp) REVERT: A 566 LEU cc_start: 0.6609 (tt) cc_final: 0.6366 (tt) REVERT: A 577 LYS cc_start: 0.7083 (mtmm) cc_final: 0.6629 (mtmm) REVERT: A 606 MET cc_start: 0.7280 (tpt) cc_final: 0.6949 (tpp) REVERT: A 621 MET cc_start: 0.5575 (mmp) cc_final: 0.5156 (mmt) REVERT: A 636 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8315 (mm-30) REVERT: A 639 ARG cc_start: 0.7262 (ttp80) cc_final: 0.7039 (ttp80) REVERT: A 640 GLN cc_start: 0.8405 (pp30) cc_final: 0.7988 (pp30) REVERT: A 645 ASP cc_start: 0.7247 (t0) cc_final: 0.6835 (t0) REVERT: A 672 ASP cc_start: 0.7749 (p0) cc_final: 0.7504 (p0) REVERT: A 680 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 683 MET cc_start: 0.8313 (tmm) cc_final: 0.8033 (tmm) REVERT: A 684 ILE cc_start: 0.8266 (pt) cc_final: 0.7940 (pt) REVERT: B 18 GLN cc_start: 0.7172 (mp10) cc_final: 0.6857 (mp10) REVERT: B 69 LYS cc_start: 0.8056 (mptt) cc_final: 0.7849 (mptt) REVERT: B 71 LEU cc_start: 0.8152 (tt) cc_final: 0.7878 (tt) REVERT: B 72 LYS cc_start: 0.7853 (pttt) cc_final: 0.7554 (pttt) REVERT: B 133 PHE cc_start: 0.6364 (t80) cc_final: 0.5977 (t80) REVERT: B 139 VAL cc_start: 0.8065 (t) cc_final: 0.7861 (m) REVERT: B 145 VAL cc_start: 0.6567 (t) cc_final: 0.6316 (p) REVERT: B 153 GLU cc_start: 0.8155 (mp0) cc_final: 0.7766 (mp0) REVERT: B 157 TRP cc_start: 0.7335 (t60) cc_final: 0.6754 (t60) REVERT: B 200 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6704 (tm-30) REVERT: B 342 ASP cc_start: 0.6285 (p0) cc_final: 0.5911 (p0) REVERT: B 359 ARG cc_start: 0.7119 (ttp-170) cc_final: 0.6860 (ttp-170) REVERT: B 394 MET cc_start: 0.7060 (ttm) cc_final: 0.6652 (tpp) REVERT: B 428 LYS cc_start: 0.6937 (mmmt) cc_final: 0.6638 (mmmt) REVERT: B 448 ARG cc_start: 0.6054 (ttm-80) cc_final: 0.5845 (ttm-80) REVERT: B 471 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7118 (tm-30) REVERT: B 475 ARG cc_start: 0.7320 (pmt170) cc_final: 0.5995 (pmt170) REVERT: B 552 LYS cc_start: 0.7589 (pttm) cc_final: 0.7356 (pttm) REVERT: B 553 MET cc_start: 0.5571 (tmm) cc_final: 0.5204 (tmm) REVERT: B 567 MET cc_start: 0.6229 (ppp) cc_final: 0.5957 (ppp) REVERT: B 613 ASP cc_start: 0.6150 (p0) cc_final: 0.5634 (p0) REVERT: B 620 MET cc_start: 0.4649 (pmm) cc_final: 0.3897 (pmm) REVERT: B 637 THR cc_start: 0.8589 (p) cc_final: 0.8383 (p) REVERT: B 652 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8700 (mttt) REVERT: C 3 ASP cc_start: 0.7598 (t70) cc_final: 0.7345 (t0) REVERT: C 39 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7760 (ttp80) REVERT: C 43 PHE cc_start: 0.7650 (t80) cc_final: 0.7377 (t80) REVERT: C 46 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 106 ARG cc_start: 0.7487 (tmt-80) cc_final: 0.7229 (tpt90) REVERT: C 107 LYS cc_start: 0.7474 (mtmm) cc_final: 0.7131 (mtmm) REVERT: C 231 ARG cc_start: 0.4928 (ttp80) cc_final: 0.4023 (mmm160) REVERT: C 249 MET cc_start: 0.3638 (tpp) cc_final: 0.3431 (tpp) REVERT: C 253 ASN cc_start: 0.6594 (m110) cc_final: 0.6131 (m110) REVERT: K 646 LEU cc_start: 0.5195 (tp) cc_final: 0.4948 (tt) REVERT: P 80 TYR cc_start: 0.7806 (m-80) cc_final: 0.7521 (m-80) REVERT: P 134 MET cc_start: 0.6917 (ppp) cc_final: 0.6425 (ppp) outliers start: 5 outliers final: 1 residues processed: 405 average time/residue: 0.3591 time to fit residues: 205.6395 Evaluate side-chains 372 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 370 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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: 1.9990 chunk 60 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 53 optimal weight: 0.0670 chunk 195 optimal weight: 0.9980 chunk 211 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 193 optimal weight: 0.0470 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 0.0270 overall best weight: 0.6276 ------------------------------------------------------------------------------- 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 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN C 34 GLN C 188 ASN ** K 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.2389 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= 0.182 Angle : 0.610 8.337 24245 Z= 0.319 Chirality : 0.043 0.241 2636 Planarity : 0.004 0.094 3109 Dihedral : 7.194 82.794 2430 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.45 % Favored : 92.31 % Rotamer: Outliers : 0.21 % Allowed : 4.17 % Favored : 95.63 % 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: -1.57 (0.18), residues: 2147 helix: 0.19 (0.17), residues: 974 sheet: -0.89 (0.34), residues: 241 loop : -2.47 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 98 HIS 0.004 0.001 HIS B 149 PHE 0.049 0.002 PHE P 331 TYR 0.025 0.001 TYR C 189 ARG 0.008 0.000 ARG C 36 *********************** 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 415 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 411 time to evaluate : 1.948 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 25 MET cc_start: 0.7689 (tpt) cc_final: 0.7325 (tpt) REVERT: A 74 ASP cc_start: 0.7302 (m-30) cc_final: 0.6918 (p0) REVERT: A 75 ILE cc_start: 0.8148 (tp) cc_final: 0.7820 (tp) REVERT: A 95 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7262 (mtpp) REVERT: A 114 MET cc_start: 0.7926 (tpp) cc_final: 0.7725 (tpp) REVERT: A 144 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7817 (m) REVERT: A 158 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6788 (mm-30) REVERT: A 289 TRP cc_start: 0.6810 (p90) cc_final: 0.6267 (p90) REVERT: A 337 ARG cc_start: 0.7223 (mtt-85) cc_final: 0.6731 (mtt-85) REVERT: A 375 ASN cc_start: 0.7879 (t0) cc_final: 0.7661 (t0) REVERT: A 380 VAL cc_start: 0.8010 (t) cc_final: 0.7564 (m) REVERT: A 383 SER cc_start: 0.8095 (t) cc_final: 0.7798 (t) REVERT: A 392 ARG cc_start: 0.7861 (mmt90) cc_final: 0.7420 (mmt90) REVERT: A 421 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 424 GLU cc_start: 0.7255 (mp0) cc_final: 0.6947 (tm-30) REVERT: A 431 GLU cc_start: 0.7264 (tp30) cc_final: 0.6753 (tp30) REVERT: A 557 LYS cc_start: 0.8062 (pttp) cc_final: 0.7801 (pttp) REVERT: A 577 LYS cc_start: 0.7020 (mtmm) cc_final: 0.6601 (mtmm) REVERT: A 636 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 640 GLN cc_start: 0.8417 (pp30) cc_final: 0.8115 (pp30) REVERT: A 672 ASP cc_start: 0.7712 (p0) cc_final: 0.7478 (p0) REVERT: A 680 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8165 (tt) REVERT: A 683 MET cc_start: 0.8310 (tmm) cc_final: 0.8002 (tmm) REVERT: A 684 ILE cc_start: 0.8249 (pt) cc_final: 0.7941 (pt) REVERT: B 18 GLN cc_start: 0.7222 (mp10) cc_final: 0.6905 (mp10) REVERT: B 56 TYR cc_start: 0.6645 (t80) cc_final: 0.6379 (t80) REVERT: B 58 SER cc_start: 0.5850 (t) cc_final: 0.5427 (p) REVERT: B 69 LYS cc_start: 0.8069 (mptt) cc_final: 0.7830 (mptt) REVERT: B 72 LYS cc_start: 0.7854 (pttt) cc_final: 0.7337 (pttt) REVERT: B 93 MET cc_start: 0.6715 (mmm) cc_final: 0.6329 (mmm) REVERT: B 125 MET cc_start: 0.6972 (ttm) cc_final: 0.6328 (tpp) REVERT: B 133 PHE cc_start: 0.6378 (t80) cc_final: 0.5997 (t80) REVERT: B 145 VAL cc_start: 0.6742 (t) cc_final: 0.6519 (p) REVERT: B 153 GLU cc_start: 0.8213 (mp0) cc_final: 0.7814 (mp0) REVERT: B 200 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 204 LYS cc_start: 0.7734 (tmtt) cc_final: 0.7228 (tmtt) REVERT: B 342 ASP cc_start: 0.6362 (p0) cc_final: 0.6003 (p0) REVERT: B 359 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6788 (ttp-170) REVERT: B 393 GLU cc_start: 0.6138 (mm-30) cc_final: 0.5828 (mm-30) REVERT: B 394 MET cc_start: 0.6979 (ttm) cc_final: 0.6759 (tpp) REVERT: B 428 LYS cc_start: 0.6927 (mmmt) cc_final: 0.6675 (mmmt) REVERT: B 441 ILE cc_start: 0.7949 (tp) cc_final: 0.7711 (tt) REVERT: B 465 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 475 ARG cc_start: 0.7288 (pmt170) cc_final: 0.6540 (pmt170) REVERT: B 489 GLU cc_start: 0.6429 (mm-30) cc_final: 0.5831 (mm-30) REVERT: B 493 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6803 (tm-30) REVERT: B 529 ASP cc_start: 0.6567 (m-30) cc_final: 0.6282 (m-30) REVERT: B 550 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7222 (mmtp) REVERT: B 552 LYS cc_start: 0.7585 (pttm) cc_final: 0.7317 (pttm) REVERT: B 553 MET cc_start: 0.5586 (tmm) cc_final: 0.5281 (tmm) REVERT: B 567 MET cc_start: 0.6160 (ppp) cc_final: 0.5858 (ppp) REVERT: B 613 ASP cc_start: 0.6281 (p0) cc_final: 0.5766 (p0) REVERT: B 674 GLN cc_start: 0.7359 (tm-30) cc_final: 0.6924 (tm-30) REVERT: C 3 ASP cc_start: 0.7607 (t70) cc_final: 0.7317 (t0) REVERT: C 39 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7599 (ttp80) REVERT: C 42 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7371 (tm-30) REVERT: C 48 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: C 106 ARG cc_start: 0.7539 (tmt-80) cc_final: 0.7308 (tmt-80) REVERT: C 107 LYS cc_start: 0.7524 (mtmm) cc_final: 0.6966 (mtmm) REVERT: C 249 MET cc_start: 0.3733 (tpp) cc_final: 0.3114 (tmm) REVERT: C 253 ASN cc_start: 0.6786 (m110) cc_final: 0.5793 (m110) REVERT: P 38 TYR cc_start: 0.7509 (m-80) cc_final: 0.7306 (m-80) REVERT: P 39 PHE cc_start: 0.5074 (t80) cc_final: 0.4833 (t80) REVERT: P 80 TYR cc_start: 0.7777 (m-80) cc_final: 0.7496 (m-80) REVERT: P 134 MET cc_start: 0.6915 (ppp) cc_final: 0.6384 (ppp) REVERT: P 331 PHE cc_start: 0.7651 (m-80) cc_final: 0.7409 (m-80) outliers start: 4 outliers final: 0 residues processed: 413 average time/residue: 0.3633 time to fit residues: 210.9362 Evaluate side-chains 374 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 371 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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: 10.0000 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 30.0000 chunk 196 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** 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** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** 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: 0.6215 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18024 Z= 0.181 Angle : 0.604 7.059 24245 Z= 0.317 Chirality : 0.042 0.164 2636 Planarity : 0.005 0.128 3109 Dihedral : 7.075 80.167 2430 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.96 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -1.44 (0.18), residues: 2147 helix: 0.32 (0.17), residues: 964 sheet: -0.61 (0.35), residues: 225 loop : -2.44 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 7 HIS 0.003 0.001 HIS B 320 PHE 0.032 0.002 PHE P 331 TYR 0.022 0.001 TYR C 189 ARG 0.020 0.001 ARG C 36 *********************** 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 396 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.889 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 18 GLN cc_start: 0.6380 (mp10) cc_final: 0.6020 (mp10) REVERT: A 25 MET cc_start: 0.7634 (tpt) cc_final: 0.7216 (tpt) REVERT: A 72 LYS cc_start: 0.7009 (ptmm) cc_final: 0.6578 (ptmt) REVERT: A 95 LYS cc_start: 0.7617 (ttmm) cc_final: 0.7242 (mtpp) REVERT: A 289 TRP cc_start: 0.6782 (p90) cc_final: 0.6166 (p90) REVERT: A 375 ASN cc_start: 0.7843 (t0) cc_final: 0.7606 (t0) REVERT: A 380 VAL cc_start: 0.7995 (t) cc_final: 0.7532 (m) REVERT: A 383 SER cc_start: 0.7997 (t) cc_final: 0.7762 (t) REVERT: A 394 MET cc_start: 0.6798 (ppp) cc_final: 0.6342 (ppp) REVERT: A 395 LEU cc_start: 0.7392 (mt) cc_final: 0.6658 (mt) REVERT: A 421 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 424 GLU cc_start: 0.7265 (mp0) cc_final: 0.6961 (tm-30) REVERT: A 431 GLU cc_start: 0.7282 (tp30) cc_final: 0.6716 (tp30) REVERT: A 446 THR cc_start: 0.8862 (t) cc_final: 0.8630 (p) REVERT: A 457 TYR cc_start: 0.6381 (m-80) cc_final: 0.6048 (m-80) REVERT: A 557 LYS cc_start: 0.8165 (pttp) cc_final: 0.7806 (pttp) REVERT: A 602 MET cc_start: 0.6746 (tpt) cc_final: 0.6516 (tpt) REVERT: A 606 MET cc_start: 0.7492 (tpp) cc_final: 0.7139 (tpt) REVERT: A 636 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8295 (mm-30) REVERT: A 639 ARG cc_start: 0.7366 (ttp80) cc_final: 0.7079 (ttp80) REVERT: A 640 GLN cc_start: 0.8529 (pp30) cc_final: 0.7929 (pp30) REVERT: A 680 ILE cc_start: 0.8574 (mp) cc_final: 0.8270 (mt) REVERT: A 683 MET cc_start: 0.8244 (tmm) cc_final: 0.7949 (tmm) REVERT: A 684 ILE cc_start: 0.8259 (pt) cc_final: 0.7929 (pt) REVERT: B 18 GLN cc_start: 0.7266 (mp10) cc_final: 0.6956 (mp10) REVERT: B 58 SER cc_start: 0.5848 (t) cc_final: 0.5398 (p) REVERT: B 69 LYS cc_start: 0.8136 (mptt) cc_final: 0.7680 (mptt) REVERT: B 70 GLU cc_start: 0.7753 (pm20) cc_final: 0.7414 (pp20) REVERT: B 71 LEU cc_start: 0.8228 (mp) cc_final: 0.7326 (tt) REVERT: B 93 MET cc_start: 0.6855 (mmm) cc_final: 0.6415 (mmm) REVERT: B 125 MET cc_start: 0.6966 (ttm) cc_final: 0.6476 (ttm) REVERT: B 153 GLU cc_start: 0.8235 (mp0) cc_final: 0.7828 (mp0) REVERT: B 157 TRP cc_start: 0.7424 (t60) cc_final: 0.6889 (t60) REVERT: B 168 ARG cc_start: 0.6897 (ptm-80) cc_final: 0.6524 (ptm-80) REVERT: B 200 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6613 (tm-30) REVERT: B 203 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7037 (ttmm) REVERT: B 204 LYS cc_start: 0.7601 (tmtt) cc_final: 0.7107 (tmtt) REVERT: B 342 ASP cc_start: 0.6519 (p0) cc_final: 0.6191 (p0) REVERT: B 393 GLU cc_start: 0.6106 (mm-30) cc_final: 0.5810 (mm-30) REVERT: B 394 MET cc_start: 0.7031 (ttm) cc_final: 0.6802 (tpp) REVERT: B 428 LYS cc_start: 0.6935 (mmmt) cc_final: 0.6688 (mmmt) REVERT: B 475 ARG cc_start: 0.7348 (pmt170) cc_final: 0.6641 (pmt170) REVERT: B 489 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5812 (mm-30) REVERT: B 493 GLN cc_start: 0.7125 (tm-30) cc_final: 0.6865 (tm-30) REVERT: B 552 LYS cc_start: 0.7569 (pttm) cc_final: 0.7285 (pttm) REVERT: B 553 MET cc_start: 0.5668 (tmm) cc_final: 0.5369 (tmm) REVERT: B 567 MET cc_start: 0.6098 (ppp) cc_final: 0.5791 (ppp) REVERT: C 3 ASP cc_start: 0.7638 (t70) cc_final: 0.7345 (t0) REVERT: C 39 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7574 (ttp80) REVERT: C 46 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7309 (mm-30) REVERT: C 106 ARG cc_start: 0.7671 (tmt-80) cc_final: 0.6913 (tmt-80) REVERT: C 107 LYS cc_start: 0.7521 (mtmm) cc_final: 0.6855 (mtmm) REVERT: C 128 MET cc_start: 0.6128 (ttp) cc_final: 0.5715 (tmm) REVERT: C 249 MET cc_start: 0.3921 (tpp) cc_final: 0.3286 (tmm) REVERT: C 253 ASN cc_start: 0.6679 (m110) cc_final: 0.5697 (m110) REVERT: P 39 PHE cc_start: 0.5006 (t80) cc_final: 0.4793 (t80) REVERT: P 80 TYR cc_start: 0.7819 (m-80) cc_final: 0.7534 (m-80) REVERT: P 134 MET cc_start: 0.7008 (ppp) cc_final: 0.6454 (ppp) REVERT: P 331 PHE cc_start: 0.7672 (m-80) cc_final: 0.7374 (m-80) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.3487 time to fit residues: 194.8171 Evaluate side-chains 360 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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: 0.8980 chunk 117 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 186 optimal weight: 0.3980 chunk 52 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 609 GLN B 425 ASN ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** 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: 0.6208 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18024 Z= 0.160 Angle : 0.596 9.572 24245 Z= 0.308 Chirality : 0.042 0.170 2636 Planarity : 0.004 0.091 3109 Dihedral : 7.037 81.461 2430 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.50 % Rotamer: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % 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: -1.30 (0.18), residues: 2147 helix: 0.38 (0.17), residues: 977 sheet: -0.44 (0.36), residues: 218 loop : -2.36 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 7 HIS 0.003 0.001 HIS C 180 PHE 0.027 0.001 PHE P 331 TYR 0.017 0.001 TYR P 38 ARG 0.011 0.000 ARG C 36 *********************** 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 388 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 386 time to evaluate : 2.012 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: symmetry clash REVERT: A 18 GLN cc_start: 0.6353 (mp10) cc_final: 0.5965 (mp10) REVERT: A 25 MET cc_start: 0.7699 (tpt) cc_final: 0.6949 (tmm) REVERT: A 29 ILE cc_start: 0.7529 (tp) cc_final: 0.7245 (tp) REVERT: A 115 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 289 TRP cc_start: 0.6707 (p90) cc_final: 0.6064 (p90) REVERT: A 375 ASN cc_start: 0.7799 (t0) cc_final: 0.7591 (t0) REVERT: A 380 VAL cc_start: 0.7960 (t) cc_final: 0.7473 (m) REVERT: A 383 SER cc_start: 0.7976 (t) cc_final: 0.7738 (t) REVERT: A 394 MET cc_start: 0.6802 (ppp) cc_final: 0.6400 (ppp) REVERT: A 395 LEU cc_start: 0.7396 (mt) cc_final: 0.6649 (mt) REVERT: A 421 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 424 GLU cc_start: 0.7261 (mp0) cc_final: 0.6982 (tm-30) REVERT: A 431 GLU cc_start: 0.7329 (tp30) cc_final: 0.6727 (tp30) REVERT: A 454 LEU cc_start: 0.8184 (mp) cc_final: 0.7952 (mp) REVERT: A 557 LYS cc_start: 0.8224 (pttp) cc_final: 0.7842 (pttp) REVERT: A 577 LYS cc_start: 0.7028 (mtmm) cc_final: 0.6598 (mtmm) REVERT: A 602 MET cc_start: 0.6836 (tpt) cc_final: 0.6572 (tpt) REVERT: A 606 MET cc_start: 0.7574 (tpp) cc_final: 0.7235 (tpt) REVERT: A 636 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8431 (mm-30) REVERT: A 640 GLN cc_start: 0.8471 (pp30) cc_final: 0.7959 (pp30) REVERT: A 680 ILE cc_start: 0.8566 (mp) cc_final: 0.8348 (mt) REVERT: A 683 MET cc_start: 0.8218 (tmm) cc_final: 0.7971 (tmm) REVERT: A 684 ILE cc_start: 0.8253 (pt) cc_final: 0.8016 (pt) REVERT: B 18 GLN cc_start: 0.7283 (mp10) cc_final: 0.6939 (mp10) REVERT: B 58 SER cc_start: 0.5932 (t) cc_final: 0.5431 (p) REVERT: B 69 LYS cc_start: 0.8211 (mptt) cc_final: 0.7743 (mptt) REVERT: B 70 GLU cc_start: 0.7665 (pm20) cc_final: 0.7313 (pp20) REVERT: B 71 LEU cc_start: 0.8201 (mp) cc_final: 0.7247 (tt) REVERT: B 93 MET cc_start: 0.6808 (mmm) cc_final: 0.6379 (mmm) REVERT: B 125 MET cc_start: 0.6794 (ttm) cc_final: 0.6022 (tpp) REVERT: B 133 PHE cc_start: 0.6431 (t80) cc_final: 0.6133 (t80) REVERT: B 153 GLU cc_start: 0.8271 (mp0) cc_final: 0.7852 (mp0) REVERT: B 168 ARG cc_start: 0.6920 (ptm-80) cc_final: 0.6518 (ptm-80) REVERT: B 200 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6544 (tm-30) REVERT: B 203 LYS cc_start: 0.7520 (mmtt) cc_final: 0.7062 (ttmm) REVERT: B 204 LYS cc_start: 0.7642 (tmtt) cc_final: 0.7128 (tmtt) REVERT: B 342 ASP cc_start: 0.6517 (p0) cc_final: 0.6259 (p0) REVERT: B 393 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5870 (mm-30) REVERT: B 394 MET cc_start: 0.7245 (ttm) cc_final: 0.6987 (tpp) REVERT: B 395 LEU cc_start: 0.7680 (tt) cc_final: 0.7464 (tt) REVERT: B 471 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6918 (tm-30) REVERT: B 489 GLU cc_start: 0.6421 (mm-30) cc_final: 0.5799 (mm-30) REVERT: B 493 GLN cc_start: 0.7068 (tm-30) cc_final: 0.6837 (tm-30) REVERT: B 550 LYS cc_start: 0.7548 (mmtp) cc_final: 0.7109 (mmtp) REVERT: B 552 LYS cc_start: 0.7599 (pttm) cc_final: 0.7302 (pttm) REVERT: B 553 MET cc_start: 0.5613 (tmm) cc_final: 0.5343 (tmm) REVERT: B 567 MET cc_start: 0.6116 (ppp) cc_final: 0.5814 (ppp) REVERT: C 3 ASP cc_start: 0.7638 (t70) cc_final: 0.7351 (t0) REVERT: C 39 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7593 (ttp80) REVERT: C 46 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7377 (mm-30) REVERT: C 106 ARG cc_start: 0.7631 (tmt-80) cc_final: 0.7246 (tmt-80) REVERT: C 107 LYS cc_start: 0.7599 (mtmm) cc_final: 0.7203 (mtmm) REVERT: C 128 MET cc_start: 0.6107 (ttp) cc_final: 0.5616 (tmm) REVERT: C 249 MET cc_start: 0.3822 (tpp) cc_final: 0.3220 (tmm) REVERT: C 253 ASN cc_start: 0.6668 (m110) cc_final: 0.5690 (m110) REVERT: K 537 LEU cc_start: 0.6632 (tp) cc_final: 0.6277 (tp) REVERT: K 668 MET cc_start: 0.2674 (tmm) cc_final: 0.1651 (ptm) REVERT: P 39 PHE cc_start: 0.5071 (t80) cc_final: 0.4864 (t80) REVERT: P 80 TYR cc_start: 0.7775 (m-80) cc_final: 0.7493 (m-80) REVERT: P 134 MET cc_start: 0.7041 (ppp) cc_final: 0.6451 (ppp) REVERT: P 331 PHE cc_start: 0.7674 (m-80) cc_final: 0.7430 (m-80) outliers start: 2 outliers final: 0 residues processed: 387 average time/residue: 0.3487 time to fit residues: 191.6090 Evaluate side-chains 366 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.094 ------------------------------------------------------------------------------- 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: 2.9990 chunk 187 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 HIS ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN K 709 GLN P 246 GLN ** P 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18024 Z= 0.303 Angle : 0.677 8.256 24245 Z= 0.360 Chirality : 0.046 0.211 2636 Planarity : 0.005 0.097 3109 Dihedral : 7.355 81.468 2430 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.64 % Favored : 90.22 % Rotamer: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % 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: 0.15 (0.16), residues: 970 sheet: -0.61 (0.36), residues: 222 loop : -2.48 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 98 HIS 0.006 0.001 HIS B 320 PHE 0.041 0.002 PHE A 32 TYR 0.031 0.002 TYR A 373 ARG 0.009 0.001 ARG C 36 *********************** 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 400 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 399 time to evaluate : 1.935 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 18 GLN cc_start: 0.6339 (mp10) cc_final: 0.5955 (mp10) REVERT: A 23 GLN cc_start: 0.8104 (mp10) cc_final: 0.7846 (mp10) REVERT: A 25 MET cc_start: 0.7690 (tpt) cc_final: 0.7175 (tpt) REVERT: A 74 ASP cc_start: 0.7454 (m-30) cc_final: 0.7168 (p0) REVERT: A 75 ILE cc_start: 0.8174 (tp) cc_final: 0.7953 (tp) REVERT: A 93 MET cc_start: 0.7981 (mmm) cc_final: 0.7654 (mmm) REVERT: A 292 ASN cc_start: 0.7868 (t0) cc_final: 0.7130 (t0) REVERT: A 309 THR cc_start: 0.7981 (p) cc_final: 0.7731 (p) REVERT: A 358 ARG cc_start: 0.6715 (mtt180) cc_final: 0.6347 (mtt180) REVERT: A 375 ASN cc_start: 0.7900 (t0) cc_final: 0.7664 (t0) REVERT: A 380 VAL cc_start: 0.8032 (t) cc_final: 0.7566 (m) REVERT: A 384 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7613 (mm-30) REVERT: A 392 ARG cc_start: 0.7984 (mmt90) cc_final: 0.7269 (tpp-160) REVERT: A 394 MET cc_start: 0.6734 (ppp) cc_final: 0.6406 (ppp) REVERT: A 395 LEU cc_start: 0.7397 (mt) cc_final: 0.6661 (mt) REVERT: A 402 LYS cc_start: 0.8073 (pttm) cc_final: 0.7730 (mptt) REVERT: A 407 ASN cc_start: 0.7742 (m110) cc_final: 0.7375 (m-40) REVERT: A 421 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 431 GLU cc_start: 0.7305 (tp30) cc_final: 0.6724 (tp30) REVERT: A 454 LEU cc_start: 0.8181 (mp) cc_final: 0.7976 (mp) REVERT: A 557 LYS cc_start: 0.8310 (pttp) cc_final: 0.7861 (pttp) REVERT: A 577 LYS cc_start: 0.7105 (mtmm) cc_final: 0.6842 (mtmm) REVERT: A 606 MET cc_start: 0.7628 (tpp) cc_final: 0.7394 (tpt) REVERT: A 620 MET cc_start: 0.7427 (mmt) cc_final: 0.7101 (mmt) REVERT: A 621 MET cc_start: 0.6013 (mmt) cc_final: 0.5507 (mpp) REVERT: A 636 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8501 (mm-30) REVERT: A 640 GLN cc_start: 0.8397 (pp30) cc_final: 0.7902 (pp30) REVERT: A 668 PHE cc_start: 0.8269 (m-10) cc_final: 0.8057 (m-10) REVERT: A 672 ASP cc_start: 0.7804 (p0) cc_final: 0.7507 (p0) REVERT: A 680 ILE cc_start: 0.8582 (mp) cc_final: 0.8091 (mp) REVERT: A 683 MET cc_start: 0.8214 (tmm) cc_final: 0.7955 (tmm) REVERT: A 684 ILE cc_start: 0.8251 (pt) cc_final: 0.7907 (pt) REVERT: B 18 GLN cc_start: 0.7236 (mp10) cc_final: 0.6916 (mp10) REVERT: B 69 LYS cc_start: 0.8269 (mptt) cc_final: 0.7793 (mptt) REVERT: B 74 ASP cc_start: 0.5641 (t70) cc_final: 0.4759 (t70) REVERT: B 93 MET cc_start: 0.6844 (mmm) cc_final: 0.6077 (mmm) REVERT: B 95 LYS cc_start: 0.8227 (ptmt) cc_final: 0.7767 (ptmt) REVERT: B 97 ASP cc_start: 0.8284 (t0) cc_final: 0.8064 (t0) REVERT: B 125 MET cc_start: 0.7163 (ttm) cc_final: 0.6677 (ttm) REVERT: B 133 PHE cc_start: 0.6258 (t80) cc_final: 0.5978 (t80) REVERT: B 153 GLU cc_start: 0.8308 (mp0) cc_final: 0.8085 (mp0) REVERT: B 154 GLN cc_start: 0.7376 (tp40) cc_final: 0.7004 (tp40) REVERT: B 200 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6488 (tm-30) REVERT: B 203 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7140 (ttmm) REVERT: B 204 LYS cc_start: 0.7551 (tmtt) cc_final: 0.7077 (tmtt) REVERT: B 428 LYS cc_start: 0.6935 (mmmt) cc_final: 0.6647 (mmmt) REVERT: B 465 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7050 (mm-30) REVERT: B 471 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6520 (tm-30) REVERT: B 475 ARG cc_start: 0.7358 (pmt170) cc_final: 0.5995 (pmt170) REVERT: B 489 GLU cc_start: 0.6479 (mm-30) cc_final: 0.5915 (mm-30) REVERT: B 552 LYS cc_start: 0.7703 (pttm) cc_final: 0.7370 (pttm) REVERT: B 652 LYS cc_start: 0.9024 (mtmm) cc_final: 0.8678 (mttp) REVERT: C 3 ASP cc_start: 0.7644 (t70) cc_final: 0.7307 (t0) REVERT: C 39 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7359 (ttp80) REVERT: C 46 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7449 (mm-30) REVERT: C 112 MET cc_start: 0.8118 (mmm) cc_final: 0.7803 (mmp) REVERT: C 128 MET cc_start: 0.6086 (ttp) cc_final: 0.5529 (tmm) REVERT: C 249 MET cc_start: 0.3795 (tpp) cc_final: 0.3104 (tmm) REVERT: C 253 ASN cc_start: 0.6838 (m110) cc_final: 0.5834 (m110) REVERT: K 537 LEU cc_start: 0.6817 (tp) cc_final: 0.6512 (tp) REVERT: K 668 MET cc_start: 0.2735 (tmm) cc_final: 0.1759 (ptm) REVERT: P 80 TYR cc_start: 0.7890 (m-80) cc_final: 0.7600 (m-80) REVERT: P 134 MET cc_start: 0.7138 (ppp) cc_final: 0.6537 (ppp) REVERT: P 331 PHE cc_start: 0.7679 (m-80) cc_final: 0.7462 (m-80) outliers start: 1 outliers final: 1 residues processed: 400 average time/residue: 0.3495 time to fit residues: 197.7861 Evaluate side-chains 368 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 367 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 116 optimal weight: 0.0170 chunk 207 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 217 GLN P 46 ASN P 246 GLN ** P 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.3722 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= 0.167 Angle : 0.625 10.246 24245 Z= 0.322 Chirality : 0.043 0.194 2636 Planarity : 0.005 0.131 3109 Dihedral : 6.826 79.587 2430 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 0.10 % Allowed : 1.90 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.40 (0.18), residues: 2147 helix: 0.33 (0.17), residues: 971 sheet: -0.65 (0.36), residues: 227 loop : -2.39 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 98 HIS 0.004 0.001 HIS A 184 PHE 0.020 0.001 PHE P 331 TYR 0.016 0.001 TYR A 485 ARG 0.022 0.001 ARG C 36 *********************** 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 400 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 398 time to evaluate : 1.828 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 18 GLN cc_start: 0.6432 (mp10) cc_final: 0.6001 (mp10) REVERT: A 23 GLN cc_start: 0.8036 (mp10) cc_final: 0.7766 (mp10) REVERT: A 25 MET cc_start: 0.7542 (tpt) cc_final: 0.6826 (tmm) REVERT: A 75 ILE cc_start: 0.8270 (tp) cc_final: 0.8031 (tp) REVERT: A 93 MET cc_start: 0.7970 (mmm) cc_final: 0.7632 (mmm) REVERT: A 95 LYS cc_start: 0.7785 (ttmm) cc_final: 0.7528 (mtmm) REVERT: A 168 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7850 (tmm-80) REVERT: A 289 TRP cc_start: 0.6710 (p90) cc_final: 0.5878 (p90) REVERT: A 292 ASN cc_start: 0.7835 (t0) cc_final: 0.7075 (t0) REVERT: A 358 ARG cc_start: 0.6690 (mtt180) cc_final: 0.6468 (mtt180) REVERT: A 378 ARG cc_start: 0.6816 (mmm-85) cc_final: 0.6562 (mtp180) REVERT: A 380 VAL cc_start: 0.7954 (t) cc_final: 0.7426 (m) REVERT: A 384 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 394 MET cc_start: 0.6798 (ppp) cc_final: 0.6413 (ppp) REVERT: A 395 LEU cc_start: 0.7356 (mt) cc_final: 0.6544 (mt) REVERT: A 407 ASN cc_start: 0.7771 (m110) cc_final: 0.7350 (m-40) REVERT: A 421 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 431 GLU cc_start: 0.7299 (tp30) cc_final: 0.6683 (tp30) REVERT: A 454 LEU cc_start: 0.8092 (mp) cc_final: 0.7890 (mp) REVERT: A 475 ARG cc_start: 0.7225 (mtm110) cc_final: 0.7011 (mtm-85) REVERT: A 557 LYS cc_start: 0.8305 (pttp) cc_final: 0.7847 (pttp) REVERT: A 566 LEU cc_start: 0.6153 (tt) cc_final: 0.5908 (tt) REVERT: A 577 LYS cc_start: 0.7069 (mtmm) cc_final: 0.6740 (mtmm) REVERT: A 606 MET cc_start: 0.7595 (tpp) cc_final: 0.7284 (tpp) REVERT: A 636 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8488 (mm-30) REVERT: A 640 GLN cc_start: 0.8350 (pp30) cc_final: 0.7866 (pp30) REVERT: A 668 PHE cc_start: 0.8180 (m-10) cc_final: 0.7910 (m-10) REVERT: A 680 ILE cc_start: 0.8589 (mp) cc_final: 0.8250 (mp) REVERT: A 683 MET cc_start: 0.8213 (tmm) cc_final: 0.7928 (tmm) REVERT: B 18 GLN cc_start: 0.7261 (mp10) cc_final: 0.6919 (mp10) REVERT: B 25 MET cc_start: 0.7091 (tpp) cc_final: 0.6636 (tpp) REVERT: B 69 LYS cc_start: 0.8093 (mptt) cc_final: 0.7766 (mptt) REVERT: B 70 GLU cc_start: 0.7705 (pp20) cc_final: 0.7039 (pp20) REVERT: B 71 LEU cc_start: 0.7990 (mp) cc_final: 0.7410 (tt) REVERT: B 74 ASP cc_start: 0.5753 (t70) cc_final: 0.4847 (t70) REVERT: B 93 MET cc_start: 0.6703 (mmm) cc_final: 0.5963 (mmm) REVERT: B 95 LYS cc_start: 0.8188 (ptmt) cc_final: 0.7685 (ptmt) REVERT: B 97 ASP cc_start: 0.8273 (t0) cc_final: 0.8021 (t0) REVERT: B 133 PHE cc_start: 0.6315 (t80) cc_final: 0.6024 (t80) REVERT: B 143 VAL cc_start: 0.5690 (m) cc_final: 0.5479 (m) REVERT: B 153 GLU cc_start: 0.8321 (mp0) cc_final: 0.8103 (mp0) REVERT: B 154 GLN cc_start: 0.7390 (tp40) cc_final: 0.7054 (tp40) REVERT: B 200 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6514 (tm-30) REVERT: B 203 LYS cc_start: 0.7540 (mmtt) cc_final: 0.7128 (ttmm) REVERT: B 204 LYS cc_start: 0.7565 (tmtt) cc_final: 0.7132 (tmtt) REVERT: B 300 GLU cc_start: 0.6939 (mp0) cc_final: 0.6639 (mp0) REVERT: B 393 GLU cc_start: 0.6189 (mm-30) cc_final: 0.5734 (mm-30) REVERT: B 428 LYS cc_start: 0.6899 (mmmt) cc_final: 0.6598 (mmmt) REVERT: B 465 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 471 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6772 (tm-30) REVERT: B 489 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5722 (mm-30) REVERT: B 493 GLN cc_start: 0.6911 (tm-30) cc_final: 0.6682 (tm-30) REVERT: B 552 LYS cc_start: 0.7615 (pttm) cc_final: 0.7296 (pttm) REVERT: B 567 MET cc_start: 0.6165 (ppp) cc_final: 0.5919 (ppp) REVERT: C 3 ASP cc_start: 0.7614 (t70) cc_final: 0.7286 (t0) REVERT: C 39 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7282 (ttp80) REVERT: C 46 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 112 MET cc_start: 0.8118 (mmm) cc_final: 0.7911 (mmp) REVERT: C 128 MET cc_start: 0.6032 (ttp) cc_final: 0.5428 (tmm) REVERT: C 249 MET cc_start: 0.3853 (tpp) cc_final: 0.3251 (tmm) REVERT: C 253 ASN cc_start: 0.6490 (m110) cc_final: 0.5505 (m110) REVERT: K 646 LEU cc_start: 0.5694 (mt) cc_final: 0.5311 (mt) REVERT: K 668 MET cc_start: 0.2570 (tmm) cc_final: 0.1588 (ptm) REVERT: P 80 TYR cc_start: 0.7822 (m-80) cc_final: 0.7526 (m-80) REVERT: P 134 MET cc_start: 0.7127 (ppp) cc_final: 0.6551 (ppp) REVERT: P 331 PHE cc_start: 0.7669 (m-80) cc_final: 0.7463 (m-80) outliers start: 2 outliers final: 1 residues processed: 399 average time/residue: 0.3576 time to fit residues: 201.4833 Evaluate side-chains 374 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 141 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** 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 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** P 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18024 Z= 0.328 Angle : 0.712 11.467 24245 Z= 0.375 Chirality : 0.047 0.200 2636 Planarity : 0.006 0.149 3109 Dihedral : 7.050 78.268 2430 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.48 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.64 (0.18), residues: 2147 helix: 0.11 (0.16), residues: 972 sheet: -0.60 (0.37), residues: 222 loop : -2.54 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 98 HIS 0.008 0.001 HIS B 625 PHE 0.042 0.002 PHE A 32 TYR 0.030 0.002 TYR A 373 ARG 0.021 0.001 ARG C 36 *********************** 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 394 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.101 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 18 GLN cc_start: 0.6399 (mp10) cc_final: 0.6198 (mp10) REVERT: A 25 MET cc_start: 0.7660 (tpt) cc_final: 0.7185 (tpt) REVERT: A 76 ILE cc_start: 0.7395 (mm) cc_final: 0.7179 (mm) REVERT: A 93 MET cc_start: 0.8043 (mmm) cc_final: 0.7617 (mmm) REVERT: A 168 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7874 (tmm-80) REVERT: A 194 GLU cc_start: 0.7704 (pm20) cc_final: 0.7428 (pm20) REVERT: A 289 TRP cc_start: 0.6771 (p90) cc_final: 0.6127 (p90) REVERT: A 292 ASN cc_start: 0.7869 (t0) cc_final: 0.7140 (t0) REVERT: A 299 GLU cc_start: 0.6760 (pp20) cc_final: 0.6305 (pp20) REVERT: A 358 ARG cc_start: 0.6810 (mtt180) cc_final: 0.6579 (mtt180) REVERT: A 364 ASP cc_start: 0.8093 (p0) cc_final: 0.7423 (p0) REVERT: A 380 VAL cc_start: 0.8027 (t) cc_final: 0.7545 (m) REVERT: A 384 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 392 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7257 (tpp-160) REVERT: A 394 MET cc_start: 0.6732 (ppp) cc_final: 0.6409 (ppp) REVERT: A 395 LEU cc_start: 0.7446 (mt) cc_final: 0.6614 (mt) REVERT: A 402 LYS cc_start: 0.8048 (pttm) cc_final: 0.7720 (mptt) REVERT: A 407 ASN cc_start: 0.7775 (m110) cc_final: 0.7423 (m-40) REVERT: A 431 GLU cc_start: 0.7294 (tp30) cc_final: 0.6711 (tp30) REVERT: A 446 THR cc_start: 0.8802 (t) cc_final: 0.8584 (p) REVERT: A 557 LYS cc_start: 0.8294 (pttp) cc_final: 0.7901 (pttp) REVERT: A 577 LYS cc_start: 0.7146 (mtmm) cc_final: 0.6697 (mtmm) REVERT: A 609 GLN cc_start: 0.6953 (pp30) cc_final: 0.6622 (pp30) REVERT: A 620 MET cc_start: 0.7099 (mmt) cc_final: 0.6561 (mmt) REVERT: A 635 VAL cc_start: 0.7915 (p) cc_final: 0.7525 (p) REVERT: A 636 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8546 (mm-30) REVERT: A 640 GLN cc_start: 0.8376 (pp30) cc_final: 0.7901 (pp30) REVERT: A 668 PHE cc_start: 0.8263 (m-10) cc_final: 0.8026 (m-10) REVERT: A 672 ASP cc_start: 0.7777 (p0) cc_final: 0.7512 (p0) REVERT: A 680 ILE cc_start: 0.8606 (mp) cc_final: 0.8167 (mp) REVERT: A 682 ARG cc_start: 0.8433 (ptm-80) cc_final: 0.8210 (ttp-110) REVERT: A 683 MET cc_start: 0.8331 (tmm) cc_final: 0.8001 (tmm) REVERT: A 684 ILE cc_start: 0.8184 (pt) cc_final: 0.7825 (pt) REVERT: B 18 GLN cc_start: 0.7237 (mp10) cc_final: 0.6918 (mp10) REVERT: B 25 MET cc_start: 0.7076 (tpp) cc_final: 0.6712 (tpp) REVERT: B 69 LYS cc_start: 0.8126 (mptt) cc_final: 0.7817 (mptt) REVERT: B 70 GLU cc_start: 0.7763 (pp20) cc_final: 0.7390 (pp20) REVERT: B 74 ASP cc_start: 0.5674 (t70) cc_final: 0.5016 (t70) REVERT: B 93 MET cc_start: 0.6713 (mmm) cc_final: 0.5953 (mmm) REVERT: B 95 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7655 (ptmt) REVERT: B 97 ASP cc_start: 0.8353 (t0) cc_final: 0.8147 (t0) REVERT: B 102 LEU cc_start: 0.6946 (tt) cc_final: 0.6626 (tt) REVERT: B 133 PHE cc_start: 0.6401 (t80) cc_final: 0.6109 (t80) REVERT: B 153 GLU cc_start: 0.8296 (mp0) cc_final: 0.7843 (mp0) REVERT: B 154 GLN cc_start: 0.7273 (tp40) cc_final: 0.6888 (tp40) REVERT: B 157 TRP cc_start: 0.7409 (t60) cc_final: 0.6747 (t60) REVERT: B 200 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6477 (tm-30) REVERT: B 203 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7193 (ttmm) REVERT: B 204 LYS cc_start: 0.7569 (tmtt) cc_final: 0.7229 (tmtt) REVERT: B 428 LYS cc_start: 0.6894 (mmmt) cc_final: 0.6566 (mmmt) REVERT: B 465 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7065 (mm-30) REVERT: B 471 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6771 (tm-30) REVERT: B 489 GLU cc_start: 0.6364 (mm-30) cc_final: 0.5859 (mm-30) REVERT: B 492 GLU cc_start: 0.7039 (tp30) cc_final: 0.6612 (tp30) REVERT: B 552 LYS cc_start: 0.7740 (pttm) cc_final: 0.7410 (pttm) REVERT: B 553 MET cc_start: 0.5708 (tpp) cc_final: 0.5361 (tmm) REVERT: B 567 MET cc_start: 0.6091 (ppp) cc_final: 0.5800 (ppp) REVERT: B 652 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8717 (mttp) REVERT: C 46 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 108 LYS cc_start: 0.6918 (mtmm) cc_final: 0.6621 (ptmm) REVERT: C 112 MET cc_start: 0.8195 (mmm) cc_final: 0.7883 (mmp) REVERT: C 128 MET cc_start: 0.6133 (ttp) cc_final: 0.5416 (tmm) REVERT: C 217 GLN cc_start: 0.8788 (mm110) cc_final: 0.8520 (mm-40) REVERT: C 249 MET cc_start: 0.3809 (tpp) cc_final: 0.3164 (tmm) REVERT: C 253 ASN cc_start: 0.6657 (m110) cc_final: 0.5753 (m110) REVERT: K 537 LEU cc_start: 0.6884 (tp) cc_final: 0.6575 (tp) REVERT: K 668 MET cc_start: 0.2761 (tmm) cc_final: 0.1879 (ptm) REVERT: P 80 TYR cc_start: 0.7939 (m-80) cc_final: 0.7633 (m-80) REVERT: P 134 MET cc_start: 0.7239 (ppp) cc_final: 0.6673 (ppp) REVERT: P 331 PHE cc_start: 0.7661 (m-80) cc_final: 0.7460 (m-80) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.3565 time to fit residues: 198.7025 Evaluate side-chains 375 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 2.637 ------------------------------------------------------------------------------- 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: 0.1980 chunk 181 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN ** 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18024 Z= 0.179 Angle : 0.651 10.707 24245 Z= 0.336 Chirality : 0.044 0.191 2636 Planarity : 0.005 0.141 3109 Dihedral : 6.653 78.435 2430 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.01 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.48 (0.18), residues: 2147 helix: 0.24 (0.17), residues: 975 sheet: -0.67 (0.37), residues: 222 loop : -2.42 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 98 HIS 0.007 0.001 HIS K 568 PHE 0.018 0.001 PHE A 32 TYR 0.021 0.001 TYR A 373 ARG 0.015 0.001 ARG C 36 *********************** 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 373 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.216 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 18 GLN cc_start: 0.6482 (mp10) cc_final: 0.6095 (mp10) REVERT: A 23 GLN cc_start: 0.7968 (mp10) cc_final: 0.7634 (mp10) REVERT: A 25 MET cc_start: 0.7574 (tpt) cc_final: 0.7108 (tpt) REVERT: A 93 MET cc_start: 0.7978 (mmm) cc_final: 0.7555 (mmm) REVERT: A 158 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6969 (mm-30) REVERT: A 165 PHE cc_start: 0.7729 (p90) cc_final: 0.7099 (p90) REVERT: A 168 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7712 (tmm-80) REVERT: A 289 TRP cc_start: 0.6712 (p90) cc_final: 0.5972 (p90) REVERT: A 292 ASN cc_start: 0.7864 (t0) cc_final: 0.7116 (t0) REVERT: A 363 MET cc_start: 0.8484 (ptm) cc_final: 0.8233 (ptp) REVERT: A 364 ASP cc_start: 0.8152 (p0) cc_final: 0.7562 (p0) REVERT: A 375 ASN cc_start: 0.7778 (t0) cc_final: 0.7516 (t0) REVERT: A 380 VAL cc_start: 0.7977 (t) cc_final: 0.7467 (m) REVERT: A 384 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 392 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7241 (tpp-160) REVERT: A 394 MET cc_start: 0.6816 (ppp) cc_final: 0.6463 (ppp) REVERT: A 395 LEU cc_start: 0.7429 (mt) cc_final: 0.6599 (mt) REVERT: A 402 LYS cc_start: 0.7955 (pttm) cc_final: 0.7683 (mptt) REVERT: A 431 GLU cc_start: 0.7326 (tp30) cc_final: 0.6699 (tp30) REVERT: A 466 MET cc_start: 0.7826 (tpt) cc_final: 0.7310 (tpt) REVERT: A 557 LYS cc_start: 0.8331 (pttp) cc_final: 0.7840 (pttp) REVERT: A 577 LYS cc_start: 0.7038 (mtmm) cc_final: 0.6612 (mtmm) REVERT: A 606 MET cc_start: 0.7478 (tpt) cc_final: 0.7237 (tpp) REVERT: A 620 MET cc_start: 0.7146 (mmt) cc_final: 0.6449 (mmt) REVERT: A 636 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8525 (mm-30) REVERT: A 640 GLN cc_start: 0.8332 (pp30) cc_final: 0.7843 (pp30) REVERT: A 680 ILE cc_start: 0.8556 (mp) cc_final: 0.8084 (mp) REVERT: A 683 MET cc_start: 0.8300 (tmm) cc_final: 0.7954 (tmm) REVERT: A 684 ILE cc_start: 0.8157 (pt) cc_final: 0.7764 (pt) REVERT: B 18 GLN cc_start: 0.7219 (mp10) cc_final: 0.6855 (mp-120) REVERT: B 25 MET cc_start: 0.6991 (tpp) cc_final: 0.6679 (tpp) REVERT: B 69 LYS cc_start: 0.8043 (mptt) cc_final: 0.7756 (mptt) REVERT: B 70 GLU cc_start: 0.7722 (pp20) cc_final: 0.7393 (pp20) REVERT: B 74 ASP cc_start: 0.5910 (t70) cc_final: 0.4938 (t0) REVERT: B 93 MET cc_start: 0.6569 (mmm) cc_final: 0.5885 (mmm) REVERT: B 95 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7563 (ptmt) REVERT: B 97 ASP cc_start: 0.8315 (t0) cc_final: 0.8077 (t0) REVERT: B 102 LEU cc_start: 0.6929 (tt) cc_final: 0.6573 (tt) REVERT: B 133 PHE cc_start: 0.6454 (t80) cc_final: 0.6203 (t80) REVERT: B 139 VAL cc_start: 0.8186 (t) cc_final: 0.7930 (m) REVERT: B 153 GLU cc_start: 0.8314 (mp0) cc_final: 0.8085 (mp0) REVERT: B 154 GLN cc_start: 0.7245 (tp40) cc_final: 0.6921 (tp40) REVERT: B 157 TRP cc_start: 0.7382 (t60) cc_final: 0.6727 (t60) REVERT: B 200 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6458 (tm-30) REVERT: B 203 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7112 (ttmm) REVERT: B 204 LYS cc_start: 0.7505 (tmtt) cc_final: 0.7105 (tmtt) REVERT: B 428 LYS cc_start: 0.6980 (mmmt) cc_final: 0.6654 (mmmt) REVERT: B 465 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6990 (mm-30) REVERT: B 471 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6737 (tm-30) REVERT: B 489 GLU cc_start: 0.6205 (mm-30) cc_final: 0.5698 (mm-30) REVERT: B 492 GLU cc_start: 0.7035 (tp30) cc_final: 0.6595 (tp30) REVERT: B 502 ARG cc_start: 0.7261 (tpp80) cc_final: 0.6720 (tpp80) REVERT: B 552 LYS cc_start: 0.7719 (pttm) cc_final: 0.7401 (pttm) REVERT: B 553 MET cc_start: 0.5805 (tpp) cc_final: 0.5413 (tmm) REVERT: B 567 MET cc_start: 0.6042 (ppp) cc_final: 0.5748 (ppp) REVERT: C 38 GLU cc_start: 0.7749 (pp20) cc_final: 0.7254 (pp20) REVERT: C 46 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7329 (mm-30) REVERT: C 106 ARG cc_start: 0.7795 (tmt-80) cc_final: 0.7062 (ttp80) REVERT: C 108 LYS cc_start: 0.7085 (mtmm) cc_final: 0.6634 (ptmm) REVERT: C 112 MET cc_start: 0.8170 (mmm) cc_final: 0.7880 (mmp) REVERT: C 128 MET cc_start: 0.6155 (ttp) cc_final: 0.5273 (tmm) REVERT: C 217 GLN cc_start: 0.8751 (mm110) cc_final: 0.8509 (mm-40) REVERT: C 249 MET cc_start: 0.3712 (tpp) cc_final: 0.3054 (tmm) REVERT: C 253 ASN cc_start: 0.6475 (m110) cc_final: 0.5605 (m110) REVERT: K 668 MET cc_start: 0.2770 (tmm) cc_final: 0.1903 (ptm) REVERT: P 80 TYR cc_start: 0.7838 (m-80) cc_final: 0.7536 (m-80) REVERT: P 134 MET cc_start: 0.7212 (ppp) cc_final: 0.6671 (ppp) REVERT: P 331 PHE cc_start: 0.7645 (m-80) cc_final: 0.7441 (m-80) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.3806 time to fit residues: 201.2023 Evaluate side-chains 361 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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: 3.9990 chunk 124 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 0.0670 chunk 214 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 104 optimal weight: 0.2980 chunk 135 optimal weight: 5.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS ** 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 C 146 GLN P 46 ASN ** 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: 0.6256 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18024 Z= 0.190 Angle : 0.645 11.669 24245 Z= 0.336 Chirality : 0.044 0.209 2636 Planarity : 0.005 0.133 3109 Dihedral : 7.594 178.336 2430 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.99 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % 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 (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: 0.28 (0.17), residues: 975 sheet: -0.65 (0.36), residues: 222 loop : -2.38 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 98 HIS 0.006 0.001 HIS A 149 PHE 0.023 0.001 PHE A 32 TYR 0.022 0.001 TYR A 373 ARG 0.014 0.001 ARG C 36 ********************** 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 384 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.969 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 18 GLN cc_start: 0.6522 (mp10) cc_final: 0.6313 (mp10) REVERT: A 23 GLN cc_start: 0.8035 (mp10) cc_final: 0.7751 (mp10) REVERT: A 25 MET cc_start: 0.7620 (tpt) cc_final: 0.7169 (tpt) REVERT: A 95 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7492 (mtmm) REVERT: A 165 PHE cc_start: 0.7769 (p90) cc_final: 0.7227 (p90) REVERT: A 168 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7684 (tmm-80) REVERT: A 289 TRP cc_start: 0.6735 (p90) cc_final: 0.6057 (p90) REVERT: A 292 ASN cc_start: 0.7839 (t0) cc_final: 0.7082 (t0) REVERT: A 363 MET cc_start: 0.8436 (ptm) cc_final: 0.8220 (ptp) REVERT: A 364 ASP cc_start: 0.8076 (p0) cc_final: 0.7553 (p0) REVERT: A 375 ASN cc_start: 0.7788 (t0) cc_final: 0.7473 (t0) REVERT: A 378 ARG cc_start: 0.6839 (mtp180) cc_final: 0.6420 (mtp85) REVERT: A 380 VAL cc_start: 0.7982 (t) cc_final: 0.7496 (m) REVERT: A 384 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 392 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7234 (tpp-160) REVERT: A 394 MET cc_start: 0.6829 (ppp) cc_final: 0.6457 (ppp) REVERT: A 395 LEU cc_start: 0.7424 (mt) cc_final: 0.6585 (mt) REVERT: A 402 LYS cc_start: 0.7958 (pttm) cc_final: 0.7706 (mptt) REVERT: A 557 LYS cc_start: 0.8350 (pttp) cc_final: 0.7854 (pttp) REVERT: A 577 LYS cc_start: 0.7041 (mtmm) cc_final: 0.6599 (mtmm) REVERT: A 606 MET cc_start: 0.7478 (tpt) cc_final: 0.7240 (tpp) REVERT: A 609 GLN cc_start: 0.7047 (pp30) cc_final: 0.6748 (pp30) REVERT: A 620 MET cc_start: 0.7128 (mmt) cc_final: 0.6528 (mmt) REVERT: A 636 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8509 (mm-30) REVERT: A 640 GLN cc_start: 0.8338 (pp30) cc_final: 0.7866 (pp30) REVERT: A 680 ILE cc_start: 0.8558 (mp) cc_final: 0.8101 (mp) REVERT: A 683 MET cc_start: 0.8308 (tmm) cc_final: 0.7964 (tmm) REVERT: A 684 ILE cc_start: 0.8165 (pt) cc_final: 0.7770 (pt) REVERT: B 18 GLN cc_start: 0.7252 (mp10) cc_final: 0.6882 (mp10) REVERT: B 25 MET cc_start: 0.7004 (tpp) cc_final: 0.6632 (tpp) REVERT: B 69 LYS cc_start: 0.7949 (mptt) cc_final: 0.7699 (mptt) REVERT: B 70 GLU cc_start: 0.7700 (pp20) cc_final: 0.7379 (pp20) REVERT: B 74 ASP cc_start: 0.5684 (t70) cc_final: 0.4996 (t70) REVERT: B 93 MET cc_start: 0.6515 (mmm) cc_final: 0.5871 (mmm) REVERT: B 95 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7589 (ptmt) REVERT: B 97 ASP cc_start: 0.8309 (t0) cc_final: 0.8095 (t0) REVERT: B 102 LEU cc_start: 0.6941 (tt) cc_final: 0.6536 (tt) REVERT: B 133 PHE cc_start: 0.6462 (t80) cc_final: 0.6200 (t80) REVERT: B 139 VAL cc_start: 0.8184 (t) cc_final: 0.7931 (m) REVERT: B 153 GLU cc_start: 0.8321 (mp0) cc_final: 0.8085 (mp0) REVERT: B 154 GLN cc_start: 0.7246 (tp40) cc_final: 0.6918 (tp40) REVERT: B 157 TRP cc_start: 0.7398 (t60) cc_final: 0.6780 (t60) REVERT: B 200 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6461 (tm-30) REVERT: B 203 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7080 (ttmm) REVERT: B 204 LYS cc_start: 0.7572 (tmtt) cc_final: 0.7152 (tmtt) REVERT: B 428 LYS cc_start: 0.6891 (mmmt) cc_final: 0.6568 (mmmt) REVERT: B 465 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7010 (mm-30) REVERT: B 471 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6757 (tm-30) REVERT: B 489 GLU cc_start: 0.6263 (mm-30) cc_final: 0.5763 (mm-30) REVERT: B 492 GLU cc_start: 0.7030 (tp30) cc_final: 0.6580 (tp30) REVERT: B 550 LYS cc_start: 0.7429 (mmtp) cc_final: 0.6992 (mmtp) REVERT: B 552 LYS cc_start: 0.7721 (pttm) cc_final: 0.7409 (pttm) REVERT: B 567 MET cc_start: 0.6037 (ppp) cc_final: 0.5737 (ppp) REVERT: C 11 GLU cc_start: 0.7710 (tt0) cc_final: 0.6968 (tm-30) REVERT: C 38 GLU cc_start: 0.7747 (pp20) cc_final: 0.7235 (pp20) REVERT: C 46 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7489 (mm-30) REVERT: C 106 ARG cc_start: 0.7685 (tmt-80) cc_final: 0.7001 (ttp80) REVERT: C 108 LYS cc_start: 0.7061 (mtmm) cc_final: 0.6550 (ptmm) REVERT: C 112 MET cc_start: 0.8185 (mmm) cc_final: 0.7889 (mmp) REVERT: C 217 GLN cc_start: 0.8745 (mm110) cc_final: 0.8506 (mm-40) REVERT: C 249 MET cc_start: 0.3572 (tpp) cc_final: 0.2975 (tmm) REVERT: C 253 ASN cc_start: 0.6455 (m110) cc_final: 0.5465 (m110) REVERT: K 537 LEU cc_start: 0.6941 (tp) cc_final: 0.6632 (tp) REVERT: K 668 MET cc_start: 0.2771 (tmm) cc_final: 0.1913 (ptm) REVERT: P 80 TYR cc_start: 0.7865 (m-80) cc_final: 0.7565 (m-80) REVERT: P 134 MET cc_start: 0.7207 (ppp) cc_final: 0.6665 (ppp) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.3561 time to fit residues: 193.9272 Evaluate side-chains 370 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9545 > 50: distance: 82 - 91: 34.860 distance: 91 - 92: 68.253 distance: 92 - 95: 61.940 distance: 93 - 94: 56.613 distance: 95 - 96: 48.037 distance: 96 - 97: 31.402 distance: 96 - 98: 34.037 distance: 99 - 100: 39.481 distance: 100 - 101: 41.308 distance: 101 - 102: 56.763 distance: 101 - 103: 55.614 distance: 104 - 105: 42.379 distance: 105 - 106: 47.303 distance: 105 - 112: 15.791 distance: 107 - 108: 57.532 distance: 108 - 109: 39.771 distance: 109 - 110: 58.472 distance: 110 - 111: 48.107 distance: 112 - 113: 12.958 distance: 113 - 114: 41.167 distance: 113 - 116: 26.218 distance: 114 - 115: 15.307 distance: 114 - 118: 42.317 distance: 116 - 117: 23.661 distance: 118 - 119: 38.795 distance: 119 - 120: 39.943 distance: 119 - 122: 58.501 distance: 120 - 121: 38.804 distance: 120 - 126: 39.923 distance: 122 - 123: 41.703 distance: 123 - 124: 39.260 distance: 123 - 125: 56.588 distance: 127 - 128: 40.684 distance: 127 - 130: 50.570 distance: 128 - 133: 28.533 distance: 130 - 131: 47.063 distance: 130 - 132: 20.338 distance: 133 - 134: 41.165 distance: 134 - 135: 61.457 distance: 134 - 137: 13.241 distance: 135 - 136: 37.364 distance: 135 - 139: 57.372 distance: 139 - 140: 11.180 distance: 140 - 141: 38.388 distance: 140 - 143: 22.204 distance: 141 - 142: 8.300 distance: 141 - 146: 41.470 distance: 146 - 147: 36.335 distance: 147 - 148: 34.130 distance: 147 - 150: 40.972 distance: 148 - 149: 40.466 distance: 150 - 151: 39.779 distance: 150 - 152: 42.020 distance: 154 - 155: 56.449 distance: 154 - 157: 38.590 distance: 155 - 156: 13.774 distance: 155 - 162: 33.767 distance: 157 - 158: 22.505 distance: 158 - 159: 20.385 distance: 159 - 160: 39.956