Starting phenix.real_space_refine on Mon Apr 8 12:01:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/04_2024/6c23_7334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/04_2024/6c23_7334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/04_2024/6c23_7334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/04_2024/6c23_7334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/04_2024/6c23_7334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c23_7334/04_2024/6c23_7334_updated.pdb" } resolution = 3.9 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= 0.004 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8471 2.51 5 N 2389 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 685": "NH1" <-> "NH2" Residue "L PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 414": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13440 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 860 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 181 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2406 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2877 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 349} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "N" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3058 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "O" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 51 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "P" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 484 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 496 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 63} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 674 Classifications: {'peptide': 135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 134} Link IDs: {'TRANS': 134} Chain breaks: 6 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1307 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain breaks: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 7.77, per 1000 atoms: 0.58 Number of scatterers: 13440 At special positions: 0 Unit cell: (146.16, 109.2, 111.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2496 8.00 N 2389 7.00 C 8471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 453 " distance=2.07 Simple disulfide: pdb=" SG CYS K 289 " - pdb=" SG CYS K 294 " distance=2.01 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 530 " distance=2.05 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 547 " distance=2.03 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 549 " distance=2.02 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 549 " distance=2.03 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 553 " distance=2.05 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 429 " distance=2.07 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 2.4 seconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB UNK Z 25 " Number of C-beta restraints generated: 3500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 20 sheets defined 20.7% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'K' and resid 274 through 283 removed outlier: 5.206A pdb=" N SER K 280 " --> pdb=" O GLN K 276 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE K 281 " --> pdb=" O SER K 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 447 removed outlier: 3.513A pdb=" N ILE K 444 " --> pdb=" O PHE K 440 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY K 445 " --> pdb=" O ARG K 441 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR K 446 " --> pdb=" O VAL K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 457 Processing helix chain 'K' and resid 463 through 476 Processing helix chain 'K' and resid 535 through 538 No H-bonds generated for 'chain 'K' and resid 535 through 538' Processing helix chain 'K' and resid 572 through 575 No H-bonds generated for 'chain 'K' and resid 572 through 575' Processing helix chain 'K' and resid 605 through 608 No H-bonds generated for 'chain 'K' and resid 605 through 608' Processing helix chain 'K' and resid 648 through 661 removed outlier: 3.932A pdb=" N VAL K 657 " --> pdb=" O ARG K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 683 through 686 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 268 through 278 Processing helix chain 'L' and resid 282 through 284 No H-bonds generated for 'chain 'L' and resid 282 through 284' Processing helix chain 'M' and resid 577 through 579 No H-bonds generated for 'chain 'M' and resid 577 through 579' Processing helix chain 'M' and resid 592 through 602 removed outlier: 3.540A pdb=" N GLU M 601 " --> pdb=" O ILE M 597 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU M 602 " --> pdb=" O THR M 598 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 624 Processing helix chain 'M' and resid 629 through 650 removed outlier: 3.708A pdb=" N ASN M 633 " --> pdb=" O ASP M 629 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET M 637 " --> pdb=" O ASN M 633 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN M 645 " --> pdb=" O GLU M 641 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS M 646 " --> pdb=" O ASN M 642 " (cutoff:3.500A) Processing helix chain 'M' and resid 653 through 664 Processing helix chain 'M' and resid 671 through 681 Processing helix chain 'N' and resid 5 through 30 removed outlier: 3.556A pdb=" N ALA N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Proline residue: N 29 - end of helix Processing helix chain 'N' and resid 154 through 156 No H-bonds generated for 'chain 'N' and resid 154 through 156' Processing helix chain 'N' and resid 356 through 361 Processing helix chain 'P' and resid 244 through 256 removed outlier: 4.807A pdb=" N LEU P 249 " --> pdb=" O GLU P 246 " (cutoff:3.500A) Proline residue: P 250 - end of helix removed outlier: 3.544A pdb=" N GLU P 256 " --> pdb=" O TRP P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 280 No H-bonds generated for 'chain 'P' and resid 278 through 280' Processing helix chain 'Q' and resid 83 through 104 removed outlier: 4.354A pdb=" N LYS Q 92 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) Proline residue: Q 93 - end of helix Processing helix chain 'C' and resid 18 through 62 removed outlier: 3.712A pdb=" N LEU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.557A pdb=" N LEU C 149 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 150 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 Processing helix chain 'C' and resid 221 through 230 removed outlier: 4.213A pdb=" N ALA C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'B' and resid 108 through 111 No H-bonds generated for 'chain 'B' and resid 108 through 111' Processing sheet with id= A, first strand: chain 'A' and resid 474 through 477 Processing sheet with id= B, first strand: chain 'K' and resid 614 through 618 Processing sheet with id= C, first strand: chain 'K' and resid 644 through 646 Processing sheet with id= D, first strand: chain 'K' and resid 696 through 702 Processing sheet with id= E, first strand: chain 'L' and resid 82 through 84 Processing sheet with id= F, first strand: chain 'L' and resid 98 through 101 removed outlier: 3.686A pdb=" N GLY L 98 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU L 111 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 124 through 126 Processing sheet with id= H, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.936A pdb=" N GLY L 167 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE L 171 " --> pdb=" O GLY L 167 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 205 through 210 removed outlier: 4.469A pdb=" N ALA L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN L 219 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU L 225 " --> pdb=" O ASN L 219 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN L 292 " --> pdb=" O ILE L 228 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 260 through 264 Processing sheet with id= K, first strand: chain 'L' and resid 312 through 315 Processing sheet with id= L, first strand: chain 'L' and resid 331 through 333 Processing sheet with id= M, first strand: chain 'N' and resid 65 through 67 Processing sheet with id= N, first strand: chain 'N' and resid 78 through 80 Processing sheet with id= O, first strand: chain 'N' and resid 139 through 142 Processing sheet with id= P, first strand: chain 'N' and resid 267 through 270 removed outlier: 4.442A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA N 247 " --> pdb=" O LYS N 251 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE N 243 " --> pdb=" O TRP N 255 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'N' and resid 288 through 292 removed outlier: 3.846A pdb=" N HIS N 311 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP N 302 " --> pdb=" O LYS N 309 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LYS N 309 " --> pdb=" O ASP N 302 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'N' and resid 320 through 323 removed outlier: 7.034A pdb=" N SER N 336 " --> pdb=" O PHE N 321 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL N 323 " --> pdb=" O ALA N 334 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA N 334 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP N 346 " --> pdb=" O LEU N 366 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU N 366 " --> pdb=" O ASP N 346 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'N' and resid 32 through 39 removed outlier: 6.329A pdb=" N GLN N 403 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL N 35 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL N 401 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR N 37 " --> pdb=" O MET N 399 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET N 399 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Z' and resid 31 through 36 removed outlier: 7.166A pdb=" N UNK Z 58 " --> pdb=" O UNK Z 32 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N UNK Z 34 " --> pdb=" O UNK Z 58 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N UNK Z 60 " --> pdb=" O UNK Z 34 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N UNK Z 36 " --> pdb=" O UNK Z 60 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N UNK Z 62 " --> pdb=" O UNK Z 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N UNK Z 86 " --> pdb=" O UNK Z 61 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N UNK Z 63 " --> pdb=" O UNK Z 86 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N UNK Z 88 " --> pdb=" O UNK Z 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= T 320 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2273 1.29 - 1.43: 3651 1.43 - 1.56: 7691 1.56 - 1.70: 7 1.70 - 1.84: 114 Bond restraints: 13736 Sorted by residual: bond pdb=" CA GLY L 234 " pdb=" C GLY L 234 " ideal model delta sigma weight residual 1.514 1.149 0.366 1.41e-02 5.03e+03 6.72e+02 bond pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " ideal model delta sigma weight residual 1.458 1.168 0.290 1.90e-02 2.77e+03 2.32e+02 bond pdb=" CA UNK Z 25 " pdb=" C UNK Z 25 " ideal model delta sigma weight residual 1.525 1.206 0.319 2.10e-02 2.27e+03 2.31e+02 bond pdb=" CA CYS N 391 " pdb=" C CYS N 391 " ideal model delta sigma weight residual 1.522 1.453 0.069 1.19e-02 7.06e+03 3.39e+01 bond pdb=" CA ASN L 146 " pdb=" C ASN L 146 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.10e-02 8.26e+03 3.33e+01 ... (remaining 13731 not shown) Histogram of bond angle deviations from ideal: 78.75 - 91.57: 2 91.57 - 104.39: 257 104.39 - 117.22: 9982 117.22 - 130.04: 8318 130.04 - 142.87: 142 Bond angle restraints: 18701 Sorted by residual: angle pdb=" N UNK Z 25 " pdb=" CA UNK Z 25 " pdb=" CB UNK Z 25 " ideal model delta sigma weight residual 110.50 78.75 31.75 1.70e+00 3.46e-01 3.49e+02 angle pdb=" C UNK Z 25 " pdb=" CA UNK Z 25 " pdb=" CB UNK Z 25 " ideal model delta sigma weight residual 110.08 142.87 -32.79 1.90e+00 2.77e-01 2.98e+02 angle pdb=" CA GLY L 234 " pdb=" C GLY L 234 " pdb=" O GLY L 234 " ideal model delta sigma weight residual 120.57 98.19 22.38 1.74e+00 3.30e-01 1.65e+02 angle pdb=" C UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta sigma weight residual 110.08 88.67 21.41 1.90e+00 2.77e-01 1.27e+02 angle pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta sigma weight residual 110.50 129.03 -18.53 1.70e+00 3.46e-01 1.19e+02 ... (remaining 18696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 7529 16.61 - 33.22: 568 33.22 - 49.83: 82 49.83 - 66.43: 16 66.43 - 83.04: 8 Dihedral angle restraints: 8203 sinusoidal: 2855 harmonic: 5348 Sorted by residual: dihedral pdb=" N UNK Z 24 " pdb=" C UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta harmonic sigma weight residual 122.80 171.90 -49.10 0 2.50e+00 1.60e-01 3.86e+02 dihedral pdb=" C UNK Z 24 " pdb=" N UNK Z 24 " pdb=" CA UNK Z 24 " pdb=" CB UNK Z 24 " ideal model delta harmonic sigma weight residual -122.60 -169.56 46.96 0 2.50e+00 1.60e-01 3.53e+02 dihedral pdb=" CA HIS C 129 " pdb=" C HIS C 129 " pdb=" N ASN C 130 " pdb=" CA ASN C 130 " ideal model delta harmonic sigma weight residual -180.00 -125.52 -54.48 0 5.00e+00 4.00e-02 1.19e+02 ... (remaining 8200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.508: 2110 0.508 - 1.016: 2 1.016 - 1.524: 0 1.524 - 2.032: 0 2.032 - 2.540: 2 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CA UNK Z 25 " pdb=" N UNK Z 25 " pdb=" C UNK Z 25 " pdb=" CB UNK Z 25 " both_signs ideal model delta sigma weight residual False 2.52 -0.02 2.54 2.00e-01 2.50e+01 1.61e+02 chirality pdb=" CA UNK Z 24 " pdb=" N UNK Z 24 " pdb=" C UNK Z 24 " pdb=" CB UNK Z 24 " both_signs ideal model delta sigma weight residual False 2.52 0.24 2.28 2.00e-01 2.50e+01 1.30e+02 chirality pdb=" CA TYR L 148 " pdb=" N TYR L 148 " pdb=" C TYR L 148 " pdb=" CB TYR L 148 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.47e+00 ... (remaining 2111 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 148 " 0.055 2.00e-02 2.50e+03 2.89e-02 1.66e+01 pdb=" CG TYR L 148 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR L 148 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 148 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR L 148 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 148 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR L 148 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 151 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO E 152 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 380 " -0.034 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE N 380 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE N 380 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE N 380 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE N 380 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE N 380 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE N 380 " -0.011 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 8 1.80 - 2.57: 188 2.57 - 3.35: 17309 3.35 - 4.12: 31584 4.12 - 4.90: 56716 Nonbonded interactions: 105805 Sorted by model distance: nonbonded pdb=" O VAL N 151 " pdb=" OD1 ASP N 170 " model vdw 1.020 3.040 nonbonded pdb=" O LEU K 443 " pdb=" CD1 TYR K 447 " model vdw 1.548 3.340 nonbonded pdb=" CD1 TRP L 389 " pdb=" O LYS L 400 " model vdw 1.593 3.260 nonbonded pdb=" ND1 HIS K 593 " pdb=" CB SER K 596 " model vdw 1.644 3.520 nonbonded pdb=" C SER K 729 " pdb=" OE1 GLN K 730 " model vdw 1.693 3.270 ... (remaining 105800 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=0.49 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: 5.210 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: 0.000 Extract box with map and model: 5.730 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 38.850 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.013 0.366 13736 Z= 0.838 Angle : 1.586 32.789 18701 Z= 0.964 Chirality : 0.114 2.540 2114 Planarity : 0.006 0.081 2439 Dihedral : 12.198 78.205 4679 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 1.57 % Allowed : 14.68 % Favored : 83.75 % Rotamer: Outliers : 1.02 % Allowed : 5.18 % Favored : 93.80 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -4.76 (0.17), residues: 1655 helix: -1.81 (0.24), residues: 336 sheet: -3.79 (0.23), residues: 317 loop : -3.60 (0.16), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP K 624 HIS 0.014 0.003 HIS A 471 PHE 0.040 0.005 PHE N 380 TYR 0.055 0.006 TYR L 148 ARG 0.011 0.001 ARG Q 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 464 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8784 (mt) cc_final: 0.8420 (mt) REVERT: A 429 PHE cc_start: 0.8016 (m-10) cc_final: 0.7708 (t80) REVERT: A 459 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8565 (mmtp) REVERT: A 468 LYS cc_start: 0.8922 (mttt) cc_final: 0.8680 (tttp) REVERT: A 499 TYR cc_start: 0.8617 (t80) cc_final: 0.8150 (t80) REVERT: E 155 GLU cc_start: 0.8116 (tt0) cc_final: 0.7551 (tm-30) REVERT: K 536 CYS cc_start: 0.7517 (m) cc_final: 0.7181 (p) REVERT: K 581 ASP cc_start: 0.7351 (t0) cc_final: 0.5909 (m-30) REVERT: K 602 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8229 (mmpt) REVERT: K 605 SER cc_start: 0.9050 (m) cc_final: 0.8751 (t) REVERT: K 607 GLN cc_start: 0.9035 (mt0) cc_final: 0.8833 (mt0) REVERT: K 644 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8039 (mt-10) REVERT: K 662 MET cc_start: 0.7687 (tpp) cc_final: 0.7086 (tpp) REVERT: K 694 ASN cc_start: 0.8709 (p0) cc_final: 0.7868 (p0) REVERT: L 89 LYS cc_start: 0.8295 (tttm) cc_final: 0.8053 (tmtt) REVERT: L 145 GLU cc_start: 0.8464 (pt0) cc_final: 0.8242 (pt0) REVERT: L 181 GLN cc_start: 0.8534 (tt0) cc_final: 0.8242 (mm-40) REVERT: L 191 ASN cc_start: 0.9143 (m110) cc_final: 0.8935 (m110) REVERT: L 238 GLU cc_start: 0.9060 (pt0) cc_final: 0.8688 (pt0) REVERT: L 250 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8729 (tttp) REVERT: L 262 LEU cc_start: 0.9270 (mt) cc_final: 0.8835 (mt) REVERT: L 292 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8559 (tp-100) REVERT: L 307 ASN cc_start: 0.8514 (t0) cc_final: 0.8196 (t0) REVERT: L 342 LYS cc_start: 0.9065 (mptm) cc_final: 0.8746 (tptt) REVERT: L 382 GLN cc_start: 0.8072 (pt0) cc_final: 0.7705 (pt0) REVERT: L 436 ARG cc_start: 0.8734 (tmt90) cc_final: 0.8417 (ttt-90) REVERT: M 569 ASP cc_start: 0.8928 (p0) cc_final: 0.8598 (p0) REVERT: M 620 HIS cc_start: 0.8714 (t-90) cc_final: 0.8450 (t-90) REVERT: M 642 ASN cc_start: 0.8450 (m-40) cc_final: 0.8250 (m-40) REVERT: M 653 CYS cc_start: 0.8344 (m) cc_final: 0.7379 (t) REVERT: M 676 LYS cc_start: 0.8879 (tttt) cc_final: 0.8482 (tptp) REVERT: N 37 THR cc_start: 0.9347 (m) cc_final: 0.9134 (p) REVERT: N 41 GLU cc_start: 0.8864 (pt0) cc_final: 0.8493 (tp30) REVERT: N 48 GLN cc_start: 0.8304 (tp40) cc_final: 0.8065 (tt0) REVERT: N 55 ARG cc_start: 0.8630 (pmm-80) cc_final: 0.7681 (ptp90) REVERT: N 64 HIS cc_start: 0.8514 (m-70) cc_final: 0.8161 (m90) REVERT: N 65 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.7830 (mpt180) REVERT: N 66 LEU cc_start: 0.9335 (mm) cc_final: 0.9084 (mt) REVERT: N 122 ASN cc_start: 0.8616 (m110) cc_final: 0.8326 (p0) REVERT: N 172 ARG cc_start: 0.8829 (ttt180) cc_final: 0.8607 (mmm-85) REVERT: N 310 LEU cc_start: 0.9292 (mp) cc_final: 0.8965 (tt) REVERT: N 342 LEU cc_start: 0.9600 (tt) cc_final: 0.9336 (tt) REVERT: N 379 ASP cc_start: 0.8829 (t0) cc_final: 0.8404 (t0) REVERT: N 385 ASN cc_start: 0.8526 (m-40) cc_final: 0.8023 (t0) REVERT: N 396 ASP cc_start: 0.9062 (p0) cc_final: 0.8783 (p0) REVERT: O 28 PHE cc_start: 0.5537 (m-10) cc_final: 0.4950 (t80) REVERT: Q 117 TYR cc_start: 0.8738 (p90) cc_final: 0.8461 (p90) REVERT: C 36 ASP cc_start: 0.8647 (m-30) cc_final: 0.8433 (p0) REVERT: C 55 ILE cc_start: 0.9502 (mt) cc_final: 0.9035 (mt) REVERT: C 61 LYS cc_start: 0.9112 (mttt) cc_final: 0.8837 (mtmm) REVERT: C 64 ARG cc_start: 0.8327 (mtt90) cc_final: 0.7871 (mmm160) REVERT: C 65 ILE cc_start: 0.8287 (mm) cc_final: 0.7875 (tt) REVERT: C 230 MET cc_start: 0.7700 (mmp) cc_final: 0.7220 (mmm) outliers start: 13 outliers final: 4 residues processed: 474 average time/residue: 0.3096 time to fit residues: 200.2644 Evaluate side-chains 319 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 315 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 668 ASN Chi-restraints excluded: chain N residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 30.0000 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 0.0370 chunk 103 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 668 ASN L 94 GLN L 136 GLN L 213 HIS ** L 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 397 HIS M 655 ASN N 18 ASN N 64 HIS N 188 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 HIS N 343 ASN P 268 HIS Q 83 HIS C 45 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13736 Z= 0.324 Angle : 0.793 11.093 18701 Z= 0.415 Chirality : 0.049 0.207 2114 Planarity : 0.005 0.064 2439 Dihedral : 7.281 53.381 1927 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.37 % Favored : 90.27 % Rotamer: Outliers : 4.78 % Allowed : 13.73 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.31 % 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: -3.73 (0.18), residues: 1655 helix: -0.59 (0.26), residues: 354 sheet: -3.18 (0.25), residues: 304 loop : -3.10 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 345 HIS 0.007 0.001 HIS N 157 PHE 0.017 0.002 PHE C 120 TYR 0.032 0.002 TYR L 148 ARG 0.006 0.001 ARG K 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 351 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8517 (mmtp) REVERT: A 468 LYS cc_start: 0.8961 (mttt) cc_final: 0.8677 (tttp) REVERT: A 487 ILE cc_start: 0.9055 (mt) cc_final: 0.8786 (mp) REVERT: E 155 GLU cc_start: 0.7926 (tt0) cc_final: 0.7364 (tm-30) REVERT: K 581 ASP cc_start: 0.7280 (t0) cc_final: 0.5701 (m-30) REVERT: K 605 SER cc_start: 0.9008 (m) cc_final: 0.8785 (t) REVERT: K 632 VAL cc_start: 0.8826 (m) cc_final: 0.8613 (m) REVERT: K 721 GLU cc_start: 0.9036 (tt0) cc_final: 0.8619 (tt0) REVERT: L 145 GLU cc_start: 0.8349 (pt0) cc_final: 0.8108 (pt0) REVERT: L 181 GLN cc_start: 0.8486 (tt0) cc_final: 0.8148 (mm-40) REVERT: L 233 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7808 (mm-30) REVERT: L 250 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8479 (tttp) REVERT: L 251 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8127 (mt) REVERT: L 256 MET cc_start: 0.9056 (ttm) cc_final: 0.8646 (ttm) REVERT: L 341 ASP cc_start: 0.9049 (m-30) cc_final: 0.8557 (t70) REVERT: L 357 ASP cc_start: 0.8833 (m-30) cc_final: 0.8630 (t0) REVERT: M 595 LYS cc_start: 0.9121 (tttp) cc_final: 0.8912 (tppp) REVERT: M 599 GLN cc_start: 0.8737 (tp40) cc_final: 0.8444 (tp40) REVERT: M 634 HIS cc_start: 0.8986 (t-90) cc_final: 0.8470 (t-170) REVERT: M 641 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8842 (tm-30) REVERT: M 653 CYS cc_start: 0.8384 (m) cc_final: 0.7436 (t) REVERT: M 676 LYS cc_start: 0.9007 (tttt) cc_final: 0.8496 (tptp) REVERT: N 41 GLU cc_start: 0.8896 (pt0) cc_final: 0.8429 (tm-30) REVERT: N 122 ASN cc_start: 0.8644 (m110) cc_final: 0.8307 (p0) REVERT: N 270 ASP cc_start: 0.8809 (m-30) cc_final: 0.8456 (t0) REVERT: N 302 ASP cc_start: 0.8710 (t0) cc_final: 0.8168 (p0) REVERT: N 354 GLN cc_start: 0.7841 (pt0) cc_final: 0.7065 (pt0) REVERT: N 379 ASP cc_start: 0.8766 (t0) cc_final: 0.8336 (t0) REVERT: N 385 ASN cc_start: 0.8575 (m-40) cc_final: 0.8095 (t0) REVERT: N 396 ASP cc_start: 0.9055 (p0) cc_final: 0.8802 (p0) REVERT: N 399 MET cc_start: 0.9292 (ttp) cc_final: 0.9077 (ppp) REVERT: C 61 LYS cc_start: 0.9135 (mttt) cc_final: 0.8873 (mtmm) REVERT: C 64 ARG cc_start: 0.8376 (mtt90) cc_final: 0.8118 (mmm160) REVERT: C 65 ILE cc_start: 0.8312 (mm) cc_final: 0.7887 (tt) outliers start: 61 outliers final: 35 residues processed: 380 average time/residue: 0.2601 time to fit residues: 142.8574 Evaluate side-chains 328 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 292 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 700 MET Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 607 ASN Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN N 188 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13736 Z= 0.283 Angle : 0.745 10.120 18701 Z= 0.383 Chirality : 0.046 0.184 2114 Planarity : 0.004 0.053 2439 Dihedral : 6.630 51.342 1925 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.57 % Favored : 89.06 % Rotamer: Outliers : 5.18 % Allowed : 15.84 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % 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: -3.21 (0.19), residues: 1655 helix: -0.05 (0.27), residues: 351 sheet: -2.76 (0.27), residues: 286 loop : -2.85 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 218 HIS 0.005 0.001 HIS A 466 PHE 0.030 0.002 PHE M 656 TYR 0.029 0.002 TYR L 148 ARG 0.007 0.001 ARG L 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 321 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8522 (mmtp) REVERT: A 476 PHE cc_start: 0.7626 (m-80) cc_final: 0.7358 (m-80) REVERT: A 487 ILE cc_start: 0.9097 (mt) cc_final: 0.8836 (mp) REVERT: K 293 ASP cc_start: 0.8287 (t70) cc_final: 0.7921 (t70) REVERT: K 581 ASP cc_start: 0.7013 (t0) cc_final: 0.5650 (m-30) REVERT: K 685 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8671 (ptm160) REVERT: K 721 GLU cc_start: 0.9062 (tt0) cc_final: 0.8646 (tt0) REVERT: L 145 GLU cc_start: 0.8407 (pt0) cc_final: 0.8183 (pt0) REVERT: L 153 THR cc_start: 0.9538 (t) cc_final: 0.9048 (m) REVERT: L 181 GLN cc_start: 0.8448 (tt0) cc_final: 0.8110 (mm-40) REVERT: L 250 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8405 (tttp) REVERT: L 251 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8275 (mt) REVERT: L 256 MET cc_start: 0.9106 (ttm) cc_final: 0.8793 (ttm) REVERT: L 257 ASP cc_start: 0.8791 (p0) cc_final: 0.8488 (p0) REVERT: L 341 ASP cc_start: 0.8916 (m-30) cc_final: 0.8390 (t70) REVERT: L 357 ASP cc_start: 0.8908 (m-30) cc_final: 0.8517 (t0) REVERT: M 568 SER cc_start: 0.8905 (p) cc_final: 0.8527 (p) REVERT: M 599 GLN cc_start: 0.8762 (tp40) cc_final: 0.8412 (tp40) REVERT: M 634 HIS cc_start: 0.8945 (t-90) cc_final: 0.8385 (t-170) REVERT: M 653 CYS cc_start: 0.8390 (m) cc_final: 0.7424 (t) REVERT: M 676 LYS cc_start: 0.8986 (tttt) cc_final: 0.8498 (tptp) REVERT: N 22 LYS cc_start: 0.9158 (tppt) cc_final: 0.8813 (tppp) REVERT: N 41 GLU cc_start: 0.8866 (pt0) cc_final: 0.8516 (tt0) REVERT: N 66 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8974 (mt) REVERT: N 122 ASN cc_start: 0.8649 (m110) cc_final: 0.8247 (p0) REVERT: N 270 ASP cc_start: 0.8809 (m-30) cc_final: 0.8493 (t0) REVERT: N 354 GLN cc_start: 0.7650 (pt0) cc_final: 0.6995 (pt0) REVERT: N 379 ASP cc_start: 0.8837 (t0) cc_final: 0.8403 (t0) REVERT: N 385 ASN cc_start: 0.8550 (m-40) cc_final: 0.8097 (t0) REVERT: N 396 ASP cc_start: 0.8915 (p0) cc_final: 0.8700 (p0) REVERT: N 399 MET cc_start: 0.9332 (ttp) cc_final: 0.9052 (ppp) REVERT: P 286 ARG cc_start: 0.8077 (tmt-80) cc_final: 0.7572 (tmt-80) REVERT: P 288 MET cc_start: 0.8025 (mmp) cc_final: 0.7410 (mmp) REVERT: C 61 LYS cc_start: 0.9156 (mttt) cc_final: 0.8925 (mtmm) REVERT: C 64 ARG cc_start: 0.8615 (mtt90) cc_final: 0.8287 (mmm160) REVERT: C 65 ILE cc_start: 0.8729 (mm) cc_final: 0.8250 (tt) REVERT: C 99 LYS cc_start: 0.8742 (tppp) cc_final: 0.8192 (tptp) outliers start: 66 outliers final: 47 residues processed: 356 average time/residue: 0.2905 time to fit residues: 154.5409 Evaluate side-chains 337 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 287 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain K residue 700 MET Chi-restraints excluded: chain K residue 705 ASP Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 607 ASN Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain M residue 655 ASN Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 168 ASN Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 301 TRP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 0.0770 chunk 108 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 171 optimal weight: 50.0000 chunk 84 optimal weight: 7.9990 chunk 153 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS K 689 HIS L 191 ASN M 659 HIS N 38 HIS ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 HIS ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13736 Z= 0.378 Angle : 0.778 10.093 18701 Z= 0.403 Chirality : 0.047 0.198 2114 Planarity : 0.005 0.062 2439 Dihedral : 6.738 54.364 1925 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.00 % Favored : 88.64 % Rotamer: Outliers : 6.98 % Allowed : 17.96 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.25 % 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: -3.19 (0.19), residues: 1655 helix: -0.02 (0.27), residues: 348 sheet: -2.82 (0.25), residues: 312 loop : -2.79 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 218 HIS 0.007 0.001 HIS A 466 PHE 0.024 0.002 PHE N 243 TYR 0.033 0.002 TYR L 148 ARG 0.007 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 302 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8067 (m-10) cc_final: 0.7822 (m-10) REVERT: A 459 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8470 (mmtp) REVERT: A 487 ILE cc_start: 0.9045 (mt) cc_final: 0.8771 (mp) REVERT: K 276 GLN cc_start: 0.9122 (mm110) cc_final: 0.8133 (tp-100) REVERT: K 432 TRP cc_start: 0.6976 (m100) cc_final: 0.6658 (m100) REVERT: K 685 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8750 (ptm160) REVERT: K 701 MET cc_start: 0.9011 (tpp) cc_final: 0.8551 (tpp) REVERT: K 721 GLU cc_start: 0.9204 (tt0) cc_final: 0.8900 (tt0) REVERT: L 148 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7722 (p90) REVERT: L 181 GLN cc_start: 0.8452 (tt0) cc_final: 0.8126 (mm-40) REVERT: L 276 GLU cc_start: 0.9110 (tp30) cc_final: 0.8881 (tp30) REVERT: L 341 ASP cc_start: 0.8851 (m-30) cc_final: 0.8314 (t70) REVERT: L 357 ASP cc_start: 0.8881 (m-30) cc_final: 0.8521 (t0) REVERT: M 569 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8489 (p0) REVERT: M 586 GLU cc_start: 0.7339 (tt0) cc_final: 0.6292 (mm-30) REVERT: M 599 GLN cc_start: 0.8906 (tp40) cc_final: 0.8485 (tp-100) REVERT: M 634 HIS cc_start: 0.8936 (t-90) cc_final: 0.8499 (t-170) REVERT: M 653 CYS cc_start: 0.8061 (m) cc_final: 0.7123 (t) REVERT: M 676 LYS cc_start: 0.9086 (tttt) cc_final: 0.8586 (tptp) REVERT: N 122 ASN cc_start: 0.8714 (m110) cc_final: 0.8339 (p0) REVERT: N 177 GLN cc_start: 0.8780 (mp10) cc_final: 0.8426 (tm-30) REVERT: N 270 ASP cc_start: 0.8771 (m-30) cc_final: 0.8440 (t0) REVERT: N 379 ASP cc_start: 0.8848 (t0) cc_final: 0.8418 (t0) REVERT: N 385 ASN cc_start: 0.8707 (m-40) cc_final: 0.8232 (t0) REVERT: P 281 ASP cc_start: 0.9160 (p0) cc_final: 0.8914 (p0) REVERT: C 61 LYS cc_start: 0.9142 (mttt) cc_final: 0.8880 (mtmm) REVERT: C 64 ARG cc_start: 0.8701 (mtt90) cc_final: 0.8270 (mmm160) REVERT: C 65 ILE cc_start: 0.8880 (mm) cc_final: 0.8456 (mp) REVERT: C 99 LYS cc_start: 0.8820 (tppp) cc_final: 0.8337 (tptp) outliers start: 89 outliers final: 71 residues processed: 350 average time/residue: 0.2539 time to fit residues: 129.2851 Evaluate side-chains 354 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 280 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 685 ARG Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain K residue 700 MET Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 592 LEU Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 607 ASN Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain M residue 638 LEU Chi-restraints excluded: chain M residue 655 ASN Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 168 ASN Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 328 HIS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 389 VAL Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain N residue 394 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 50.0000 chunk 118 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 153 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 706 HIS L 160 HIS ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN M 620 HIS ** M 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 261 ASN ** P 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13736 Z= 0.386 Angle : 0.768 10.542 18701 Z= 0.398 Chirality : 0.047 0.189 2114 Planarity : 0.005 0.059 2439 Dihedral : 6.684 55.756 1925 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.69 % Favored : 88.94 % Rotamer: Outliers : 7.61 % Allowed : 19.92 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % 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: -3.17 (0.19), residues: 1655 helix: -0.04 (0.27), residues: 346 sheet: -2.80 (0.25), residues: 317 loop : -2.75 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 218 HIS 0.012 0.001 HIS M 659 PHE 0.024 0.002 PHE N 243 TYR 0.028 0.002 TYR L 148 ARG 0.006 0.001 ARG L 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 295 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8434 (mmtp) REVERT: A 487 ILE cc_start: 0.9098 (mt) cc_final: 0.8877 (mp) REVERT: K 276 GLN cc_start: 0.9159 (mm110) cc_final: 0.8171 (tp-100) REVERT: K 432 TRP cc_start: 0.7020 (m100) cc_final: 0.6678 (m100) REVERT: K 721 GLU cc_start: 0.9294 (tt0) cc_final: 0.9083 (tt0) REVERT: L 145 GLU cc_start: 0.8484 (pt0) cc_final: 0.8202 (pm20) REVERT: L 148 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7614 (p90) REVERT: L 181 GLN cc_start: 0.8497 (tt0) cc_final: 0.8169 (mm-40) REVERT: L 276 GLU cc_start: 0.9119 (tp30) cc_final: 0.8886 (tp30) REVERT: L 292 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8863 (mm-40) REVERT: L 357 ASP cc_start: 0.8757 (m-30) cc_final: 0.8400 (t0) REVERT: M 586 GLU cc_start: 0.7337 (tt0) cc_final: 0.6309 (mm-30) REVERT: M 599 GLN cc_start: 0.8933 (tp40) cc_final: 0.8486 (tp-100) REVERT: M 634 HIS cc_start: 0.8861 (t-90) cc_final: 0.8514 (t-170) REVERT: M 653 CYS cc_start: 0.8266 (m) cc_final: 0.7209 (t) REVERT: M 676 LYS cc_start: 0.9116 (tttt) cc_final: 0.8614 (tptp) REVERT: N 122 ASN cc_start: 0.8750 (m110) cc_final: 0.8345 (p0) REVERT: N 177 GLN cc_start: 0.8798 (mp10) cc_final: 0.8222 (tm-30) REVERT: N 270 ASP cc_start: 0.8793 (m-30) cc_final: 0.8433 (t0) REVERT: N 366 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8524 (tt) REVERT: N 379 ASP cc_start: 0.8840 (t0) cc_final: 0.8385 (t0) REVERT: N 385 ASN cc_start: 0.8690 (m-40) cc_final: 0.8201 (t0) REVERT: N 399 MET cc_start: 0.9332 (ttp) cc_final: 0.9016 (ppp) REVERT: P 281 ASP cc_start: 0.9194 (p0) cc_final: 0.8958 (p0) REVERT: Q 118 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8427 (mpp) REVERT: C 65 ILE cc_start: 0.8784 (mm) cc_final: 0.8286 (tt) REVERT: C 99 LYS cc_start: 0.8845 (tppp) cc_final: 0.8317 (tptp) REVERT: C 117 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8400 (mm-40) outliers start: 97 outliers final: 78 residues processed: 348 average time/residue: 0.2418 time to fit residues: 124.1863 Evaluate side-chains 359 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 278 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain K residue 700 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 592 LEU Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 607 ASN Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 629 ASP Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain M residue 638 LEU Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 253 MET Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 328 HIS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 389 VAL Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 288 MET Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 149 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.7980 chunk 154 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 171 optimal weight: 40.0000 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS L 160 HIS M 659 HIS N 261 ASN ** P 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13736 Z= 0.203 Angle : 0.694 10.913 18701 Z= 0.352 Chirality : 0.044 0.176 2114 Planarity : 0.004 0.050 2439 Dihedral : 6.112 58.542 1925 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.94 % Favored : 90.69 % Rotamer: Outliers : 4.55 % Allowed : 23.37 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % 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: -2.80 (0.19), residues: 1655 helix: 0.18 (0.28), residues: 348 sheet: -2.42 (0.28), residues: 297 loop : -2.56 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 218 HIS 0.008 0.001 HIS N 157 PHE 0.024 0.001 PHE N 243 TYR 0.026 0.001 TYR Q 117 ARG 0.007 0.001 ARG L 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 321 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8410 (mmtp) REVERT: A 487 ILE cc_start: 0.9112 (mt) cc_final: 0.8890 (mp) REVERT: K 276 GLN cc_start: 0.9107 (mm110) cc_final: 0.8148 (tp-100) REVERT: K 293 ASP cc_start: 0.8233 (t70) cc_final: 0.8021 (t70) REVERT: K 432 TRP cc_start: 0.6942 (m100) cc_final: 0.6585 (m100) REVERT: K 636 GLU cc_start: 0.8656 (tt0) cc_final: 0.8453 (tt0) REVERT: K 721 GLU cc_start: 0.9101 (tt0) cc_final: 0.8847 (tt0) REVERT: L 181 GLN cc_start: 0.8499 (tt0) cc_final: 0.8158 (mm-40) REVERT: L 251 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8322 (mt) REVERT: L 357 ASP cc_start: 0.8640 (m-30) cc_final: 0.8382 (t0) REVERT: L 390 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6915 (p0) REVERT: M 568 SER cc_start: 0.9056 (p) cc_final: 0.8592 (m) REVERT: M 586 GLU cc_start: 0.7240 (tt0) cc_final: 0.6373 (mm-30) REVERT: M 634 HIS cc_start: 0.8743 (t-90) cc_final: 0.8460 (t70) REVERT: M 641 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8737 (tm-30) REVERT: M 653 CYS cc_start: 0.8082 (m) cc_final: 0.7096 (t) REVERT: M 676 LYS cc_start: 0.9138 (tttt) cc_final: 0.8713 (tptp) REVERT: N 22 LYS cc_start: 0.9154 (tptt) cc_final: 0.8772 (tppp) REVERT: N 85 GLN cc_start: 0.7315 (tt0) cc_final: 0.7049 (mt0) REVERT: N 122 ASN cc_start: 0.8724 (m110) cc_final: 0.8218 (p0) REVERT: N 177 GLN cc_start: 0.8712 (mp10) cc_final: 0.8138 (tm-30) REVERT: N 270 ASP cc_start: 0.8798 (m-30) cc_final: 0.8440 (t0) REVERT: N 318 ASP cc_start: 0.8431 (t0) cc_final: 0.8186 (t0) REVERT: N 366 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8547 (tt) REVERT: N 379 ASP cc_start: 0.8790 (t0) cc_final: 0.8280 (t0) REVERT: N 385 ASN cc_start: 0.8500 (m-40) cc_final: 0.8204 (t0) REVERT: N 399 MET cc_start: 0.9272 (ttp) cc_final: 0.9019 (ppp) REVERT: P 281 ASP cc_start: 0.9134 (p0) cc_final: 0.8900 (p0) REVERT: C 54 GLU cc_start: 0.9275 (tm-30) cc_final: 0.9053 (tm-30) REVERT: C 65 ILE cc_start: 0.8830 (mm) cc_final: 0.8349 (tt) REVERT: C 66 GLN cc_start: 0.9141 (pt0) cc_final: 0.8834 (pm20) REVERT: C 99 LYS cc_start: 0.8848 (tppp) cc_final: 0.8359 (tptp) REVERT: C 116 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8059 (tp) outliers start: 58 outliers final: 43 residues processed: 349 average time/residue: 0.2416 time to fit residues: 124.1306 Evaluate side-chains 335 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 288 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 160 HIS Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 390 ASP Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 629 ASP Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 398 ILE Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 10.0000 chunk 19 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 50.0000 chunk 95 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 106 optimal weight: 0.0000 chunk 104 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS L 191 ASN L 292 GLN N 261 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13736 Z= 0.345 Angle : 0.750 11.181 18701 Z= 0.383 Chirality : 0.046 0.212 2114 Planarity : 0.004 0.047 2439 Dihedral : 6.269 54.722 1925 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.69 % Favored : 88.94 % Rotamer: Outliers : 5.80 % Allowed : 23.61 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % 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: -2.92 (0.19), residues: 1655 helix: 0.08 (0.27), residues: 350 sheet: -2.53 (0.27), residues: 308 loop : -2.62 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 205 HIS 0.008 0.001 HIS M 659 PHE 0.034 0.002 PHE M 626 TYR 0.027 0.002 TYR L 148 ARG 0.004 0.001 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 292 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8433 (mmtp) REVERT: A 487 ILE cc_start: 0.9152 (mt) cc_final: 0.8941 (mp) REVERT: K 276 GLN cc_start: 0.9123 (mm110) cc_final: 0.8227 (tp-100) REVERT: K 636 GLU cc_start: 0.8731 (tt0) cc_final: 0.8428 (tt0) REVERT: L 145 GLU cc_start: 0.8486 (pm20) cc_final: 0.8166 (pm20) REVERT: L 148 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7791 (p90) REVERT: L 181 GLN cc_start: 0.8512 (tt0) cc_final: 0.8181 (mm-40) REVERT: L 292 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8907 (mm-40) REVERT: L 357 ASP cc_start: 0.8665 (m-30) cc_final: 0.8425 (t0) REVERT: L 360 GLN cc_start: 0.8708 (mt0) cc_final: 0.8134 (mp10) REVERT: L 390 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6945 (p0) REVERT: M 586 GLU cc_start: 0.7351 (tt0) cc_final: 0.6542 (mm-30) REVERT: M 634 HIS cc_start: 0.8731 (t-90) cc_final: 0.8398 (t-170) REVERT: M 653 CYS cc_start: 0.8272 (m) cc_final: 0.7235 (t) REVERT: M 676 LYS cc_start: 0.9137 (tttt) cc_final: 0.8684 (tptp) REVERT: N 122 ASN cc_start: 0.8751 (m110) cc_final: 0.8335 (p0) REVERT: N 177 GLN cc_start: 0.8805 (mp10) cc_final: 0.8195 (tm-30) REVERT: N 270 ASP cc_start: 0.8837 (m-30) cc_final: 0.8499 (t0) REVERT: N 366 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8599 (tt) REVERT: N 379 ASP cc_start: 0.8797 (t0) cc_final: 0.8323 (t0) REVERT: N 385 ASN cc_start: 0.8623 (m-40) cc_final: 0.8289 (t0) REVERT: N 399 MET cc_start: 0.9320 (ttp) cc_final: 0.9013 (ppp) REVERT: Q 118 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8511 (mpp) REVERT: C 54 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9039 (tm-30) REVERT: C 65 ILE cc_start: 0.8891 (mm) cc_final: 0.8425 (tt) REVERT: C 99 LYS cc_start: 0.8875 (tppp) cc_final: 0.8343 (tptp) REVERT: C 121 MET cc_start: 0.8885 (tpt) cc_final: 0.8075 (mtp) outliers start: 74 outliers final: 62 residues processed: 332 average time/residue: 0.2444 time to fit residues: 120.8110 Evaluate side-chains 352 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 286 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 586 LEU Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 390 ASP Chi-restraints excluded: chain L residue 407 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 629 ASP Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 328 HIS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 389 VAL Chi-restraints excluded: chain N residue 398 ILE Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 659 HIS ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13736 Z= 0.229 Angle : 0.702 10.570 18701 Z= 0.356 Chirality : 0.045 0.179 2114 Planarity : 0.004 0.042 2439 Dihedral : 5.966 57.082 1925 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.31 % Favored : 90.39 % Rotamer: Outliers : 5.18 % Allowed : 24.24 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % 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: -2.73 (0.19), residues: 1655 helix: 0.24 (0.28), residues: 351 sheet: -2.26 (0.29), residues: 288 loop : -2.56 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 205 HIS 0.005 0.001 HIS L 160 PHE 0.026 0.001 PHE M 626 TYR 0.030 0.001 TYR Q 117 ARG 0.004 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 314 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8402 (mmtp) REVERT: A 487 ILE cc_start: 0.9140 (mt) cc_final: 0.8933 (mp) REVERT: K 276 GLN cc_start: 0.9063 (mm110) cc_final: 0.8208 (tp-100) REVERT: K 432 TRP cc_start: 0.6898 (m100) cc_final: 0.6482 (m100) REVERT: K 636 GLU cc_start: 0.8661 (tt0) cc_final: 0.8365 (tt0) REVERT: K 705 ASP cc_start: 0.9040 (t70) cc_final: 0.8550 (p0) REVERT: L 148 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7806 (p90) REVERT: L 181 GLN cc_start: 0.8501 (tt0) cc_final: 0.8179 (mm-40) REVERT: L 184 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8075 (ttmm) REVERT: L 251 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8291 (mt) REVERT: L 336 MET cc_start: 0.7034 (tmm) cc_final: 0.6800 (tpp) REVERT: L 357 ASP cc_start: 0.8614 (m-30) cc_final: 0.8392 (t0) REVERT: L 374 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8851 (mm-40) REVERT: L 390 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6269 (m-30) REVERT: M 586 GLU cc_start: 0.7293 (tt0) cc_final: 0.6631 (mm-30) REVERT: M 634 HIS cc_start: 0.8734 (t-90) cc_final: 0.8409 (t-170) REVERT: M 641 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8788 (tm-30) REVERT: M 653 CYS cc_start: 0.8175 (m) cc_final: 0.7059 (t) REVERT: M 676 LYS cc_start: 0.9110 (tttt) cc_final: 0.8703 (tptp) REVERT: N 85 GLN cc_start: 0.7371 (tt0) cc_final: 0.7092 (mt0) REVERT: N 177 GLN cc_start: 0.8738 (mp10) cc_final: 0.8117 (tm-30) REVERT: N 270 ASP cc_start: 0.8840 (m-30) cc_final: 0.8493 (t0) REVERT: N 342 LEU cc_start: 0.9477 (tp) cc_final: 0.9087 (tt) REVERT: N 366 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8645 (tt) REVERT: N 379 ASP cc_start: 0.8801 (t0) cc_final: 0.8273 (t0) REVERT: N 385 ASN cc_start: 0.8501 (m-40) cc_final: 0.8221 (t0) REVERT: N 396 ASP cc_start: 0.9040 (p0) cc_final: 0.8836 (t70) REVERT: N 399 MET cc_start: 0.9311 (ttp) cc_final: 0.9059 (ppp) REVERT: Q 118 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8574 (mpp) REVERT: C 54 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9037 (tm-30) REVERT: C 65 ILE cc_start: 0.9039 (mm) cc_final: 0.8494 (tt) REVERT: C 99 LYS cc_start: 0.8876 (tppp) cc_final: 0.8390 (tptp) REVERT: C 121 MET cc_start: 0.8900 (tpt) cc_final: 0.8006 (mtp) outliers start: 66 outliers final: 52 residues processed: 352 average time/residue: 0.2362 time to fit residues: 123.2222 Evaluate side-chains 346 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 288 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 390 ASP Chi-restraints excluded: chain L residue 397 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 629 ASP Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 398 ILE Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 144 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 40.0000 chunk 149 optimal weight: 40.0000 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 chunk 104 optimal weight: 0.0570 chunk 168 optimal weight: 9.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 620 HIS M 659 HIS N 261 ASN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13736 Z= 0.291 Angle : 0.743 11.895 18701 Z= 0.377 Chirality : 0.046 0.208 2114 Planarity : 0.004 0.042 2439 Dihedral : 6.041 56.180 1925 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.69 % Favored : 89.00 % Rotamer: Outliers : 6.27 % Allowed : 23.37 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % 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: -2.77 (0.19), residues: 1655 helix: 0.13 (0.27), residues: 351 sheet: -2.22 (0.29), residues: 297 loop : -2.58 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 218 HIS 0.005 0.001 HIS A 466 PHE 0.025 0.002 PHE A 429 TYR 0.023 0.002 TYR L 148 ARG 0.004 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 294 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8408 (mmtp) REVERT: A 487 ILE cc_start: 0.9144 (mt) cc_final: 0.8937 (mp) REVERT: K 276 GLN cc_start: 0.9087 (mm110) cc_final: 0.8247 (tp-100) REVERT: K 432 TRP cc_start: 0.6935 (m100) cc_final: 0.6500 (m100) REVERT: K 636 GLU cc_start: 0.8704 (tt0) cc_final: 0.8420 (tt0) REVERT: K 705 ASP cc_start: 0.9048 (t70) cc_final: 0.8545 (p0) REVERT: L 148 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7881 (p90) REVERT: L 181 GLN cc_start: 0.8472 (tt0) cc_final: 0.8198 (mm-40) REVERT: L 184 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8080 (ttmm) REVERT: L 251 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8236 (mt) REVERT: L 374 GLN cc_start: 0.9250 (mm-40) cc_final: 0.8941 (mm-40) REVERT: L 390 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: M 586 GLU cc_start: 0.7232 (tt0) cc_final: 0.6686 (mm-30) REVERT: M 634 HIS cc_start: 0.8755 (t-90) cc_final: 0.8459 (t-170) REVERT: M 641 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8789 (tm-30) REVERT: M 653 CYS cc_start: 0.8267 (m) cc_final: 0.7118 (t) REVERT: M 676 LYS cc_start: 0.9119 (tttt) cc_final: 0.8698 (tptp) REVERT: N 41 GLU cc_start: 0.8854 (pt0) cc_final: 0.8294 (tm-30) REVERT: N 85 GLN cc_start: 0.7366 (tt0) cc_final: 0.7069 (mt0) REVERT: N 177 GLN cc_start: 0.8772 (mp10) cc_final: 0.8131 (tm-30) REVERT: N 270 ASP cc_start: 0.8872 (m-30) cc_final: 0.8503 (t0) REVERT: N 342 LEU cc_start: 0.9487 (tp) cc_final: 0.9219 (tt) REVERT: N 366 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8679 (tt) REVERT: N 379 ASP cc_start: 0.8783 (t0) cc_final: 0.8299 (t0) REVERT: N 385 ASN cc_start: 0.8563 (m-40) cc_final: 0.8280 (t0) REVERT: N 396 ASP cc_start: 0.9052 (p0) cc_final: 0.8794 (t70) REVERT: N 399 MET cc_start: 0.9330 (ttp) cc_final: 0.9088 (ppp) REVERT: C 54 GLU cc_start: 0.9325 (tm-30) cc_final: 0.9082 (tm-30) REVERT: C 99 LYS cc_start: 0.8901 (tppp) cc_final: 0.8364 (tptp) REVERT: C 121 MET cc_start: 0.8906 (tpt) cc_final: 0.7943 (mtp) outliers start: 80 outliers final: 65 residues processed: 341 average time/residue: 0.2364 time to fit residues: 119.7392 Evaluate side-chains 354 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 284 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 160 HIS Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 315 LEU Chi-restraints excluded: chain L residue 390 ASP Chi-restraints excluded: chain L residue 397 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 629 ASP Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 328 HIS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 398 ILE Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 176 optimal weight: 0.0050 chunk 162 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 40.0000 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 620 HIS N 261 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13736 Z= 0.252 Angle : 0.727 10.923 18701 Z= 0.370 Chirality : 0.045 0.241 2114 Planarity : 0.004 0.043 2439 Dihedral : 5.964 57.459 1925 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.67 % Favored : 90.09 % Rotamer: Outliers : 5.18 % Allowed : 24.39 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % 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: -2.68 (0.19), residues: 1655 helix: 0.01 (0.27), residues: 363 sheet: -2.16 (0.29), residues: 295 loop : -2.46 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 218 HIS 0.008 0.001 HIS M 659 PHE 0.041 0.002 PHE M 656 TYR 0.022 0.002 TYR L 308 ARG 0.004 0.000 ARG A 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 292 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8373 (mmtp) REVERT: A 487 ILE cc_start: 0.9131 (mt) cc_final: 0.8929 (mp) REVERT: K 276 GLN cc_start: 0.9096 (mm110) cc_final: 0.8255 (tp-100) REVERT: K 432 TRP cc_start: 0.6965 (m100) cc_final: 0.6490 (m100) REVERT: K 636 GLU cc_start: 0.8689 (tt0) cc_final: 0.8367 (tt0) REVERT: K 705 ASP cc_start: 0.9055 (t70) cc_final: 0.8559 (p0) REVERT: L 148 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7889 (p90) REVERT: L 181 GLN cc_start: 0.8470 (tt0) cc_final: 0.8225 (mm-40) REVERT: L 184 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8063 (ttmm) REVERT: L 251 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8292 (mt) REVERT: L 374 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8949 (mm-40) REVERT: L 390 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6370 (m-30) REVERT: M 586 GLU cc_start: 0.7117 (tt0) cc_final: 0.6706 (mm-30) REVERT: M 631 GLN cc_start: 0.7786 (mt0) cc_final: 0.7247 (mt0) REVERT: M 634 HIS cc_start: 0.8773 (t-90) cc_final: 0.8443 (t-170) REVERT: M 641 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8786 (tm-30) REVERT: M 653 CYS cc_start: 0.8289 (m) cc_final: 0.7122 (t) REVERT: M 676 LYS cc_start: 0.9123 (tttt) cc_final: 0.8716 (tptp) REVERT: N 41 GLU cc_start: 0.8859 (pt0) cc_final: 0.8282 (tm-30) REVERT: N 270 ASP cc_start: 0.8868 (m-30) cc_final: 0.8496 (t0) REVERT: N 342 LEU cc_start: 0.9477 (tp) cc_final: 0.9206 (tt) REVERT: N 366 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8670 (tt) REVERT: N 379 ASP cc_start: 0.8797 (t0) cc_final: 0.8291 (t0) REVERT: N 385 ASN cc_start: 0.8524 (m-40) cc_final: 0.8249 (t0) REVERT: N 396 ASP cc_start: 0.9022 (p0) cc_final: 0.8786 (t70) REVERT: N 399 MET cc_start: 0.9326 (ttp) cc_final: 0.9101 (ppp) REVERT: C 54 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9079 (tm-30) REVERT: C 65 ILE cc_start: 0.8706 (mp) cc_final: 0.8495 (mp) REVERT: C 99 LYS cc_start: 0.8891 (tppp) cc_final: 0.8361 (tptp) REVERT: C 121 MET cc_start: 0.8899 (tpt) cc_final: 0.7910 (mtp) outliers start: 66 outliers final: 58 residues processed: 329 average time/residue: 0.2448 time to fit residues: 119.3555 Evaluate side-chains 349 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 286 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 525 HIS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 599 VAL Chi-restraints excluded: chain K residue 642 CYS Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 691 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 160 HIS Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 390 ASP Chi-restraints excluded: chain L residue 397 HIS Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 600 ILE Chi-restraints excluded: chain M residue 610 GLU Chi-restraints excluded: chain M residue 627 ILE Chi-restraints excluded: chain M residue 629 ASP Chi-restraints excluded: chain M residue 637 MET Chi-restraints excluded: chain M residue 638 LEU Chi-restraints excluded: chain M residue 659 HIS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 133 MET Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 246 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 328 HIS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 398 ILE Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 118 MET Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 144 optimal weight: 50.0000 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 689 HIS ** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 620 HIS M 659 HIS ** N 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.133906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110681 restraints weight = 26773.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110620 restraints weight = 24050.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111573 restraints weight = 25196.059| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13736 Z= 0.277 Angle : 0.737 10.624 18701 Z= 0.375 Chirality : 0.046 0.238 2114 Planarity : 0.004 0.042 2439 Dihedral : 5.969 57.499 1925 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.15 % Favored : 89.61 % Rotamer: Outliers : 5.96 % Allowed : 23.69 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.19 % 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: -2.65 (0.19), residues: 1655 helix: 0.15 (0.27), residues: 351 sheet: -2.12 (0.29), residues: 295 loop : -2.47 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 218 HIS 0.005 0.001 HIS A 466 PHE 0.026 0.002 PHE A 429 TYR 0.030 0.002 TYR L 308 ARG 0.004 0.000 ARG E 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3029.72 seconds wall clock time: 60 minutes 10.52 seconds (3610.52 seconds total)