Starting phenix.real_space_refine on Sat Jan 20 07:39:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr0_14875/01_2024/7zr0_14875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr0_14875/01_2024/7zr0_14875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr0_14875/01_2024/7zr0_14875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr0_14875/01_2024/7zr0_14875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr0_14875/01_2024/7zr0_14875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr0_14875/01_2024/7zr0_14875_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 73 5.16 5 C 8870 2.51 5 N 2388 2.21 5 O 2714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 542": "OE1" <-> "OE2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B GLU 627": "OE1" <-> "OE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 660": "OE1" <-> "OE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 14052 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5132 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "B" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5112 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 1 Chain: "C" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2243 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain: "K" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1503 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.41, per 1000 atoms: 0.53 Number of scatterers: 14052 At special positions: 0 Unit cell: (118.68, 126.42, 139.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 7 15.00 O 2714 8.00 N 2388 7.00 C 8870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 2.4 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 11 sheets defined 39.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 36 through 60 removed outlier: 4.364A pdb=" N SER A 48 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 49 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 57 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 58 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 59 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 400 through 420 removed outlier: 3.553A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 432 removed outlier: 3.748A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 440 No H-bonds generated for 'chain 'A' and resid 437 through 440' Processing helix chain 'A' and resid 448 through 451 No H-bonds generated for 'chain 'A' and resid 448 through 451' Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.747A pdb=" N ARG A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 614 through 617 No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 633 through 644 removed outlier: 4.106A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.529A pdb=" N SER A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 686 removed outlier: 3.578A pdb=" N SER A 677 " --> pdb=" O PRO A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 39 through 60 removed outlier: 3.733A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.784A pdb=" N GLU B 303 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 398 through 419 removed outlier: 3.602A pdb=" N ARG B 405 " --> pdb=" O LYS B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.602A pdb=" N LYS B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.530A pdb=" N VAL B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 469 through 475' Processing helix chain 'B' and resid 500 through 503 No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 517 through 524 removed outlier: 4.001A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 563 through 570 removed outlier: 3.538A pdb=" N LYS B 568 " --> pdb=" O CYS B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 removed outlier: 3.669A pdb=" N ALA B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 620 No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.570A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 Processing helix chain 'B' and resid 673 through 688 removed outlier: 3.638A pdb=" N MET B 683 " --> pdb=" O ARG B 679 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 71 Processing helix chain 'C' and resid 79 through 111 removed outlier: 3.642A pdb=" N LYS C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 119 No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 140 through 163 Processing helix chain 'C' and resid 169 through 181 Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 203 through 226 Processing helix chain 'C' and resid 235 through 242 Processing helix chain 'C' and resid 246 through 265 Processing helix chain 'K' and resid 537 through 542 removed outlier: 3.580A pdb=" N LEU K 541 " --> pdb=" O LEU K 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 550 through 569 Processing helix chain 'K' and resid 635 through 651 Processing helix chain 'K' and resid 662 through 670 Processing helix chain 'K' and resid 688 through 696 Processing helix chain 'K' and resid 707 through 720 removed outlier: 3.830A pdb=" N SER K 720 " --> pdb=" O LEU K 716 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 73 through 75 Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.614A pdb=" N THR A 83 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 318 through 324 removed outlier: 3.859A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 329 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 378 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 532 through 535 removed outlier: 3.657A pdb=" N TYR A 485 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 73 through 75 Processing sheet with id= F, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= G, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.005A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 143 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 159 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 329 through 331 Processing sheet with id= I, first strand: chain 'B' and resid 533 through 535 removed outlier: 5.661A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 511 " --> pdb=" O ILE B 486 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 578 through 580 removed outlier: 8.638A pdb=" N THR B 579 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU B 626 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.831A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1317 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: 3.53 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 1 1.05 - 1.24: 1742 1.24 - 1.43: 4127 1.43 - 1.62: 8299 1.62 - 1.81: 124 Bond restraints: 14293 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 0.858 0.634 5.00e-02 4.00e+02 1.61e+02 bond pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 1.503 1.257 0.246 3.40e-02 8.65e+02 5.25e+01 bond pdb=" N PRO A 77 " pdb=" CD PRO A 77 " ideal model delta sigma weight residual 1.473 1.399 0.074 1.40e-02 5.10e+03 2.80e+01 bond pdb=" N PRO B 79 " pdb=" CD PRO B 79 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.26e+01 bond pdb=" C MET C 112 " pdb=" N PRO C 113 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.25e-02 6.40e+03 9.40e+00 ... (remaining 14288 not shown) Histogram of bond angle deviations from ideal: 77.07 - 97.65: 2 97.65 - 118.22: 10935 118.22 - 138.80: 8276 138.80 - 159.38: 2 159.38 - 179.95: 1 Bond angle restraints: 19216 Sorted by residual: angle pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO A 79 " pdb=" CD PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 103.20 78.91 24.29 1.50e+00 4.44e-01 2.62e+02 angle pdb=" CA PRO A 79 " pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 104.50 77.07 27.43 1.90e+00 2.77e-01 2.08e+02 angle pdb=" N ILE A 690 " pdb=" CA ILE A 690 " pdb=" C ILE A 690 " ideal model delta sigma weight residual 112.96 107.29 5.67 1.00e+00 1.00e+00 3.21e+01 angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 104.27 7.73 1.40e+00 5.10e-01 3.05e+01 ... (remaining 19211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7155 17.95 - 35.90: 1276 35.90 - 53.85: 353 53.85 - 71.80: 65 71.80 - 89.74: 30 Dihedral angle restraints: 8879 sinusoidal: 3826 harmonic: 5053 Sorted by residual: dihedral pdb=" CA THR B 309 " pdb=" C THR B 309 " pdb=" N ASN B 310 " pdb=" CA ASN B 310 " ideal model delta harmonic sigma weight residual 180.00 148.78 31.22 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA MET C 112 " pdb=" C MET C 112 " pdb=" N PRO C 113 " pdb=" CA PRO C 113 " ideal model delta harmonic sigma weight residual 180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" N PRO A 79 " pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " pdb=" CB PRO A 79 " ideal model delta sinusoidal sigma weight residual -30.00 -112.14 82.14 1 1.50e+01 4.44e-03 3.68e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1476 0.043 - 0.086: 483 0.086 - 0.130: 126 0.130 - 0.173: 18 0.173 - 0.216: 5 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CA PRO K 523 " pdb=" N PRO K 523 " pdb=" C PRO K 523 " pdb=" CB PRO K 523 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA GLU B 539 " pdb=" N GLU B 539 " pdb=" C GLU B 539 " pdb=" CB GLU B 539 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR B 190 " pdb=" CA THR B 190 " pdb=" OG1 THR B 190 " pdb=" CG2 THR B 190 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2105 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 173 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.25e+01 pdb=" N PRO B 174 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 20 " -0.051 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO C 21 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 21 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 21 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 9 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C HIS C 9 " 0.048 2.00e-02 2.50e+03 pdb=" O HIS C 9 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 10 " -0.016 2.00e-02 2.50e+03 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 143 2.59 - 3.17: 11311 3.17 - 3.74: 19922 3.74 - 4.32: 25390 4.32 - 4.90: 43677 Nonbonded interactions: 100443 Sorted by model distance: nonbonded pdb=" OG1 THR B 94 " pdb=" OD2 ASP B 152 " model vdw 2.011 2.440 nonbonded pdb=" O ILE A 690 " pdb=" OE1 GLU A 692 " model vdw 2.119 3.040 nonbonded pdb=" O LEU A 27 " pdb=" OG1 THR A 31 " model vdw 2.129 2.440 nonbonded pdb=" O LYS C 108 " pdb=" N MET C 112 " model vdw 2.177 2.520 nonbonded pdb=" O SER B 160 " pdb=" OG SER B 160 " model vdw 2.182 2.440 ... (remaining 100438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 220 or resid 273 through 692 or resid 801)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.730 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 36.390 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.007 0.634 14293 Z= 0.335 Angle : 0.995 73.851 19216 Z= 0.497 Chirality : 0.046 0.216 2108 Planarity : 0.006 0.118 2455 Dihedral : 19.990 89.744 5595 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.06 % Favored : 89.35 % Rotamer: Outliers : 0.19 % Allowed : 35.74 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.06 % 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: -2.37 (0.19), residues: 1699 helix: 0.39 (0.20), residues: 719 sheet: -2.11 (0.36), residues: 199 loop : -3.47 (0.18), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 114 HIS 0.009 0.002 HIS A 632 PHE 0.023 0.002 PHE B 165 TYR 0.026 0.002 TYR A 137 ARG 0.010 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 299 time to evaluate : 1.694 Fit side-chains REVERT: B 52 ASP cc_start: 0.8359 (t0) cc_final: 0.8020 (m-30) outliers start: 3 outliers final: 2 residues processed: 299 average time/residue: 0.2990 time to fit residues: 124.6230 Evaluate side-chains 298 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 296 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 20.0000 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.4980 chunk 154 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14293 Z= 0.215 Angle : 0.631 12.302 19216 Z= 0.332 Chirality : 0.043 0.210 2108 Planarity : 0.005 0.079 2455 Dihedral : 7.211 81.119 1936 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.01 % Favored : 90.52 % Rotamer: Outliers : 3.28 % Allowed : 33.74 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.06 % 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: -2.07 (0.20), residues: 1699 helix: 0.53 (0.20), residues: 721 sheet: -1.65 (0.40), residues: 179 loop : -3.27 (0.18), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 114 HIS 0.005 0.001 HIS A 632 PHE 0.016 0.002 PHE A 32 TYR 0.011 0.001 TYR A 373 ARG 0.004 0.000 ARG K 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 315 time to evaluate : 1.589 Fit side-chains REVERT: A 137 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6612 (t80) REVERT: A 283 ASN cc_start: 0.7760 (p0) cc_final: 0.7546 (p0) REVERT: A 443 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7058 (mt-10) REVERT: A 491 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8256 (tttm) REVERT: B 32 PHE cc_start: 0.8301 (m-80) cc_final: 0.8018 (m-10) REVERT: B 52 ASP cc_start: 0.8358 (t0) cc_final: 0.8008 (m-30) REVERT: B 277 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7570 (pt) outliers start: 51 outliers final: 26 residues processed: 341 average time/residue: 0.2861 time to fit residues: 136.4795 Evaluate side-chains 324 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 296 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.0050 chunk 47 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 124 optimal weight: 0.9980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 523 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 14293 Z= 0.153 Angle : 0.567 11.858 19216 Z= 0.294 Chirality : 0.041 0.208 2108 Planarity : 0.004 0.062 2455 Dihedral : 6.788 87.118 1934 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.53 % Favored : 90.99 % Rotamer: Outliers : 4.38 % Allowed : 33.35 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1699 helix: 0.74 (0.20), residues: 714 sheet: -1.24 (0.40), residues: 181 loop : -3.08 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 114 HIS 0.004 0.001 HIS B 632 PHE 0.010 0.001 PHE A 32 TYR 0.010 0.001 TYR K 640 ARG 0.003 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 309 time to evaluate : 1.734 Fit side-chains REVERT: A 79 PRO cc_start: 0.8621 (Cg_endo) cc_final: 0.8392 (Cg_exo) REVERT: A 137 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6489 (t80) REVERT: A 303 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: A 311 ASP cc_start: 0.7343 (t0) cc_final: 0.6956 (t70) REVERT: A 491 LYS cc_start: 0.8464 (tmtt) cc_final: 0.8163 (tttm) REVERT: B 80 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: B 114 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7306 (tpp) REVERT: B 277 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7504 (pt) REVERT: K 618 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6369 (mt) outliers start: 68 outliers final: 28 residues processed: 350 average time/residue: 0.2862 time to fit residues: 140.6020 Evaluate side-chains 330 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 618 LEU Chi-restraints excluded: chain K residue 689 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 523 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14293 Z= 0.353 Angle : 0.669 12.288 19216 Z= 0.349 Chirality : 0.046 0.201 2108 Planarity : 0.005 0.064 2455 Dihedral : 7.004 78.624 1932 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.65 % Favored : 89.82 % Rotamer: Outliers : 5.47 % Allowed : 31.94 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.20), residues: 1699 helix: 0.47 (0.20), residues: 725 sheet: -1.19 (0.39), residues: 186 loop : -3.17 (0.18), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 157 HIS 0.007 0.001 HIS B 676 PHE 0.025 0.002 PHE A 32 TYR 0.022 0.002 TYR A 485 ARG 0.004 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 314 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: A 303 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: A 311 ASP cc_start: 0.7406 (t0) cc_final: 0.7166 (t0) REVERT: A 443 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 491 LYS cc_start: 0.8576 (tmtt) cc_final: 0.8283 (tttm) REVERT: A 574 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7062 (mtmt) REVERT: B 52 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8091 (m-30) REVERT: B 114 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7349 (tpp) REVERT: B 139 VAL cc_start: 0.8317 (m) cc_final: 0.8083 (p) REVERT: B 277 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7531 (pt) REVERT: B 385 ASP cc_start: 0.7570 (p0) cc_final: 0.7316 (p0) REVERT: B 641 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7736 (mppt) REVERT: C 14 ASP cc_start: 0.8294 (p0) cc_final: 0.8076 (p0) REVERT: C 18 GLU cc_start: 0.8134 (pp20) cc_final: 0.7629 (tm-30) REVERT: C 112 MET cc_start: 0.4437 (mtp) cc_final: 0.4199 (mtp) REVERT: K 618 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6600 (mt) REVERT: K 700 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6230 (mttt) outliers start: 85 outliers final: 55 residues processed: 368 average time/residue: 0.2860 time to fit residues: 147.2602 Evaluate side-chains 367 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 304 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 618 LEU Chi-restraints excluded: chain K residue 668 MET Chi-restraints excluded: chain K residue 689 MET Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 700 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN K 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14293 Z= 0.235 Angle : 0.615 13.336 19216 Z= 0.318 Chirality : 0.043 0.206 2108 Planarity : 0.004 0.065 2455 Dihedral : 6.853 82.080 1932 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.71 % Favored : 90.82 % Rotamer: Outliers : 5.34 % Allowed : 32.39 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.20), residues: 1699 helix: 0.53 (0.20), residues: 730 sheet: -1.07 (0.41), residues: 183 loop : -3.19 (0.18), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 114 HIS 0.005 0.001 HIS B 676 PHE 0.017 0.002 PHE A 32 TYR 0.013 0.001 TYR A 485 ARG 0.005 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 319 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 303 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: A 443 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 491 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8231 (tttm) REVERT: A 574 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7074 (mtmt) REVERT: A 606 MET cc_start: 0.8587 (mmt) cc_final: 0.8316 (mmt) REVERT: B 52 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: B 80 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: B 114 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7319 (tpp) REVERT: B 277 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7508 (pt) REVERT: B 364 ASP cc_start: 0.7855 (p0) cc_final: 0.7606 (p0) REVERT: B 385 ASP cc_start: 0.7524 (p0) cc_final: 0.7255 (p0) REVERT: B 555 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6754 (tm-30) REVERT: B 641 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7714 (mppt) REVERT: C 14 ASP cc_start: 0.8275 (p0) cc_final: 0.8072 (p0) REVERT: C 18 GLU cc_start: 0.8108 (pp20) cc_final: 0.7674 (tm-30) REVERT: C 112 MET cc_start: 0.4309 (mtp) cc_final: 0.4086 (mtp) REVERT: K 564 MET cc_start: 0.7945 (tpp) cc_final: 0.7331 (tpp) REVERT: K 689 MET cc_start: 0.5657 (OUTLIER) cc_final: 0.5213 (ttt) REVERT: K 700 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6100 (mttt) outliers start: 83 outliers final: 55 residues processed: 371 average time/residue: 0.2964 time to fit residues: 154.3908 Evaluate side-chains 376 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 312 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 524 GLN Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 668 MET Chi-restraints excluded: chain K residue 689 MET Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 700 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.0040 chunk 147 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 609 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 130 ASN C 146 GLN C 253 ASN K 585 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14293 Z= 0.182 Angle : 0.600 13.795 19216 Z= 0.307 Chirality : 0.042 0.211 2108 Planarity : 0.004 0.062 2455 Dihedral : 6.671 86.734 1932 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.95 % Favored : 90.64 % Rotamer: Outliers : 5.09 % Allowed : 32.97 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.20), residues: 1699 helix: 0.68 (0.20), residues: 727 sheet: -0.78 (0.41), residues: 179 loop : -3.13 (0.18), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 114 HIS 0.005 0.001 HIS B 632 PHE 0.013 0.001 PHE A 32 TYR 0.011 0.001 TYR C 155 ARG 0.004 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 309 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 137 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6602 (t80) REVERT: A 303 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: A 443 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 491 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8193 (tttm) REVERT: A 518 ASP cc_start: 0.7695 (m-30) cc_final: 0.7494 (m-30) REVERT: B 52 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: B 80 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: B 114 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7393 (tpp) REVERT: B 364 ASP cc_start: 0.7823 (p0) cc_final: 0.7565 (p0) REVERT: B 385 ASP cc_start: 0.7483 (p0) cc_final: 0.7208 (p0) REVERT: B 555 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6548 (tm-30) REVERT: B 641 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7702 (mppt) REVERT: C 14 ASP cc_start: 0.8282 (p0) cc_final: 0.8063 (p0) REVERT: C 18 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: C 112 MET cc_start: 0.4123 (mtp) cc_final: 0.3915 (mtp) REVERT: K 564 MET cc_start: 0.7928 (tpp) cc_final: 0.7309 (tpp) REVERT: K 689 MET cc_start: 0.5553 (OUTLIER) cc_final: 0.5035 (ttt) REVERT: K 700 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5964 (mttt) outliers start: 79 outliers final: 55 residues processed: 359 average time/residue: 0.2874 time to fit residues: 144.7324 Evaluate side-chains 369 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 305 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 668 MET Chi-restraints excluded: chain K residue 689 MET Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 700 LYS Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 120 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 0.0270 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN K 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14293 Z= 0.191 Angle : 0.594 14.348 19216 Z= 0.306 Chirality : 0.042 0.224 2108 Planarity : 0.004 0.062 2455 Dihedral : 6.628 87.819 1932 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.01 % Favored : 90.58 % Rotamer: Outliers : 5.09 % Allowed : 33.35 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1699 helix: 0.70 (0.20), residues: 730 sheet: -0.79 (0.41), residues: 184 loop : -3.08 (0.18), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 114 HIS 0.004 0.001 HIS B 632 PHE 0.014 0.001 PHE A 32 TYR 0.011 0.001 TYR C 155 ARG 0.004 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 309 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 137 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6610 (t80) REVERT: A 303 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: A 311 ASP cc_start: 0.7205 (t0) cc_final: 0.6908 (t70) REVERT: A 328 GLU cc_start: 0.7294 (pt0) cc_final: 0.6990 (pt0) REVERT: A 443 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7057 (mt-10) REVERT: B 52 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: B 80 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: B 139 VAL cc_start: 0.8210 (p) cc_final: 0.7907 (m) REVERT: B 370 ILE cc_start: 0.8305 (pt) cc_final: 0.8026 (tt) REVERT: B 385 ASP cc_start: 0.7475 (p0) cc_final: 0.7199 (p0) REVERT: B 555 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6520 (tm-30) REVERT: B 641 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7691 (mppt) REVERT: C 14 ASP cc_start: 0.8287 (p0) cc_final: 0.8054 (p0) REVERT: C 18 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: K 700 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5935 (mttt) outliers start: 79 outliers final: 60 residues processed: 360 average time/residue: 0.2923 time to fit residues: 147.3898 Evaluate side-chains 375 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 308 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 700 LYS Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 128 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14293 Z= 0.171 Angle : 0.582 14.168 19216 Z= 0.298 Chirality : 0.041 0.220 2108 Planarity : 0.004 0.061 2455 Dihedral : 6.488 87.619 1932 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.77 % Favored : 90.94 % Rotamer: Outliers : 4.64 % Allowed : 33.87 % Favored : 61.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1699 helix: 0.78 (0.20), residues: 732 sheet: -0.69 (0.41), residues: 184 loop : -2.99 (0.19), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 114 HIS 0.004 0.001 HIS B 632 PHE 0.011 0.001 PHE A 32 TYR 0.012 0.001 TYR C 155 ARG 0.004 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 307 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 137 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6784 (t80) REVERT: A 303 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: A 311 ASP cc_start: 0.7272 (t0) cc_final: 0.6957 (t70) REVERT: A 328 GLU cc_start: 0.7309 (pt0) cc_final: 0.7001 (pt0) REVERT: A 443 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7041 (mt-10) REVERT: A 606 MET cc_start: 0.8579 (mmt) cc_final: 0.8294 (mmt) REVERT: B 52 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: B 80 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: B 114 MET cc_start: 0.7657 (tpp) cc_final: 0.7299 (tpp) REVERT: B 385 ASP cc_start: 0.7329 (p0) cc_final: 0.7059 (p0) REVERT: B 555 GLU cc_start: 0.6780 (tm-30) cc_final: 0.6436 (tm-30) REVERT: B 641 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7698 (mppt) REVERT: C 14 ASP cc_start: 0.8281 (p0) cc_final: 0.8029 (p0) REVERT: C 18 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: K 700 LYS cc_start: 0.6371 (OUTLIER) cc_final: 0.5896 (mttt) outliers start: 72 outliers final: 58 residues processed: 355 average time/residue: 0.2969 time to fit residues: 147.6136 Evaluate side-chains 362 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 297 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 577 LEU Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 700 LYS Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 91 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14293 Z= 0.317 Angle : 0.666 14.607 19216 Z= 0.343 Chirality : 0.045 0.241 2108 Planarity : 0.005 0.062 2455 Dihedral : 6.817 82.565 1932 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.59 % Favored : 89.99 % Rotamer: Outliers : 5.54 % Allowed : 33.42 % Favored : 61.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.20), residues: 1699 helix: 0.55 (0.19), residues: 745 sheet: -0.94 (0.40), residues: 190 loop : -3.08 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 114 HIS 0.008 0.001 HIS B 676 PHE 0.024 0.002 PHE A 32 TYR 0.019 0.002 TYR A 485 ARG 0.004 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 310 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8322 (mm) cc_final: 0.8036 (mt) REVERT: A 303 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: A 328 GLU cc_start: 0.7298 (pt0) cc_final: 0.6987 (pt0) REVERT: A 574 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7068 (mtmt) REVERT: B 52 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: B 324 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7202 (mt-10) REVERT: B 370 ILE cc_start: 0.8314 (pt) cc_final: 0.8081 (tt) REVERT: B 385 ASP cc_start: 0.7426 (p0) cc_final: 0.7160 (p0) REVERT: B 451 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7814 (mp) REVERT: B 555 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6590 (tm-30) REVERT: B 641 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7640 (mppt) REVERT: C 14 ASP cc_start: 0.8296 (p0) cc_final: 0.7989 (p0) REVERT: C 18 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: K 564 MET cc_start: 0.7934 (tpp) cc_final: 0.7293 (tpp) REVERT: K 650 MET cc_start: 0.7791 (mtm) cc_final: 0.7472 (mtt) REVERT: K 700 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6019 (mmmm) outliers start: 86 outliers final: 67 residues processed: 365 average time/residue: 0.2991 time to fit residues: 152.2471 Evaluate side-chains 382 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 308 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 668 MET Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 700 LYS Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 40.0000 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14293 Z= 0.304 Angle : 0.666 13.945 19216 Z= 0.342 Chirality : 0.045 0.233 2108 Planarity : 0.005 0.067 2455 Dihedral : 6.885 80.755 1932 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.18 % Favored : 90.41 % Rotamer: Outliers : 4.76 % Allowed : 34.51 % Favored : 60.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1699 helix: 0.53 (0.19), residues: 740 sheet: -1.01 (0.39), residues: 190 loop : -3.11 (0.18), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 157 HIS 0.007 0.001 HIS B 676 PHE 0.021 0.002 PHE A 32 TYR 0.017 0.002 TYR A 485 ARG 0.004 0.000 ARG C 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 311 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8274 (mm) cc_final: 0.7969 (mt) REVERT: A 303 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: A 311 ASP cc_start: 0.7221 (t0) cc_final: 0.6917 (t70) REVERT: A 328 GLU cc_start: 0.7304 (pt0) cc_final: 0.6982 (pt0) REVERT: A 519 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 574 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7073 (mtmt) REVERT: A 606 MET cc_start: 0.8577 (mmt) cc_final: 0.8318 (mmt) REVERT: B 52 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: B 324 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7235 (mt-10) REVERT: B 370 ILE cc_start: 0.8327 (pt) cc_final: 0.8073 (tt) REVERT: B 385 ASP cc_start: 0.7416 (p0) cc_final: 0.7147 (p0) REVERT: B 451 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7820 (mp) REVERT: B 555 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6629 (tm-30) REVERT: B 641 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7605 (mppt) REVERT: C 11 GLU cc_start: 0.6752 (tt0) cc_final: 0.6042 (pt0) REVERT: C 14 ASP cc_start: 0.8286 (p0) cc_final: 0.7959 (p0) REVERT: C 18 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: K 650 MET cc_start: 0.7805 (mtm) cc_final: 0.7514 (mtt) REVERT: K 700 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6206 (mttt) outliers start: 74 outliers final: 65 residues processed: 358 average time/residue: 0.2876 time to fit residues: 144.5098 Evaluate side-chains 379 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 307 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 595 PHE Chi-restraints excluded: chain K residue 668 MET Chi-restraints excluded: chain K residue 689 MET Chi-restraints excluded: chain K residue 697 LEU Chi-restraints excluded: chain K residue 700 LYS Chi-restraints excluded: chain K residue 724 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.152115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118821 restraints weight = 20102.654| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.52 r_work: 0.3305 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 14293 Z= 0.192 Angle : 0.624 15.518 19216 Z= 0.317 Chirality : 0.042 0.247 2108 Planarity : 0.004 0.065 2455 Dihedral : 6.681 87.257 1932 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.83 % Favored : 90.82 % Rotamer: Outliers : 4.31 % Allowed : 34.96 % Favored : 60.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1699 helix: 0.67 (0.19), residues: 743 sheet: -0.94 (0.40), residues: 190 loop : -3.04 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 114 HIS 0.004 0.001 HIS B 632 PHE 0.012 0.001 PHE A 32 TYR 0.012 0.001 TYR K 640 ARG 0.004 0.000 ARG C 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.10 seconds wall clock time: 63 minutes 37.03 seconds (3817.03 seconds total)