Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 05:03:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acj_9593/07_2023/6acj_9593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acj_9593/07_2023/6acj_9593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acj_9593/07_2023/6acj_9593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acj_9593/07_2023/6acj_9593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acj_9593/07_2023/6acj_9593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acj_9593/07_2023/6acj_9593.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.871 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 164 5.16 5 C 18987 2.51 5 N 4918 2.21 5 O 5646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A ARG 1021": "NH1" <-> "NH2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1001": "NH1" <-> "NH2" Residue "B ARG 1021": "NH1" <-> "NH2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1021": "NH1" <-> "NH2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1073": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 29715 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8241 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1006} Chain breaks: 5 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 13.81, per 1000 atoms: 0.46 Number of scatterers: 29715 At special positions: 0 Unit cell: (146.52, 176.88, 219.12, 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 164 16.00 O 5646 8.00 N 4918 7.00 C 18987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.01 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.01 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.02 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.04 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.01 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.00 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.73 Conformation dependent library (CDL) restraints added in 4.7 seconds 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 43 sheets defined 27.8% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 371 through 375 removed outlier: 4.102A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.553A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 488 through 492 removed outlier: 4.030A pdb=" N GLN A 492 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 729 through 738 removed outlier: 3.842A pdb=" N ASN A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 848 through 864 Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.620A pdb=" N MET A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 removed outlier: 4.095A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.921A pdb=" N ALA A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 4.480A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 965 removed outlier: 3.515A pdb=" N SER A 964 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1013 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 371 through 377 removed outlier: 3.676A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 488 through 492 removed outlier: 4.082A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.627A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 738 removed outlier: 3.565A pdb=" N TYR B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 765 Processing helix chain 'B' and resid 798 through 808 Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 880 through 888 Processing helix chain 'B' and resid 901 through 920 Processing helix chain 'B' and resid 927 through 949 removed outlier: 4.601A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 966 removed outlier: 3.825A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1017 removed outlier: 4.197A pdb=" N VAL B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.851A pdb=" N TYR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.789A pdb=" N SER C 607 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 removed outlier: 4.079A pdb=" N ASN C 733 " --> pdb=" O THR C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 888 removed outlier: 3.571A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 removed outlier: 4.709A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 4.289A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 removed outlier: 4.035A pdb=" N LEU C 966 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1013 removed outlier: 4.125A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.598A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 63 Processing helix chain 'D' and resid 63 through 81 removed outlier: 3.856A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 102 Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.823A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.596A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 3.926A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 219 through 231 removed outlier: 4.105A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 252 removed outlier: 4.576A pdb=" N LEU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.689A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.653A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.815A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 398 through 413 removed outlier: 4.410A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 4.018A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 466 removed outlier: 4.191A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.009A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.605A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.086A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.545A pdb=" N SER D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.508A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix removed outlier: 3.617A pdb=" N ASN D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 8.267A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE A 203 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 182 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 201 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 8.267A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 194 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 59 removed outlier: 4.079A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 140 removed outlier: 5.543A pdb=" N ALA A 237 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 306 removed outlier: 3.959A pdb=" N VAL A 583 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 6.979A pdb=" N GLY A 311 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ASN A 528 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.525A pdb=" N PHE A 387 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AB1, first strand: chain 'A' and resid 650 through 651 removed outlier: 3.696A pdb=" N ILE A 650 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 705 through 710 removed outlier: 3.821A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 705 through 710 removed outlier: 3.821A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 1069 through 1070 removed outlier: 3.705A pdb=" N SER A1105 " --> pdb=" O ALA A1069 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 34 removed outlier: 8.327A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 67 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 71 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 219 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 55 through 59 removed outlier: 4.327A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.262A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 137 through 141 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 304 removed outlier: 5.694A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 637 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.955A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 345 removed outlier: 5.125A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 383 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 500 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 387 " --> pdb=" O VAL B 496 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 657 through 658 Processing sheet with id=AC6, first strand: chain 'B' and resid 700 through 701 removed outlier: 3.608A pdb=" N VAL B1050 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 710 Processing sheet with id=AC8, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AC9, first strand: chain 'B' and resid 1032 through 1033 Processing sheet with id=AD1, first strand: chain 'C' and resid 31 through 34 Processing sheet with id=AD2, first strand: chain 'C' and resid 54 through 59 removed outlier: 4.157A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AD4, first strand: chain 'C' and resid 217 through 222 removed outlier: 6.907A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR C 197 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 87 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 92 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 removed outlier: 6.318A pdb=" N GLY C 311 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASN C 528 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 341 through 345 removed outlier: 5.430A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.530A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AE2, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.974A pdb=" N SER C 703 " --> pdb=" O THR C1048 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR C1048 " --> pdb=" O SER C 703 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 705 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C1034 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AE4, first strand: chain 'C' and resid 1078 through 1079 Processing sheet with id=AE5, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE6, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.813A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 347 through 350 1047 hydrogen bonds defined for protein. 2919 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: 12.13 Time building geometry restraints manager: 13.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 4901 1.27 - 1.41: 8033 1.41 - 1.56: 17272 1.56 - 1.71: 2 1.71 - 1.85: 232 Bond restraints: 30440 Sorted by residual: bond pdb=" CA THR C 678 " pdb=" C THR C 678 " ideal model delta sigma weight residual 1.523 1.371 0.152 1.34e-02 5.57e+03 1.29e+02 bond pdb=" CA TYR C 677 " pdb=" C TYR C 677 " ideal model delta sigma weight residual 1.523 1.390 0.134 1.34e-02 5.57e+03 9.95e+01 bond pdb=" C ALA C 676 " pdb=" O ALA C 676 " ideal model delta sigma weight residual 1.235 1.121 0.114 1.26e-02 6.30e+03 8.20e+01 bond pdb=" N VAL C 642 " pdb=" CA VAL C 642 " ideal model delta sigma weight residual 1.457 1.352 0.105 1.22e-02 6.72e+03 7.39e+01 bond pdb=" C TYR C 677 " pdb=" O TYR C 677 " ideal model delta sigma weight residual 1.235 1.137 0.099 1.26e-02 6.30e+03 6.13e+01 ... (remaining 30435 not shown) Histogram of bond angle deviations from ideal: 96.17 - 104.06: 507 104.06 - 111.95: 13850 111.95 - 119.83: 12265 119.83 - 127.72: 14526 127.72 - 135.60: 268 Bond angle restraints: 41416 Sorted by residual: angle pdb=" CA HIS C 641 " pdb=" C HIS C 641 " pdb=" N VAL C 642 " ideal model delta sigma weight residual 115.29 102.64 12.65 1.18e+00 7.18e-01 1.15e+02 angle pdb=" C GLU C 647 " pdb=" N CYS C 648 " pdb=" CA CYS C 648 " ideal model delta sigma weight residual 121.54 103.65 17.89 1.91e+00 2.74e-01 8.77e+01 angle pdb=" C VAL C 642 " pdb=" CA VAL C 642 " pdb=" CB VAL C 642 " ideal model delta sigma weight residual 111.26 97.40 13.86 1.52e+00 4.33e-01 8.32e+01 angle pdb=" N ILE B 891 " pdb=" CA ILE B 891 " pdb=" C ILE B 891 " ideal model delta sigma weight residual 113.47 104.27 9.20 1.01e+00 9.80e-01 8.30e+01 angle pdb=" O HIS C 641 " pdb=" C HIS C 641 " pdb=" N VAL C 642 " ideal model delta sigma weight residual 122.29 133.67 -11.38 1.40e+00 5.10e-01 6.61e+01 ... (remaining 41411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 17027 18.08 - 36.16: 873 36.16 - 54.25: 140 54.25 - 72.33: 26 72.33 - 90.41: 9 Dihedral angle restraints: 18075 sinusoidal: 7035 harmonic: 11040 Sorted by residual: dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -113.22 -66.78 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA GLU A1074 " pdb=" C GLU A1074 " pdb=" N GLY A1075 " pdb=" CA GLY A1075 " ideal model delta harmonic sigma weight residual -180.00 -115.07 -64.93 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" CB CYS C 603 " pdb=" SG CYS C 603 " pdb=" SG CYS C 635 " pdb=" CB CYS C 635 " ideal model delta sinusoidal sigma weight residual -86.00 -176.41 90.41 1 1.00e+01 1.00e-02 9.67e+01 ... (remaining 18072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 4534 0.166 - 0.333: 90 0.333 - 0.499: 2 0.499 - 0.666: 1 0.666 - 0.832: 1 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CA TYR C 646 " pdb=" N TYR C 646 " pdb=" C TYR C 646 " pdb=" CB TYR C 646 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CA TYR C 677 " pdb=" N TYR C 677 " pdb=" C TYR C 677 " pdb=" CB TYR C 677 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CB VAL C 642 " pdb=" CA VAL C 642 " pdb=" CG1 VAL C 642 " pdb=" CG2 VAL C 642 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 4625 not shown) Planarity restraints: 5366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 678 " 0.027 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C THR C 678 " -0.091 2.00e-02 2.50e+03 pdb=" O THR C 678 " 0.035 2.00e-02 2.50e+03 pdb=" N MET C 679 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 677 " -0.017 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR C 677 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR C 677 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 677 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 677 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 677 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR C 677 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR C 677 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 641 " 0.018 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C HIS C 641 " -0.072 2.00e-02 2.50e+03 pdb=" O HIS C 641 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL C 642 " 0.025 2.00e-02 2.50e+03 ... (remaining 5363 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 104 2.36 - 3.00: 16089 3.00 - 3.63: 45193 3.63 - 4.27: 69455 4.27 - 4.90: 110117 Nonbonded interactions: 240958 Sorted by model distance: nonbonded pdb=" OE1 GLU C 647 " pdb=" OG SER C 680 " model vdw 1.731 2.440 nonbonded pdb=" O GLU C 647 " pdb=" CB CYS C 648 " model vdw 1.774 3.440 nonbonded pdb=" O GLY C 655 " pdb=" O THR C 678 " model vdw 1.827 3.040 nonbonded pdb=" CB TYR C 646 " pdb=" CE2 TYR C 677 " model vdw 1.896 3.740 nonbonded pdb=" OG1 THR C 678 " pdb=" N MET C 679 " model vdw 2.034 2.520 ... (remaining 240953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = (chain 'B' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.090 Check model and map are aligned: 0.490 Set scattering table: 0.270 Process input model: 75.380 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.010 0.152 30440 Z= 0.625 Angle : 1.335 17.888 41416 Z= 0.757 Chirality : 0.069 0.832 4628 Planarity : 0.009 0.078 5366 Dihedral : 11.276 77.450 10850 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.59 % Allowed : 16.76 % Favored : 82.66 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 1.45 % 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 (0.11), residues: 3754 helix: -2.38 (0.13), residues: 955 sheet: -2.32 (0.23), residues: 452 loop : -3.93 (0.10), residues: 2347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 603 time to evaluate : 3.667 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 620 average time/residue: 0.4282 time to fit residues: 419.0943 Evaluate side-chains 326 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 319 time to evaluate : 3.512 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2713 time to fit residues: 8.1500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 341 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 181 HIS A 301 GLN A 589 ASN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN A 737 GLN A 759 ASN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 877 GLN A 889 ASN A 907 ASN A 931 GLN A 935 ASN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN B 70 HIS B 135 ASN ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 GLN ** B 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B 939 GLN B1095 GLN B1101 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 155 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 357 ASN C 473 ASN C 479 ASN C 632 GLN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 915 GLN ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C 993 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN D 239 HIS D 250 ASN D 437 ASN D 526 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 30440 Z= 0.261 Angle : 0.801 10.699 41416 Z= 0.429 Chirality : 0.049 0.270 4628 Planarity : 0.006 0.065 5366 Dihedral : 8.250 67.332 4064 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.05 % Favored : 86.65 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.89 (0.12), residues: 3754 helix: -1.05 (0.15), residues: 971 sheet: -2.09 (0.23), residues: 473 loop : -3.62 (0.11), residues: 2310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 473 time to evaluate : 3.787 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 477 average time/residue: 0.4118 time to fit residues: 315.7360 Evaluate side-chains 319 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 316 time to evaluate : 3.830 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3037 time to fit residues: 6.3748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 232 optimal weight: 0.0670 chunk 94 optimal weight: 2.9990 chunk 342 optimal weight: 30.0000 chunk 369 optimal weight: 40.0000 chunk 304 optimal weight: 2.9990 chunk 339 optimal weight: 40.0000 chunk 116 optimal weight: 7.9990 chunk 274 optimal weight: 0.0670 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 505 ASN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN B 744 GLN B 759 ASN ** B 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN C 546 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN C 939 GLN C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 522 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 30440 Z= 0.237 Angle : 0.743 10.088 41416 Z= 0.394 Chirality : 0.047 0.252 4628 Planarity : 0.005 0.063 5366 Dihedral : 7.542 65.188 4064 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.01 % Favored : 85.75 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.45 (0.13), residues: 3754 helix: -0.41 (0.16), residues: 985 sheet: -1.91 (0.22), residues: 497 loop : -3.48 (0.11), residues: 2272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 3.328 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: symmetry clash outliers start: 4 outliers final: 2 residues processed: 423 average time/residue: 0.4080 time to fit residues: 280.5965 Evaluate side-chains 299 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 3.272 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2544 time to fit residues: 5.6041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 20.0000 chunk 257 optimal weight: 30.0000 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 343 optimal weight: 30.0000 chunk 363 optimal weight: 30.0000 chunk 179 optimal weight: 3.9990 chunk 325 optimal weight: 0.0070 chunk 97 optimal weight: 8.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN B 769 GLN B 947 GLN B 984 GLN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 549 GLN C 759 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 33 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 30440 Z= 0.237 Angle : 0.729 12.111 41416 Z= 0.384 Chirality : 0.047 0.233 4628 Planarity : 0.005 0.056 5366 Dihedral : 7.214 64.236 4064 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.51 % Favored : 86.28 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.18 (0.13), residues: 3754 helix: 0.00 (0.16), residues: 973 sheet: -1.71 (0.23), residues: 490 loop : -3.39 (0.11), residues: 2291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 408 time to evaluate : 3.311 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 409 average time/residue: 0.4051 time to fit residues: 270.0862 Evaluate side-chains 292 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 3.744 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2660 time to fit residues: 5.4759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 270 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 chunk 326 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 ASN B 947 GLN B 984 GLN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 280 GLN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 942 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 30440 Z= 0.356 Angle : 0.813 11.804 41416 Z= 0.427 Chirality : 0.049 0.238 4628 Planarity : 0.006 0.070 5366 Dihedral : 7.336 60.021 4064 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.93 % Favored : 83.83 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.23 (0.13), residues: 3754 helix: -0.16 (0.16), residues: 984 sheet: -1.72 (0.24), residues: 486 loop : -3.38 (0.12), residues: 2284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 370 time to evaluate : 4.290 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: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 372 average time/residue: 0.4245 time to fit residues: 259.7685 Evaluate side-chains 267 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2616 time to fit residues: 4.8915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 363 optimal weight: 30.0000 chunk 301 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 632 GLN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B 883 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 30440 Z= 0.326 Angle : 0.787 12.837 41416 Z= 0.413 Chirality : 0.048 0.227 4628 Planarity : 0.005 0.057 5366 Dihedral : 7.274 61.019 4064 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.89 % Favored : 84.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.20 (0.13), residues: 3754 helix: -0.08 (0.16), residues: 986 sheet: -1.66 (0.24), residues: 491 loop : -3.41 (0.12), residues: 2277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 3.532 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.4020 time to fit residues: 238.3595 Evaluate side-chains 262 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.574 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 205 optimal weight: 0.0010 chunk 306 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 362 optimal weight: 40.0000 chunk 226 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 149 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 30440 Z= 0.229 Angle : 0.719 10.901 41416 Z= 0.378 Chirality : 0.047 0.240 4628 Planarity : 0.005 0.056 5366 Dihedral : 6.918 62.039 4064 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.99 % Favored : 85.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.95 (0.13), residues: 3754 helix: 0.19 (0.16), residues: 981 sheet: -1.43 (0.24), residues: 481 loop : -3.29 (0.12), residues: 2292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 3.438 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 outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.4024 time to fit residues: 256.0549 Evaluate side-chains 271 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 246 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 284 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 149 HIS B 280 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 30440 Z= 0.291 Angle : 0.759 12.646 41416 Z= 0.397 Chirality : 0.048 0.266 4628 Planarity : 0.005 0.079 5366 Dihedral : 6.901 61.005 4064 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.89 % Favored : 84.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.98 (0.13), residues: 3754 helix: 0.20 (0.16), residues: 980 sheet: -1.51 (0.23), residues: 517 loop : -3.32 (0.12), residues: 2257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 3.449 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 outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.4108 time to fit residues: 237.1984 Evaluate side-chains 251 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 3.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 20.0000 chunk 347 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 chunk 337 optimal weight: 0.0050 chunk 203 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 319 optimal weight: 20.0000 chunk 336 optimal weight: 0.6980 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 632 GLN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 759 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 835 GLN ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 30440 Z= 0.242 Angle : 0.720 11.905 41416 Z= 0.377 Chirality : 0.047 0.229 4628 Planarity : 0.005 0.056 5366 Dihedral : 6.741 62.231 4064 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.80 % Favored : 86.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.87 (0.13), residues: 3754 helix: 0.31 (0.16), residues: 982 sheet: -1.34 (0.23), residues: 526 loop : -3.30 (0.12), residues: 2246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 3.505 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 outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.4017 time to fit residues: 233.6294 Evaluate side-chains 260 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 4.9990 chunk 357 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 20.0000 chunk 374 optimal weight: 10.0000 chunk 344 optimal weight: 30.0000 chunk 298 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 230 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 632 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 838 ASN B 947 GLN B 984 GLN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 30440 Z= 0.220 Angle : 0.715 11.401 41416 Z= 0.373 Chirality : 0.047 0.229 4628 Planarity : 0.005 0.055 5366 Dihedral : 6.583 61.297 4064 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.40 % Favored : 86.44 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 (0.13), residues: 3754 helix: 0.35 (0.17), residues: 980 sheet: -1.22 (0.24), residues: 503 loop : -3.25 (0.12), residues: 2271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 3.399 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 outliers start: 2 outliers final: 1 residues processed: 350 average time/residue: 0.4156 time to fit residues: 242.1261 Evaluate side-chains 271 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 3.478 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3389 time to fit residues: 5.3533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 9.9990 chunk 317 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 275 optimal weight: 0.0970 chunk 44 optimal weight: 0.0020 chunk 82 optimal weight: 4.9990 chunk 298 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 70 HIS B 135 ASN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 49 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.132616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.102862 restraints weight = 109584.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.102244 restraints weight = 78570.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.102924 restraints weight = 64094.416| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 30440 Z= 0.193 Angle : 0.684 11.118 41416 Z= 0.357 Chirality : 0.046 0.215 4628 Planarity : 0.005 0.055 5366 Dihedral : 6.386 60.529 4064 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.41 % Favored : 87.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.61 (0.13), residues: 3754 helix: 0.55 (0.17), residues: 968 sheet: -1.14 (0.25), residues: 501 loop : -3.12 (0.12), residues: 2285 =============================================================================== Job complete usr+sys time: 5814.12 seconds wall clock time: 107 minutes 30.91 seconds (6450.91 seconds total)