Starting phenix.real_space_refine on Sat Feb 17 20:35:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ro4_4970/02_2024/6ro4_4970_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ro4_4970/02_2024/6ro4_4970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ro4_4970/02_2024/6ro4_4970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ro4_4970/02_2024/6ro4_4970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ro4_4970/02_2024/6ro4_4970_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ro4_4970/02_2024/6ro4_4970_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 47 5.49 5 S 128 5.16 5 C 12543 2.51 5 N 3434 2.21 5 O 3665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 419": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ARG 211": "NH1" <-> "NH2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G ARG 237": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19827 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "K" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 575 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4648 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 23, 'TRANS': 551} Chain breaks: 2 Chain: "F" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 490 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "B" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5436 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 29, 'TRANS': 645} Chain breaks: 1 Chain: "E" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1857 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2182 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 15, 'TRANS': 264} Chain breaks: 3 Chain: "C" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3109 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 366} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1129 Classifications: {'peptide': 134} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 129} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13269 SG CYS E 268 79.447 101.564 111.591 1.00 68.27 S ATOM 13288 SG CYS E 271 81.397 99.772 114.156 1.00 80.25 S ATOM 13373 SG CYS E 282 82.494 102.746 111.993 1.00 96.15 S ATOM 13393 SG CYS E 285 83.161 99.662 110.883 1.00104.31 S ATOM 13161 SG CYS E 255 79.798 107.048 122.795 1.00 92.61 S ATOM 13178 SG CYS E 257 82.768 108.902 122.336 1.00109.54 S ATOM 13327 SG CYS E 276 79.016 110.564 122.274 1.00 95.56 S ATOM 14955 SG CYS D 291 59.709 108.339 119.826 1.00106.72 S ATOM 14977 SG CYS D 294 57.270 109.821 118.417 1.00113.78 S ATOM 15066 SG CYS D 305 57.353 106.787 117.090 1.00109.45 S ATOM 15089 SG CYS D 308 59.861 110.085 116.355 1.00113.96 S ATOM 15325 SG CYS D 345 90.504 77.279 135.920 1.00 86.42 S ATOM 15347 SG CYS D 348 87.448 75.217 137.026 1.00 85.40 S ATOM 15432 SG CYS D 368 88.987 73.762 134.034 1.00 96.58 S ATOM 15453 SG CYS D 371 87.108 76.362 133.960 1.00 95.34 S ATOM 15373 SG CYS D 360 94.784 85.728 129.551 1.00107.81 S ATOM 15391 SG CYS D 363 93.933 86.677 132.644 1.00108.40 S ATOM 15540 SG CYS D 382 91.039 85.558 130.609 1.00 92.12 S ATOM 15557 SG CYS D 385 92.176 88.954 130.090 1.00 95.02 S ATOM 18698 SG CYS G 105 73.202 25.228 33.520 1.00129.00 S ATOM 18722 SG CYS G 108 72.738 24.779 30.018 1.00133.28 S ATOM 18870 SG CYS G 126 70.309 27.018 31.071 1.00133.42 S ATOM 18892 SG CYS G 129 68.909 23.951 32.347 1.00138.27 S Time building chain proxies: 10.23, per 1000 atoms: 0.52 Number of scatterers: 19827 At special positions: 0 Unit cell: (117.6, 121.8, 186.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 128 16.00 P 47 15.00 O 3665 8.00 N 3434 7.00 C 12543 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=0, symmetry=0 Time building additional restraints: 7.76 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 294 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 308 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 291 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 305 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 345 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 368 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 348 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 371 " pdb=" ZN D 403 " pdb="ZN ZN D 403 " - pdb=" SG CYS D 385 " pdb="ZN ZN D 403 " - pdb=" SG CYS D 360 " pdb="ZN ZN D 403 " - pdb=" SG CYS D 382 " pdb="ZN ZN D 403 " - pdb=" SG CYS D 363 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 268 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 282 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 285 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 271 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 255 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 257 " pdb="ZN ZN E 402 " - pdb=" ND1 HIS E 258 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 276 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 105 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 108 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 129 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 126 " Number of angles added : 33 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 17 sheets defined 38.7% alpha, 8.9% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 8.33 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 4.498A pdb=" N PHE A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.614A pdb=" N TYR A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 removed outlier: 3.686A pdb=" N THR A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 133 through 139' Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.523A pdb=" N LEU A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.502A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.872A pdb=" N ARG A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.861A pdb=" N GLU A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.737A pdb=" N VAL A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 454 through 457 No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.690A pdb=" N PHE A 482 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 483 " --> pdb=" O LEU A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 483' Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.741A pdb=" N ALA A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.527A pdb=" N LEU A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 643 No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 668 through 675 removed outlier: 3.655A pdb=" N THR A 674 " --> pdb=" O MET A 670 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 716 removed outlier: 3.645A pdb=" N GLN A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 712 " --> pdb=" O GLU A 708 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 24 removed outlier: 3.598A pdb=" N GLN F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 52 through 63 removed outlier: 3.817A pdb=" N ARG F 56 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 34 removed outlier: 4.132A pdb=" N SER B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 removed outlier: 3.629A pdb=" N ALA B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 98 removed outlier: 3.577A pdb=" N ILE B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.581A pdb=" N ASP B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 197 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 215 through 221 removed outlier: 4.072A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 removed outlier: 3.523A pdb=" N ASP B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 removed outlier: 3.566A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 344 removed outlier: 3.559A pdb=" N GLU B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.869A pdb=" N ALA B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.663A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.751A pdb=" N SER B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 450 No H-bonds generated for 'chain 'B' and resid 447 through 450' Processing helix chain 'B' and resid 467 through 470 No H-bonds generated for 'chain 'B' and resid 467 through 470' Processing helix chain 'B' and resid 514 through 527 removed outlier: 4.141A pdb=" N ASN B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 523 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 552 removed outlier: 3.501A pdb=" N SER B 547 " --> pdb=" O GLN B 543 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 564 removed outlier: 3.683A pdb=" N ARG B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 587 Processing helix chain 'B' and resid 633 through 642 removed outlier: 4.041A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.745A pdb=" N LEU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B 659 " --> pdb=" O ASP B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 690 No H-bonds generated for 'chain 'B' and resid 687 through 690' Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 710 through 724 removed outlier: 3.507A pdb=" N VAL B 714 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 715 " --> pdb=" O ASP B 711 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 28 Processing helix chain 'E' and resid 35 through 48 removed outlier: 4.021A pdb=" N ALA E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.796A pdb=" N GLU E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 147 Processing helix chain 'E' and resid 171 through 185 removed outlier: 3.561A pdb=" N TYR E 174 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N MET E 175 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE E 177 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET E 178 " --> pdb=" O MET E 175 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN E 179 " --> pdb=" O ASN E 176 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 180 " --> pdb=" O PHE E 177 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE E 182 " --> pdb=" O ASN E 179 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA E 183 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN E 185 " --> pdb=" O PHE E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 209 removed outlier: 4.026A pdb=" N GLN E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS E 207 " --> pdb=" O LEU E 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP E 208 " --> pdb=" O GLN E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 235 through 240 removed outlier: 3.819A pdb=" N SER E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 235 through 240' Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 80 through 98 removed outlier: 3.510A pdb=" N LEU D 87 " --> pdb=" O CYS D 83 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 No H-bonds generated for 'chain 'D' and resid 128 through 131' Processing helix chain 'D' and resid 133 through 136 removed outlier: 3.719A pdb=" N ASP D 136 " --> pdb=" O LYS D 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 133 through 136' Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.548A pdb=" N ILE D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.985A pdb=" N ILE D 186 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 187 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 190 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.610A pdb=" N ALA D 212 " --> pdb=" O CYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 235 removed outlier: 3.584A pdb=" N GLU D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 321 removed outlier: 4.622A pdb=" N SER D 321 " --> pdb=" O HIS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.757A pdb=" N HIS D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 28 through 34 removed outlier: 3.653A pdb=" N ASP C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 removed outlier: 3.523A pdb=" N PHE C 45 " --> pdb=" O CYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.857A pdb=" N GLU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.521A pdb=" N GLN C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 160 removed outlier: 4.076A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 159 " --> pdb=" O ARG C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.606A pdb=" N GLN C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.515A pdb=" N GLN C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.560A pdb=" N LEU C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 215 " --> pdb=" O GLN C 211 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 218 " --> pdb=" O TYR C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 230 through 240 Processing helix chain 'C' and resid 256 through 268 removed outlier: 4.044A pdb=" N ASN C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 288 removed outlier: 3.821A pdb=" N ILE C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 322 through 328 Processing helix chain 'C' and resid 348 through 357 removed outlier: 3.879A pdb=" N GLN C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER C 357 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'C' and resid 385 through 399 removed outlier: 3.815A pdb=" N ASP C 389 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN C 390 " --> pdb=" O THR C 386 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG C 398 " --> pdb=" O TRP C 394 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 451 through 457 removed outlier: 3.990A pdb=" N TRP C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 147 Processing helix chain 'G' and resid 183 through 193 Processing helix chain 'G' and resid 197 through 235 removed outlier: 3.985A pdb=" N GLU G 201 " --> pdb=" O GLN G 197 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 203 " --> pdb=" O ALA G 199 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 212 " --> pdb=" O GLN G 208 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN G 216 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE G 219 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL G 223 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA G 229 " --> pdb=" O GLU G 225 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL G 230 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL G 234 " --> pdb=" O VAL G 230 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.240A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 167 through 170 removed outlier: 4.293A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.992A pdb=" N VAL A 405 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 441 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL A 339 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU A 490 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.375A pdb=" N LYS A 688 " --> pdb=" O GLU A 509 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 622 through 626 removed outlier: 7.704A pdb=" N PHE A 658 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLN A 625 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR A 660 " --> pdb=" O GLN A 625 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 8 through 11 removed outlier: 3.955A pdb=" N PHE F 44 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN F 36 " --> pdb=" O PHE F 44 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 2 through 4 Processing sheet with id= H, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.656A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 453 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS B 69 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL B 232 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE B 71 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP B 234 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS B 73 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.920A pdb=" N VAL B 204 " --> pdb=" O LEU B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 249 through 252 Processing sheet with id= K, first strand: chain 'B' and resid 490 through 493 removed outlier: 7.620A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 617 through 620 removed outlier: 6.642A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 56 through 62 removed outlier: 6.250A pdb=" N LEU E 190 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL E 163 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP E 192 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LYS E 165 " --> pdb=" O ASP E 192 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS E 194 " --> pdb=" O LYS E 165 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 114 through 118 removed outlier: 6.668A pdb=" N ILE D 106 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER D 164 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TYR D 62 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU D 166 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL D 64 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU D 168 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASP D 66 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE D 170 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG D 195 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE D 169 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER D 197 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE D 171 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D 199 " --> pdb=" O PHE D 171 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 314 through 317 removed outlier: 3.865A pdb=" N MET C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 343 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 336 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN C 345 " --> pdb=" O MET C 334 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N MET C 334 " --> pdb=" O GLN C 345 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 407 through 409 removed outlier: 3.987A pdb=" N TYR C 409 " --> pdb=" O MET C 441 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET C 441 " --> pdb=" O TYR C 409 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 435 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 442 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE C 433 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 138 through 140 472 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 7.32 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 8348 1.41 - 1.63: 11792 1.63 - 1.85: 183 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 20335 Sorted by residual: bond pdb=" CB ARG E 252 " pdb=" CG ARG E 252 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.03e+01 bond pdb=" CB PRO D 282 " pdb=" CG PRO D 282 " ideal model delta sigma weight residual 1.492 1.336 0.156 5.00e-02 4.00e+02 9.72e+00 bond pdb=" N ILE E 281 " pdb=" CA ILE E 281 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.61e+00 bond pdb=" SD MET G 118 " pdb=" CE MET G 118 " ideal model delta sigma weight residual 1.791 1.719 0.072 2.50e-02 1.60e+03 8.24e+00 bond pdb=" CG LEU D 284 " pdb=" CD2 LEU D 284 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.11e+00 ... (remaining 20330 not shown) Histogram of bond angle deviations from ideal: 73.63 - 85.72: 12 85.72 - 97.80: 1 97.80 - 109.88: 3643 109.88 - 121.97: 19948 121.97 - 134.05: 4101 Bond angle restraints: 27705 Sorted by residual: angle pdb=" N ASN G 119 " pdb=" CA ASN G 119 " pdb=" C ASN G 119 " ideal model delta sigma weight residual 114.09 105.97 8.12 1.55e+00 4.16e-01 2.75e+01 angle pdb=" C LEU D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.64e+01 angle pdb=" C ARG G 130 " pdb=" N ASP G 131 " pdb=" CA ASP G 131 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C LYS D 77 " pdb=" N PRO D 78 " pdb=" CA PRO D 78 " ideal model delta sigma weight residual 119.84 125.75 -5.91 1.25e+00 6.40e-01 2.23e+01 angle pdb=" N PRO D 78 " pdb=" CA PRO D 78 " pdb=" C PRO D 78 " ideal model delta sigma weight residual 112.47 122.14 -9.67 2.06e+00 2.36e-01 2.20e+01 ... (remaining 27700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 11542 29.44 - 58.88: 600 58.88 - 88.32: 47 88.32 - 117.76: 1 117.76 - 147.21: 4 Dihedral angle restraints: 12194 sinusoidal: 5300 harmonic: 6894 Sorted by residual: dihedral pdb=" CA ASP A 81 " pdb=" C ASP A 81 " pdb=" N GLY A 82 " pdb=" CA GLY A 82 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA PRO C 38 " pdb=" C PRO C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual 180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU B 693 " pdb=" C LEU B 693 " pdb=" N PRO B 694 " pdb=" CA PRO B 694 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 12191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2429 0.062 - 0.123: 582 0.123 - 0.185: 101 0.185 - 0.247: 19 0.247 - 0.309: 6 Chirality restraints: 3137 Sorted by residual: chirality pdb=" CA PRO D 78 " pdb=" N PRO D 78 " pdb=" C PRO D 78 " pdb=" CB PRO D 78 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA SER B 462 " pdb=" N SER B 462 " pdb=" C SER B 462 " pdb=" CB SER B 462 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU G 123 " pdb=" CB LEU G 123 " pdb=" CD1 LEU G 123 " pdb=" CD2 LEU G 123 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3134 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 134 " -0.022 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C ASP G 134 " 0.074 2.00e-02 2.50e+03 pdb=" O ASP G 134 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS G 135 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 300 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" CD GLU D 300 " 0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU D 300 " -0.023 2.00e-02 2.50e+03 pdb=" OE2 GLU D 300 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 140 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C THR G 140 " -0.062 2.00e-02 2.50e+03 pdb=" O THR G 140 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS G 141 " 0.021 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3118 2.76 - 3.29: 17557 3.29 - 3.83: 31971 3.83 - 4.36: 37954 4.36 - 4.90: 63391 Nonbonded interactions: 153991 Sorted by model distance: nonbonded pdb=" N3 DC J 18 " pdb=" NE2 HIS G 171 " model vdw 2.223 2.600 nonbonded pdb=" O ASP D 75 " pdb=" OD1 ASP D 75 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP D 73 " pdb=" N GLN D 74 " model vdw 2.284 2.520 nonbonded pdb=" O THR D 285 " pdb=" OG1 THR D 285 " model vdw 2.294 2.440 nonbonded pdb=" O THR D 176 " pdb=" OG1 THR D 176 " model vdw 2.295 2.440 ... (remaining 153986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.520 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 63.650 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.120 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:3.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.006 0.156 20335 Z= 0.404 Angle : 0.956 12.123 27705 Z= 0.532 Chirality : 0.057 0.309 3137 Planarity : 0.007 0.083 3348 Dihedral : 16.701 147.206 7718 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.75 % Favored : 92.03 % Rotamer: Outliers : 0.43 % Allowed : 6.74 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.12), residues: 2309 helix: -4.49 (0.07), residues: 964 sheet: -2.68 (0.28), residues: 295 loop : -3.30 (0.15), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 96 HIS 0.016 0.001 HIS B 613 PHE 0.038 0.002 PHE G 112 TYR 0.054 0.002 TYR G 116 ARG 0.053 0.001 ARG D 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 483 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 HIS cc_start: 0.6159 (t70) cc_final: 0.5581 (m90) REVERT: A 97 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 167 LYS cc_start: 0.8138 (tttt) cc_final: 0.7579 (mtmt) REVERT: A 291 LEU cc_start: 0.8018 (mt) cc_final: 0.7598 (mp) REVERT: A 318 PRO cc_start: 0.9052 (Cg_exo) cc_final: 0.8809 (Cg_endo) REVERT: A 322 LYS cc_start: 0.7412 (tptp) cc_final: 0.7205 (mttp) REVERT: F 51 ASN cc_start: 0.7930 (m-40) cc_final: 0.7585 (t0) REVERT: F 59 GLU cc_start: 0.7882 (tt0) cc_final: 0.6772 (tm-30) REVERT: B 380 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7720 (mmt180) REVERT: B 546 GLU cc_start: 0.6279 (tm-30) cc_final: 0.5954 (tm-30) REVERT: B 570 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 671 LYS cc_start: 0.8053 (mttt) cc_final: 0.7660 (tttp) REVERT: E 16 ASP cc_start: 0.7788 (t0) cc_final: 0.7577 (t0) REVERT: E 114 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7292 (tp30) REVERT: E 147 MET cc_start: 0.8325 (mmm) cc_final: 0.8106 (mpp) REVERT: E 158 LYS cc_start: 0.8549 (ptmt) cc_final: 0.8316 (pttp) REVERT: E 170 SER cc_start: 0.8689 (t) cc_final: 0.8461 (p) REVERT: E 226 TYR cc_start: 0.8291 (m-80) cc_final: 0.8044 (m-80) REVERT: E 236 ASP cc_start: 0.8273 (p0) cc_final: 0.7884 (p0) REVERT: E 251 TYR cc_start: 0.8399 (m-80) cc_final: 0.8040 (m-80) REVERT: D 103 GLN cc_start: 0.8567 (mp10) cc_final: 0.8111 (mt0) REVERT: D 181 ASN cc_start: 0.8576 (t0) cc_final: 0.8158 (t0) REVERT: D 321 SER cc_start: 0.8916 (m) cc_final: 0.8416 (t) REVERT: D 365 ASN cc_start: 0.6973 (m-40) cc_final: 0.6703 (m110) REVERT: C 57 MET cc_start: 0.9088 (mmm) cc_final: 0.8758 (mmt) REVERT: C 78 GLU cc_start: 0.7812 (tp30) cc_final: 0.7603 (tp30) REVERT: C 79 PHE cc_start: 0.8230 (m-80) cc_final: 0.7854 (m-80) REVERT: C 111 ASN cc_start: 0.7762 (m-40) cc_final: 0.7415 (m-40) REVERT: C 159 VAL cc_start: 0.9122 (t) cc_final: 0.8223 (p) REVERT: C 399 ASP cc_start: 0.7725 (t70) cc_final: 0.7519 (t70) REVERT: C 454 PHE cc_start: 0.7230 (t80) cc_final: 0.6618 (t80) REVERT: C 456 LYS cc_start: 0.7899 (pttm) cc_final: 0.7459 (mtpt) REVERT: G 119 ASN cc_start: 0.6112 (m-40) cc_final: 0.5457 (m110) REVERT: G 175 TRP cc_start: 0.7272 (t-100) cc_final: 0.6488 (t-100) outliers start: 9 outliers final: 4 residues processed: 490 average time/residue: 0.3714 time to fit residues: 262.1416 Evaluate side-chains 326 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 284 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 0.0670 chunk 178 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 112 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 213 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 498 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN F 54 GLN F 64 ASN B 60 GLN B 92 ASN B 114 ASN B 187 GLN B 201 HIS B 698 GLN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 HIS D 60 HIS D 147 ASN D 154 GLN D 158 HIS D 279 ASN C 68 GLN C 116 GLN C 260 ASN C 273 GLN C 390 GLN C 458 GLN G 119 ASN ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20335 Z= 0.183 Angle : 0.638 10.777 27705 Z= 0.330 Chirality : 0.043 0.167 3137 Planarity : 0.005 0.078 3348 Dihedral : 14.730 148.489 3086 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 2.36 % Allowed : 13.67 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.21 (0.14), residues: 2309 helix: -2.77 (0.13), residues: 970 sheet: -2.18 (0.29), residues: 300 loop : -2.92 (0.16), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 96 HIS 0.010 0.001 HIS E 258 PHE 0.020 0.001 PHE B 329 TYR 0.026 0.001 TYR A 581 ARG 0.006 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 376 time to evaluate : 2.305 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 167 LYS cc_start: 0.8370 (tttt) cc_final: 0.7889 (mttt) REVERT: A 187 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.8010 (t-90) REVERT: A 291 LEU cc_start: 0.7985 (mt) cc_final: 0.7685 (mp) REVERT: A 422 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6847 (tp30) REVERT: A 434 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7076 (pt0) REVERT: A 514 MET cc_start: 0.9033 (tpt) cc_final: 0.8820 (tpt) REVERT: A 535 THR cc_start: 0.8593 (m) cc_final: 0.8317 (m) REVERT: F 25 GLU cc_start: 0.7760 (pt0) cc_final: 0.7465 (pm20) REVERT: F 51 ASN cc_start: 0.8121 (m-40) cc_final: 0.7718 (t0) REVERT: F 53 LEU cc_start: 0.8137 (tp) cc_final: 0.7907 (tp) REVERT: F 59 GLU cc_start: 0.8066 (tt0) cc_final: 0.7292 (tm-30) REVERT: F 64 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7515 (p0) REVERT: B 1 MET cc_start: 0.6938 (tpt) cc_final: 0.6675 (tpp) REVERT: B 8 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 380 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7730 (mmt180) REVERT: B 405 THR cc_start: 0.9173 (t) cc_final: 0.8946 (t) REVERT: B 438 MET cc_start: 0.8351 (mtt) cc_final: 0.8078 (mtt) REVERT: B 570 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7565 (tm-30) REVERT: E 16 ASP cc_start: 0.7756 (t0) cc_final: 0.7445 (t0) REVERT: E 114 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7507 (tp30) REVERT: E 158 LYS cc_start: 0.8525 (ptmt) cc_final: 0.8217 (pttp) REVERT: E 170 SER cc_start: 0.8474 (t) cc_final: 0.8255 (p) REVERT: D 293 GLN cc_start: 0.7798 (tp40) cc_final: 0.7592 (tt0) REVERT: D 321 SER cc_start: 0.8887 (m) cc_final: 0.8504 (t) REVERT: C 78 GLU cc_start: 0.7788 (tp30) cc_final: 0.7407 (tp30) REVERT: C 79 PHE cc_start: 0.8278 (m-80) cc_final: 0.7327 (m-80) REVERT: C 111 ASN cc_start: 0.7851 (m-40) cc_final: 0.7513 (m-40) REVERT: C 282 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5731 (m-80) REVERT: C 393 LEU cc_start: 0.8733 (mm) cc_final: 0.8480 (mt) REVERT: C 438 LYS cc_start: 0.7506 (tmtt) cc_final: 0.7207 (tmtt) REVERT: G 175 TRP cc_start: 0.7541 (t-100) cc_final: 0.7277 (t-100) REVERT: G 178 MET cc_start: 0.8058 (ttp) cc_final: 0.7742 (tmm) REVERT: G 211 ARG cc_start: 0.8094 (ptp-110) cc_final: 0.7562 (ttm110) outliers start: 49 outliers final: 23 residues processed: 410 average time/residue: 0.3100 time to fit residues: 195.3400 Evaluate side-chains 359 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 331 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 213 optimal weight: 0.6980 chunk 230 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN B 148 HIS ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20335 Z= 0.304 Angle : 0.664 10.942 27705 Z= 0.338 Chirality : 0.045 0.171 3137 Planarity : 0.005 0.083 3348 Dihedral : 14.521 148.610 3082 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.88 % Favored : 92.07 % Rotamer: Outliers : 3.61 % Allowed : 14.93 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.16), residues: 2309 helix: -1.66 (0.15), residues: 998 sheet: -2.01 (0.30), residues: 296 loop : -2.76 (0.17), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 96 HIS 0.010 0.001 HIS B 118 PHE 0.019 0.001 PHE F 33 TYR 0.027 0.002 TYR A 581 ARG 0.008 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 342 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8133 (tm-30) REVERT: A 167 LYS cc_start: 0.8468 (tttt) cc_final: 0.7954 (mtmt) REVERT: A 190 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 422 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7128 (tp30) REVERT: A 514 MET cc_start: 0.9171 (tpt) cc_final: 0.8600 (tpt) REVERT: F 25 GLU cc_start: 0.7800 (pt0) cc_final: 0.7465 (pm20) REVERT: F 51 ASN cc_start: 0.8241 (m-40) cc_final: 0.7891 (t0) REVERT: F 53 LEU cc_start: 0.8355 (tp) cc_final: 0.8124 (tp) REVERT: F 59 GLU cc_start: 0.8019 (tt0) cc_final: 0.6876 (tm-30) REVERT: F 63 GLN cc_start: 0.8440 (tt0) cc_final: 0.7919 (mt0) REVERT: B 42 MET cc_start: 0.8039 (tpp) cc_final: 0.7469 (tpp) REVERT: B 81 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 380 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7763 (mmt180) REVERT: B 384 HIS cc_start: 0.8599 (t-170) cc_final: 0.8298 (t70) REVERT: B 410 TYR cc_start: 0.7753 (m-80) cc_final: 0.7549 (m-10) REVERT: B 438 MET cc_start: 0.8381 (mtt) cc_final: 0.8089 (mtt) REVERT: E 16 ASP cc_start: 0.7921 (t0) cc_final: 0.7553 (t0) REVERT: E 114 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7661 (tp30) REVERT: E 158 LYS cc_start: 0.8516 (ptmt) cc_final: 0.8149 (pttp) REVERT: E 170 SER cc_start: 0.8545 (t) cc_final: 0.8279 (p) REVERT: E 266 TYR cc_start: 0.8031 (m-10) cc_final: 0.7605 (m-80) REVERT: D 57 MET cc_start: 0.8028 (ptm) cc_final: 0.7820 (ptm) REVERT: D 77 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7096 (mmtm) REVERT: D 321 SER cc_start: 0.8995 (m) cc_final: 0.8557 (t) REVERT: C 55 TRP cc_start: 0.8022 (m100) cc_final: 0.7658 (m100) REVERT: C 111 ASN cc_start: 0.7813 (m-40) cc_final: 0.7401 (m-40) REVERT: C 163 MET cc_start: 0.8664 (mpp) cc_final: 0.8371 (mpp) REVERT: C 177 GLN cc_start: 0.7620 (pp30) cc_final: 0.7011 (tm-30) REVERT: C 334 MET cc_start: 0.8253 (mpp) cc_final: 0.7937 (mpp) REVERT: G 169 ASN cc_start: 0.8425 (t0) cc_final: 0.8209 (t0) REVERT: G 175 TRP cc_start: 0.7553 (t-100) cc_final: 0.7235 (t-100) outliers start: 75 outliers final: 51 residues processed: 397 average time/residue: 0.3046 time to fit residues: 190.5327 Evaluate side-chains 375 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 323 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 271 CYS Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 187 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20335 Z= 0.201 Angle : 0.616 12.913 27705 Z= 0.310 Chirality : 0.043 0.203 3137 Planarity : 0.004 0.078 3348 Dihedral : 14.303 149.074 3082 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.80 % Favored : 93.16 % Rotamer: Outliers : 2.94 % Allowed : 16.71 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.17), residues: 2309 helix: -0.98 (0.16), residues: 1001 sheet: -1.82 (0.30), residues: 293 loop : -2.59 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 96 HIS 0.010 0.001 HIS E 258 PHE 0.022 0.001 PHE C 454 TYR 0.023 0.001 TYR A 581 ARG 0.004 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 346 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 167 LYS cc_start: 0.8357 (tttt) cc_final: 0.7788 (mtmt) REVERT: A 187 HIS cc_start: 0.8357 (t-90) cc_final: 0.8082 (t-170) REVERT: A 372 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 514 MET cc_start: 0.9141 (tpt) cc_final: 0.8685 (tpt) REVERT: F 25 GLU cc_start: 0.7776 (pt0) cc_final: 0.7444 (pm20) REVERT: F 51 ASN cc_start: 0.8222 (m-40) cc_final: 0.7879 (t0) REVERT: F 53 LEU cc_start: 0.8448 (tp) cc_final: 0.8210 (tp) REVERT: F 59 GLU cc_start: 0.8016 (tt0) cc_final: 0.7815 (tt0) REVERT: B 380 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7754 (mmt180) REVERT: B 384 HIS cc_start: 0.8582 (t-170) cc_final: 0.8317 (t70) REVERT: B 438 MET cc_start: 0.8355 (mtt) cc_final: 0.8050 (mtt) REVERT: B 546 GLU cc_start: 0.6344 (tm-30) cc_final: 0.6095 (tm-30) REVERT: E 16 ASP cc_start: 0.7886 (t0) cc_final: 0.7595 (t0) REVERT: E 114 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7677 (tp30) REVERT: E 119 MET cc_start: 0.8457 (mmm) cc_final: 0.7575 (ptt) REVERT: E 147 MET cc_start: 0.8101 (tpp) cc_final: 0.7888 (mpp) REVERT: E 158 LYS cc_start: 0.8490 (ptmt) cc_final: 0.8119 (pttp) REVERT: E 162 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8269 (tp) REVERT: E 170 SER cc_start: 0.8282 (t) cc_final: 0.8016 (p) REVERT: E 226 TYR cc_start: 0.8339 (m-80) cc_final: 0.7977 (m-80) REVERT: E 266 TYR cc_start: 0.7989 (m-10) cc_final: 0.7582 (m-80) REVERT: D 57 MET cc_start: 0.8050 (ptm) cc_final: 0.7836 (ptm) REVERT: D 321 SER cc_start: 0.8958 (m) cc_final: 0.8525 (t) REVERT: C 79 PHE cc_start: 0.8124 (m-80) cc_final: 0.7922 (m-80) REVERT: C 111 ASN cc_start: 0.7895 (m-40) cc_final: 0.7583 (m-40) REVERT: G 211 ARG cc_start: 0.7644 (ptp-110) cc_final: 0.7284 (ttm170) outliers start: 61 outliers final: 48 residues processed: 386 average time/residue: 0.3030 time to fit residues: 181.7750 Evaluate side-chains 372 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 323 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 271 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20335 Z= 0.200 Angle : 0.600 10.165 27705 Z= 0.302 Chirality : 0.043 0.169 3137 Planarity : 0.004 0.081 3348 Dihedral : 14.188 148.906 3082 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.55 % Rotamer: Outliers : 3.23 % Allowed : 17.09 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.17), residues: 2309 helix: -0.56 (0.17), residues: 1000 sheet: -1.77 (0.30), residues: 298 loop : -2.46 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 96 HIS 0.015 0.001 HIS E 258 PHE 0.020 0.001 PHE C 433 TYR 0.029 0.001 TYR B 410 ARG 0.005 0.000 ARG G 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 341 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8324 (tm-30) REVERT: A 167 LYS cc_start: 0.8377 (tttt) cc_final: 0.7893 (mtmt) REVERT: A 372 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 514 MET cc_start: 0.9180 (tpt) cc_final: 0.8631 (tpt) REVERT: F 25 GLU cc_start: 0.7745 (pt0) cc_final: 0.7465 (pm20) REVERT: F 51 ASN cc_start: 0.8238 (m-40) cc_final: 0.7844 (t0) REVERT: F 53 LEU cc_start: 0.8492 (tp) cc_final: 0.8251 (tp) REVERT: B 238 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8096 (p0) REVERT: B 384 HIS cc_start: 0.8581 (t-170) cc_final: 0.8331 (t70) REVERT: B 427 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7281 (p) REVERT: B 438 MET cc_start: 0.8350 (mtt) cc_final: 0.8090 (mtt) REVERT: E 16 ASP cc_start: 0.7903 (t0) cc_final: 0.7522 (t0) REVERT: E 31 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7709 (mm-40) REVERT: E 68 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7291 (mtm110) REVERT: E 114 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7556 (mm-30) REVERT: E 147 MET cc_start: 0.8281 (tpp) cc_final: 0.7921 (mpp) REVERT: E 158 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8171 (pttp) REVERT: E 162 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8293 (tp) REVERT: E 170 SER cc_start: 0.8122 (t) cc_final: 0.7857 (p) REVERT: E 226 TYR cc_start: 0.8382 (m-80) cc_final: 0.7825 (m-80) REVERT: D 57 MET cc_start: 0.8096 (ptm) cc_final: 0.7842 (ptm) REVERT: D 321 SER cc_start: 0.8981 (m) cc_final: 0.8541 (t) REVERT: C 79 PHE cc_start: 0.8305 (m-80) cc_final: 0.8077 (m-80) REVERT: C 111 ASN cc_start: 0.7923 (m-40) cc_final: 0.7621 (m-40) REVERT: C 215 PHE cc_start: 0.8370 (t80) cc_final: 0.8141 (t80) REVERT: C 393 LEU cc_start: 0.8683 (mm) cc_final: 0.8478 (mt) REVERT: G 118 MET cc_start: 0.6950 (mmm) cc_final: 0.6660 (mmt) REVERT: G 169 ASN cc_start: 0.8272 (t0) cc_final: 0.8047 (t0) REVERT: G 211 ARG cc_start: 0.7649 (ptp-110) cc_final: 0.7308 (ttm170) outliers start: 67 outliers final: 54 residues processed: 383 average time/residue: 0.3136 time to fit residues: 185.8823 Evaluate side-chains 377 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 320 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 271 CYS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS A 187 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN C 458 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20335 Z= 0.245 Angle : 0.620 12.479 27705 Z= 0.311 Chirality : 0.043 0.154 3137 Planarity : 0.004 0.079 3348 Dihedral : 14.138 148.810 3082 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.95 % Allowed : 17.67 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2309 helix: -0.22 (0.17), residues: 993 sheet: -1.68 (0.31), residues: 290 loop : -2.38 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 96 HIS 0.015 0.001 HIS E 258 PHE 0.022 0.001 PHE C 433 TYR 0.030 0.001 TYR B 410 ARG 0.006 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 330 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.8173 (m-70) REVERT: A 97 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8300 (tm-30) REVERT: A 167 LYS cc_start: 0.8459 (tttt) cc_final: 0.7952 (mtmt) REVERT: A 372 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 514 MET cc_start: 0.9194 (tpt) cc_final: 0.8563 (tpt) REVERT: F 13 ASP cc_start: 0.8054 (t70) cc_final: 0.7781 (t0) REVERT: F 44 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6750 (t80) REVERT: F 51 ASN cc_start: 0.8277 (m-40) cc_final: 0.7870 (t0) REVERT: F 53 LEU cc_start: 0.8544 (tp) cc_final: 0.8322 (tp) REVERT: F 64 ASN cc_start: 0.8126 (p0) cc_final: 0.7909 (m-40) REVERT: B 28 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9009 (tt) REVERT: B 546 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5853 (tm-30) REVERT: B 554 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6885 (tp30) REVERT: E 16 ASP cc_start: 0.7913 (t0) cc_final: 0.7531 (t0) REVERT: E 31 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7779 (mm-40) REVERT: E 68 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7575 (mtm110) REVERT: E 113 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6824 (tm-30) REVERT: E 150 GLU cc_start: 0.7321 (mp0) cc_final: 0.7065 (mp0) REVERT: E 158 LYS cc_start: 0.8571 (ptmt) cc_final: 0.8189 (pttp) REVERT: E 162 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8339 (tp) REVERT: E 170 SER cc_start: 0.8142 (t) cc_final: 0.7890 (p) REVERT: D 57 MET cc_start: 0.8140 (ptm) cc_final: 0.7892 (ptm) REVERT: D 321 SER cc_start: 0.9036 (m) cc_final: 0.8550 (t) REVERT: C 79 PHE cc_start: 0.8379 (m-80) cc_final: 0.8137 (m-80) REVERT: C 111 ASN cc_start: 0.7889 (m-40) cc_final: 0.7527 (m-40) REVERT: C 393 LEU cc_start: 0.8752 (mm) cc_final: 0.8519 (mt) REVERT: G 118 MET cc_start: 0.7160 (mmm) cc_final: 0.6878 (mmt) REVERT: G 169 ASN cc_start: 0.8308 (t0) cc_final: 0.8097 (t0) REVERT: G 211 ARG cc_start: 0.7659 (ptp-110) cc_final: 0.7341 (ttm170) outliers start: 82 outliers final: 58 residues processed: 387 average time/residue: 0.3113 time to fit residues: 185.5642 Evaluate side-chains 380 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 318 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 271 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 129 optimal weight: 0.0070 chunk 166 optimal weight: 0.0870 chunk 128 optimal weight: 0.7980 chunk 191 optimal weight: 0.3980 chunk 126 optimal weight: 0.6980 chunk 226 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN F 18 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN E 25 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN G 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20335 Z= 0.159 Angle : 0.593 11.087 27705 Z= 0.295 Chirality : 0.042 0.168 3137 Planarity : 0.004 0.078 3348 Dihedral : 13.967 148.355 3082 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.32 % Allowed : 18.97 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.18), residues: 2309 helix: 0.05 (0.17), residues: 991 sheet: -1.57 (0.30), residues: 301 loop : -2.24 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 96 HIS 0.016 0.001 HIS E 258 PHE 0.022 0.001 PHE C 433 TYR 0.030 0.001 TYR B 410 ARG 0.004 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 338 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 167 LYS cc_start: 0.8395 (tttt) cc_final: 0.7883 (mtmt) REVERT: A 372 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 514 MET cc_start: 0.9194 (tpt) cc_final: 0.8744 (tpt) REVERT: A 537 ASN cc_start: 0.9055 (t0) cc_final: 0.8646 (t0) REVERT: F 13 ASP cc_start: 0.8003 (t70) cc_final: 0.7720 (t0) REVERT: F 44 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6621 (t80) REVERT: F 51 ASN cc_start: 0.8235 (m-40) cc_final: 0.7847 (t0) REVERT: F 53 LEU cc_start: 0.8542 (tp) cc_final: 0.8325 (tp) REVERT: F 64 ASN cc_start: 0.8045 (p0) cc_final: 0.7804 (m-40) REVERT: B 546 GLU cc_start: 0.6061 (tm-30) cc_final: 0.5690 (tm-30) REVERT: B 644 PHE cc_start: 0.8808 (m-80) cc_final: 0.8515 (m-80) REVERT: B 711 ASP cc_start: 0.8033 (t0) cc_final: 0.7719 (t0) REVERT: E 16 ASP cc_start: 0.7828 (t0) cc_final: 0.7484 (t0) REVERT: E 31 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7814 (mm-40) REVERT: E 68 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7561 (mtm110) REVERT: E 150 GLU cc_start: 0.7323 (mp0) cc_final: 0.7081 (mp0) REVERT: E 158 LYS cc_start: 0.8538 (ptmt) cc_final: 0.8159 (pttp) REVERT: E 162 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8298 (tp) REVERT: E 170 SER cc_start: 0.8112 (t) cc_final: 0.7845 (p) REVERT: E 226 TYR cc_start: 0.8461 (m-80) cc_final: 0.7834 (m-80) REVERT: D 57 MET cc_start: 0.8098 (ptm) cc_final: 0.7829 (ptm) REVERT: D 113 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7467 (mtm110) REVERT: D 321 SER cc_start: 0.9020 (m) cc_final: 0.8568 (t) REVERT: C 79 PHE cc_start: 0.8334 (m-80) cc_final: 0.8090 (m-80) REVERT: C 111 ASN cc_start: 0.7883 (m-40) cc_final: 0.7582 (m-40) REVERT: C 163 MET cc_start: 0.8562 (mpp) cc_final: 0.7941 (mpp) REVERT: C 315 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7676 (pt) REVERT: C 393 LEU cc_start: 0.8665 (mm) cc_final: 0.8410 (mt) REVERT: C 422 LEU cc_start: 0.8268 (mt) cc_final: 0.8063 (pp) REVERT: G 118 MET cc_start: 0.7078 (mmm) cc_final: 0.6834 (mmt) REVERT: G 169 ASN cc_start: 0.8237 (t0) cc_final: 0.8012 (t0) REVERT: G 197 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8377 (tm-30) outliers start: 69 outliers final: 54 residues processed: 382 average time/residue: 0.3043 time to fit residues: 179.5996 Evaluate side-chains 382 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 325 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 271 CYS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 187 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20335 Z= 0.195 Angle : 0.609 10.491 27705 Z= 0.301 Chirality : 0.042 0.157 3137 Planarity : 0.004 0.077 3348 Dihedral : 13.926 148.345 3082 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.27 % Allowed : 19.40 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2309 helix: 0.21 (0.17), residues: 994 sheet: -1.48 (0.31), residues: 293 loop : -2.18 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 96 HIS 0.017 0.001 HIS E 258 PHE 0.023 0.001 PHE C 433 TYR 0.029 0.001 TYR B 410 ARG 0.004 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 327 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7987 (m-70) REVERT: A 97 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 167 LYS cc_start: 0.8378 (tttt) cc_final: 0.7862 (mtmt) REVERT: A 279 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7701 (tp30) REVERT: A 372 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 514 MET cc_start: 0.9208 (tpt) cc_final: 0.8622 (tpt) REVERT: A 537 ASN cc_start: 0.9075 (t0) cc_final: 0.8666 (t0) REVERT: F 13 ASP cc_start: 0.8058 (t70) cc_final: 0.7760 (t0) REVERT: F 44 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6611 (t80) REVERT: F 51 ASN cc_start: 0.8241 (m-40) cc_final: 0.7838 (t0) REVERT: F 64 ASN cc_start: 0.8051 (p0) cc_final: 0.7846 (m-40) REVERT: B 28 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9028 (tt) REVERT: B 427 THR cc_start: 0.7537 (OUTLIER) cc_final: 0.7312 (p) REVERT: B 546 GLU cc_start: 0.6155 (tm-30) cc_final: 0.5745 (tm-30) REVERT: B 554 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6914 (tp30) REVERT: B 644 PHE cc_start: 0.8801 (m-80) cc_final: 0.8549 (m-80) REVERT: E 16 ASP cc_start: 0.7804 (t0) cc_final: 0.7483 (t0) REVERT: E 31 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7786 (mm-40) REVERT: E 68 ARG cc_start: 0.7764 (ttp-110) cc_final: 0.7409 (mtm-85) REVERT: E 114 GLU cc_start: 0.7991 (tp30) cc_final: 0.7513 (mm-30) REVERT: E 150 GLU cc_start: 0.7414 (mp0) cc_final: 0.7185 (mp0) REVERT: E 158 LYS cc_start: 0.8518 (ptmt) cc_final: 0.8117 (pttp) REVERT: E 162 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8328 (tp) REVERT: E 170 SER cc_start: 0.8142 (t) cc_final: 0.7868 (p) REVERT: E 226 TYR cc_start: 0.8503 (m-80) cc_final: 0.7823 (m-80) REVERT: E 262 ILE cc_start: 0.8139 (mt) cc_final: 0.7911 (mt) REVERT: D 57 MET cc_start: 0.8164 (ptm) cc_final: 0.7881 (ptm) REVERT: D 321 SER cc_start: 0.9025 (m) cc_final: 0.8588 (t) REVERT: C 79 PHE cc_start: 0.8337 (m-80) cc_final: 0.8093 (m-80) REVERT: C 111 ASN cc_start: 0.7877 (m-40) cc_final: 0.7589 (m-40) REVERT: C 163 MET cc_start: 0.8535 (mpp) cc_final: 0.7862 (mpp) REVERT: C 315 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7637 (pt) REVERT: C 393 LEU cc_start: 0.8714 (mm) cc_final: 0.8476 (mt) REVERT: G 118 MET cc_start: 0.7219 (mmm) cc_final: 0.6965 (mmt) REVERT: G 197 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8359 (tm-30) outliers start: 68 outliers final: 56 residues processed: 376 average time/residue: 0.3143 time to fit residues: 183.3187 Evaluate side-chains 382 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 320 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 127 optimal weight: 0.0670 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20335 Z= 0.190 Angle : 0.614 10.259 27705 Z= 0.304 Chirality : 0.043 0.272 3137 Planarity : 0.004 0.078 3348 Dihedral : 13.887 147.906 3082 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.61 % Allowed : 19.45 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2309 helix: 0.29 (0.17), residues: 1000 sheet: -1.45 (0.31), residues: 295 loop : -2.15 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 96 HIS 0.017 0.001 HIS E 258 PHE 0.024 0.001 PHE C 433 TYR 0.030 0.001 TYR B 410 ARG 0.004 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 326 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.8209 (m-70) REVERT: A 97 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8326 (tm-30) REVERT: A 167 LYS cc_start: 0.8375 (tttt) cc_final: 0.7856 (mtmt) REVERT: A 279 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7669 (tp30) REVERT: A 372 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 514 MET cc_start: 0.9208 (tpt) cc_final: 0.8629 (tpt) REVERT: A 537 ASN cc_start: 0.9084 (t0) cc_final: 0.8654 (t0) REVERT: A 700 ASP cc_start: 0.7460 (t0) cc_final: 0.7247 (t0) REVERT: F 13 ASP cc_start: 0.8093 (t70) cc_final: 0.7789 (t0) REVERT: F 44 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6622 (t80) REVERT: F 51 ASN cc_start: 0.8268 (m-40) cc_final: 0.7799 (t0) REVERT: F 55 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 28 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9027 (tt) REVERT: B 546 GLU cc_start: 0.6265 (tm-30) cc_final: 0.5631 (tm-30) REVERT: B 554 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6932 (tp30) REVERT: B 644 PHE cc_start: 0.8791 (m-80) cc_final: 0.8585 (m-80) REVERT: E 16 ASP cc_start: 0.7857 (t0) cc_final: 0.7517 (t0) REVERT: E 31 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7792 (mm-40) REVERT: E 68 ARG cc_start: 0.7766 (ttp-110) cc_final: 0.7418 (mtm-85) REVERT: E 114 GLU cc_start: 0.7994 (tp30) cc_final: 0.7534 (mm-30) REVERT: E 158 LYS cc_start: 0.8523 (ptmt) cc_final: 0.8099 (pttp) REVERT: E 162 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8326 (tp) REVERT: E 170 SER cc_start: 0.8159 (t) cc_final: 0.7878 (p) REVERT: E 226 TYR cc_start: 0.8502 (m-80) cc_final: 0.8294 (m-80) REVERT: E 262 ILE cc_start: 0.8155 (mt) cc_final: 0.7923 (mt) REVERT: D 57 MET cc_start: 0.8170 (ptm) cc_final: 0.7891 (ptm) REVERT: D 113 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7471 (mtm110) REVERT: D 321 SER cc_start: 0.8984 (m) cc_final: 0.8561 (t) REVERT: C 79 PHE cc_start: 0.8334 (m-80) cc_final: 0.8110 (m-80) REVERT: C 111 ASN cc_start: 0.7880 (m-40) cc_final: 0.7591 (m-40) REVERT: C 315 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7629 (pt) REVERT: C 393 LEU cc_start: 0.8769 (mm) cc_final: 0.8539 (mt) REVERT: C 422 LEU cc_start: 0.8289 (mt) cc_final: 0.8061 (pp) REVERT: G 113 MET cc_start: 0.5603 (mmp) cc_final: 0.5385 (mmp) REVERT: G 118 MET cc_start: 0.7319 (mmm) cc_final: 0.7032 (mmt) REVERT: G 178 MET cc_start: 0.8030 (ttp) cc_final: 0.7807 (tmm) REVERT: G 197 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8314 (tm-30) outliers start: 75 outliers final: 64 residues processed: 379 average time/residue: 0.3111 time to fit residues: 181.9456 Evaluate side-chains 388 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 319 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 271 CYS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 215 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 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 187 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20335 Z= 0.189 Angle : 0.615 10.103 27705 Z= 0.304 Chirality : 0.043 0.279 3137 Planarity : 0.004 0.077 3348 Dihedral : 13.863 147.498 3082 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.32 % Allowed : 19.64 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2309 helix: 0.38 (0.17), residues: 995 sheet: -1.40 (0.32), residues: 287 loop : -2.15 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 96 HIS 0.017 0.001 HIS E 258 PHE 0.024 0.001 PHE C 433 TYR 0.030 0.001 TYR B 410 ARG 0.004 0.000 ARG D 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4618 Ramachandran restraints generated. 2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 325 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 167 LYS cc_start: 0.8361 (tttt) cc_final: 0.7797 (mtmt) REVERT: A 279 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7699 (tp30) REVERT: A 372 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7473 (mm-30) REVERT: A 514 MET cc_start: 0.9209 (tpt) cc_final: 0.8634 (tpt) REVERT: A 537 ASN cc_start: 0.9079 (t0) cc_final: 0.8612 (t0) REVERT: F 13 ASP cc_start: 0.8119 (t70) cc_final: 0.7814 (t0) REVERT: F 44 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6733 (t80) REVERT: F 51 ASN cc_start: 0.8227 (m-40) cc_final: 0.7854 (t0) REVERT: F 55 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8055 (mm-30) REVERT: B 28 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9034 (tt) REVERT: B 546 GLU cc_start: 0.6298 (tm-30) cc_final: 0.5651 (tm-30) REVERT: B 554 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6929 (tp30) REVERT: B 570 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 644 PHE cc_start: 0.8829 (m-80) cc_final: 0.8609 (m-80) REVERT: E 16 ASP cc_start: 0.7835 (t0) cc_final: 0.7518 (t0) REVERT: E 31 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7793 (mm-40) REVERT: E 68 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7333 (mtm-85) REVERT: E 114 GLU cc_start: 0.7994 (tp30) cc_final: 0.7494 (tp30) REVERT: E 158 LYS cc_start: 0.8526 (ptmt) cc_final: 0.8107 (pttp) REVERT: E 162 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8330 (tp) REVERT: E 170 SER cc_start: 0.8158 (t) cc_final: 0.7879 (p) REVERT: E 262 ILE cc_start: 0.8163 (mt) cc_final: 0.7935 (mt) REVERT: D 57 MET cc_start: 0.8161 (ptm) cc_final: 0.7878 (ptm) REVERT: D 321 SER cc_start: 0.8977 (m) cc_final: 0.8548 (t) REVERT: D 365 ASN cc_start: 0.7141 (m-40) cc_final: 0.6546 (m110) REVERT: C 79 PHE cc_start: 0.8316 (m-80) cc_final: 0.8098 (m-80) REVERT: C 111 ASN cc_start: 0.7876 (m-40) cc_final: 0.7589 (m-40) REVERT: C 315 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7615 (pt) REVERT: C 335 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8287 (pp) REVERT: C 393 LEU cc_start: 0.8765 (mm) cc_final: 0.8537 (mt) REVERT: C 422 LEU cc_start: 0.8305 (mt) cc_final: 0.8058 (pp) REVERT: G 118 MET cc_start: 0.7316 (mmm) cc_final: 0.7031 (mmt) REVERT: G 197 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8291 (tm-30) outliers start: 69 outliers final: 62 residues processed: 372 average time/residue: 0.3025 time to fit residues: 173.9717 Evaluate side-chains 388 residues out of total 2082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 321 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 705 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 271 CYS Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 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 83 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093429 restraints weight = 32000.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097403 restraints weight = 17093.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098494 restraints weight = 11144.228| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20335 Z= 0.208 Angle : 0.617 9.964 27705 Z= 0.306 Chirality : 0.043 0.190 3137 Planarity : 0.004 0.078 3348 Dihedral : 13.867 147.014 3082 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.37 % Allowed : 19.88 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 2309 helix: 0.47 (0.18), residues: 995 sheet: -1.37 (0.32), residues: 287 loop : -2.12 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 96 HIS 0.017 0.001 HIS E 258 PHE 0.025 0.001 PHE B 93 TYR 0.029 0.001 TYR B 410 ARG 0.004 0.000 ARG B 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4307.06 seconds wall clock time: 79 minutes 28.57 seconds (4768.57 seconds total)