Starting phenix.real_space_refine on Fri Mar 15 15:41:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y04_33537/03_2024/7y04_33537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y04_33537/03_2024/7y04_33537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y04_33537/03_2024/7y04_33537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y04_33537/03_2024/7y04_33537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y04_33537/03_2024/7y04_33537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y04_33537/03_2024/7y04_33537_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 58 5.16 5 Be 2 3.05 5 C 7612 2.51 5 N 2041 2.21 5 O 2327 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12050 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5038 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 17, 'TRANS': 605} Chain breaks: 1 Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5021 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 17, 'TRANS': 603} Chain breaks: 1 Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 928 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 928 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "E" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 73 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.89, per 1000 atoms: 0.57 Number of scatterers: 12050 At special positions: 0 Unit cell: (107, 93.09, 136.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 4 15.00 F 6 9.00 O 2327 8.00 N 2041 7.00 C 7612 6.00 Be 2 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.3 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 12 sheets defined 31.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 Processing helix chain 'A' and resid 39 through 59 removed outlier: 3.655A pdb=" N LEU A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 removed outlier: 4.231A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.797A pdb=" N TYR A 137 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 195 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 300 through 309 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 400 through 420 removed outlier: 4.452A pdb=" N ARG A 405 " --> pdb=" O LYS A 402 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 409 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A 413 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 443 removed outlier: 3.811A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' 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 524 removed outlier: 4.353A pdb=" N TYR A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.653A pdb=" N LYS A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 Processing helix chain 'A' and resid 600 through 608 removed outlier: 4.264A pdb=" N ARG A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 605 " --> pdb=" O ASN A 601 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.548A pdb=" N LEU A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 663 removed outlier: 4.098A pdb=" N VAL A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 688 removed outlier: 4.210A pdb=" N ASN A 678 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 682 " --> pdb=" O ARG A 679 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 686 " --> pdb=" O MET A 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 39 through 60 removed outlier: 4.075A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.866A pdb=" N LEU B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 133 through 138 removed outlier: 3.743A pdb=" N TYR B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.544A pdb=" N SER B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 400 through 420 removed outlier: 4.216A pdb=" N ARG B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 430 removed outlier: 3.781A pdb=" N LYS B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.635A pdb=" N HIS B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 451 No H-bonds generated for 'chain 'B' and resid 448 through 451' Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.583A pdb=" N SER B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.699A pdb=" N ASN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) 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 516 through 525 removed outlier: 3.804A pdb=" N VAL B 522 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 523 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 562 through 571 Processing helix chain 'B' and resid 600 through 607 removed outlier: 3.745A pdb=" N ARG B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.757A pdb=" N GLN B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 removed outlier: 4.133A pdb=" N VAL B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 688 removed outlier: 3.848A pdb=" N LYS B 685 " --> pdb=" O TYR B 681 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 687 " --> pdb=" O MET B 683 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.525A pdb=" N THR A 214 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 215 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 280 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.588A pdb=" N VAL A 181 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 158 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 317 through 323 removed outlier: 3.844A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 329 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 533 through 535 removed outlier: 5.586A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 511 " --> pdb=" O ILE A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.583A pdb=" N THR B 214 " --> pdb=" O ILE B 73 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.693A pdb=" N ILE B 76 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 85 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 78 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 83 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 84 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 183 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.844A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 321 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 329 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 354 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 533 through 535 removed outlier: 5.664A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B 511 " --> pdb=" O ILE B 486 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.821A pdb=" N ALA C 6 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 28 through 30 Processing sheet with id= K, first strand: chain 'D' and resid 99 through 101 removed outlier: 6.867A pdb=" N ALA D 6 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 74 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.639A pdb=" N HIS D 49 " --> pdb=" O CYS D 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 47 " --> pdb=" O GLY D 42 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 849 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: 3.37 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2075 1.30 - 1.43: 3001 1.43 - 1.56: 7086 1.56 - 1.69: 10 1.69 - 1.81: 94 Bond restraints: 12266 Sorted by residual: bond pdb=" CA THR E 276 " pdb=" C THR E 276 " ideal model delta sigma weight residual 1.533 1.473 0.060 5.60e-03 3.19e+04 1.15e+02 bond pdb=" CA GLU A 13 " pdb=" CB GLU A 13 " ideal model delta sigma weight residual 1.530 1.448 0.082 1.48e-02 4.57e+03 3.08e+01 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N THR E 276 " pdb=" CA THR E 276 " ideal model delta sigma weight residual 1.457 1.425 0.032 6.40e-03 2.44e+04 2.48e+01 ... (remaining 12261 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.06: 292 107.06 - 114.51: 7277 114.51 - 121.95: 6406 121.95 - 129.40: 2462 129.40 - 136.84: 68 Bond angle restraints: 16505 Sorted by residual: angle pdb=" C THR E 276 " pdb=" CA THR E 276 " pdb=" CB THR E 276 " ideal model delta sigma weight residual 117.07 105.50 11.57 1.44e+00 4.82e-01 6.46e+01 angle pdb=" CA THR E 276 " pdb=" C THR E 276 " pdb=" N LYS E 277 " ideal model delta sigma weight residual 120.47 114.61 5.86 1.03e+00 9.43e-01 3.24e+01 angle pdb=" CA GLU A 13 " pdb=" C GLU A 13 " pdb=" N THR A 14 " ideal model delta sigma weight residual 115.86 122.91 -7.05 1.24e+00 6.50e-01 3.23e+01 angle pdb=" PA ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sigma weight residual 120.50 136.84 -16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" PA ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sigma weight residual 120.50 136.80 -16.30 3.00e+00 1.11e-01 2.95e+01 ... (remaining 16500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 7251 30.40 - 60.81: 244 60.81 - 91.21: 27 91.21 - 121.62: 1 121.62 - 152.02: 3 Dihedral angle restraints: 7526 sinusoidal: 3190 harmonic: 4336 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 147.98 152.02 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 149.00 151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 173.79 126.21 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 7523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1396 0.047 - 0.095: 312 0.095 - 0.142: 92 0.142 - 0.189: 11 0.189 - 0.236: 1 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA GLU E 273 " pdb=" N GLU E 273 " pdb=" C GLU E 273 " pdb=" CB GLU E 273 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 392 " pdb=" N ARG A 392 " pdb=" C ARG A 392 " pdb=" CB ARG A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA GLU B 418 " pdb=" N GLU B 418 " pdb=" C GLU B 418 " pdb=" CB GLU B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1809 not shown) Planarity restraints: 2105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 272 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C LEU E 272 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU E 272 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU E 273 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 274 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C ILE E 274 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE E 274 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG E 275 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 276 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C THR E 276 " 0.034 2.00e-02 2.50e+03 pdb=" O THR E 276 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS E 277 " -0.011 2.00e-02 2.50e+03 ... (remaining 2102 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1403 2.75 - 3.29: 11575 3.29 - 3.83: 17897 3.83 - 4.36: 21265 4.36 - 4.90: 37527 Nonbonded interactions: 89667 Sorted by model distance: nonbonded pdb=" OH TYR B 56 " pdb=" OE1 GLN B 118 " model vdw 2.217 2.440 nonbonded pdb=" OE1 GLU A 548 " pdb=" NZ LYS A 551 " model vdw 2.221 2.520 nonbonded pdb=" O ILE B 353 " pdb=" OG SER B 365 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR A 457 " pdb=" OD1 ASP A 518 " model vdw 2.249 2.440 nonbonded pdb=" NZ LYS A 199 " pdb=" OE2 GLU A 280 " model vdw 2.275 2.520 ... (remaining 89662 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 217 or resid 278 through 690 or resid 801 throu \ gh 802)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.730 Check model and map are aligned: 0.000 Set scattering table: 0.100 Process input model: 34.450 Find NCS groups from input model: 0.660 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 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 : 0.004 0.105 12266 Z= 0.284 Angle : 0.763 16.344 16505 Z= 0.397 Chirality : 0.044 0.236 1812 Planarity : 0.004 0.049 2105 Dihedral : 15.694 152.020 4708 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.75 % Allowed : 0.37 % Favored : 98.88 % 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: -2.60 (0.21), residues: 1461 helix: -0.78 (0.23), residues: 489 sheet: -2.78 (0.27), residues: 294 loop : -1.83 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 157 HIS 0.006 0.001 HIS D 57 PHE 0.013 0.001 PHE C 38 TYR 0.012 0.001 TYR A 681 ARG 0.007 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 1.465 Fit side-chains REVERT: A 280 GLU cc_start: 0.7466 (tt0) cc_final: 0.7220 (pt0) REVERT: A 372 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 546 ASP cc_start: 0.7582 (t70) cc_final: 0.7018 (t70) REVERT: A 550 LYS cc_start: 0.7535 (mptt) cc_final: 0.7215 (mmtt) REVERT: A 577 LYS cc_start: 0.7619 (ptmm) cc_final: 0.7231 (ptpp) REVERT: A 629 ASN cc_start: 0.8596 (t0) cc_final: 0.8238 (t0) REVERT: B 11 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5139 (pm20) REVERT: B 552 LYS cc_start: 0.8410 (tmtt) cc_final: 0.8185 (tptt) REVERT: B 553 MET cc_start: 0.9073 (tmm) cc_final: 0.8715 (tmm) REVERT: B 573 LYS cc_start: 0.8711 (tppt) cc_final: 0.8152 (ttpp) REVERT: B 629 ASN cc_start: 0.8856 (t0) cc_final: 0.8620 (t0) REVERT: C 47 PHE cc_start: 0.6818 (m-80) cc_final: 0.6386 (m-10) REVERT: C 104 ASN cc_start: 0.8057 (m-40) cc_final: 0.7844 (m-40) REVERT: D 37 THR cc_start: 0.7093 (t) cc_final: 0.6751 (p) REVERT: D 81 GLU cc_start: 0.7428 (mp0) cc_final: 0.6999 (mp0) REVERT: E 273 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: E 275 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6710 (tmt170) outliers start: 10 outliers final: 1 residues processed: 203 average time/residue: 0.2879 time to fit residues: 79.8041 Evaluate side-chains 162 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 640 GLN B 100 ASN C 57 HIS C 84 GLN D 57 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12266 Z= 0.324 Angle : 0.660 8.098 16505 Z= 0.335 Chirality : 0.045 0.175 1812 Planarity : 0.004 0.043 2105 Dihedral : 8.885 148.047 1626 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.72 % Allowed : 8.44 % Favored : 89.84 % 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: -2.49 (0.21), residues: 1461 helix: -0.68 (0.23), residues: 491 sheet: -2.50 (0.29), residues: 288 loop : -1.91 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 157 HIS 0.006 0.001 HIS B 149 PHE 0.015 0.002 PHE D 38 TYR 0.013 0.002 TYR A 426 ARG 0.008 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5437 (pm20) REVERT: A 372 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 629 ASN cc_start: 0.8691 (t0) cc_final: 0.8245 (t0) REVERT: B 100 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6493 (t0) REVERT: B 200 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 553 MET cc_start: 0.9149 (tmm) cc_final: 0.8746 (tmm) REVERT: B 573 LYS cc_start: 0.8670 (tppt) cc_final: 0.8124 (ttpp) REVERT: B 629 ASN cc_start: 0.8927 (t0) cc_final: 0.8554 (t0) REVERT: C 9 TYR cc_start: 0.6199 (p90) cc_final: 0.5920 (p90) REVERT: C 47 PHE cc_start: 0.6842 (m-80) cc_final: 0.6461 (m-10) REVERT: D 37 THR cc_start: 0.6785 (t) cc_final: 0.6489 (p) outliers start: 23 outliers final: 14 residues processed: 174 average time/residue: 0.2755 time to fit residues: 67.4408 Evaluate side-chains 161 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 106 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN B 46 ASN B 100 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12266 Z= 0.185 Angle : 0.566 6.999 16505 Z= 0.286 Chirality : 0.042 0.150 1812 Planarity : 0.003 0.037 2105 Dihedral : 7.880 139.134 1622 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.64 % Allowed : 10.98 % Favored : 87.38 % 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: -2.24 (0.21), residues: 1461 helix: -0.52 (0.24), residues: 492 sheet: -2.14 (0.29), residues: 301 loop : -1.81 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 157 HIS 0.008 0.001 HIS D 57 PHE 0.011 0.001 PHE D 38 TYR 0.010 0.001 TYR A 305 ARG 0.005 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.5667 (OUTLIER) cc_final: 0.5441 (pm20) REVERT: A 372 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 629 ASN cc_start: 0.8695 (t0) cc_final: 0.8248 (t0) REVERT: B 100 ASN cc_start: 0.6858 (OUTLIER) cc_final: 0.6564 (t0) REVERT: B 200 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6963 (tm-30) REVERT: B 424 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 553 MET cc_start: 0.9150 (tmm) cc_final: 0.8732 (tmm) REVERT: B 573 LYS cc_start: 0.8685 (tppt) cc_final: 0.8114 (ttpp) REVERT: B 602 MET cc_start: 0.7375 (tpt) cc_final: 0.7157 (tpp) REVERT: B 617 MET cc_start: 0.6996 (mpp) cc_final: 0.6695 (mpp) REVERT: B 629 ASN cc_start: 0.8845 (t0) cc_final: 0.8460 (t0) REVERT: C 9 TYR cc_start: 0.6071 (p90) cc_final: 0.5840 (p90) REVERT: C 47 PHE cc_start: 0.6822 (m-80) cc_final: 0.6526 (m-80) REVERT: D 37 THR cc_start: 0.6604 (t) cc_final: 0.6292 (p) REVERT: E 273 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: E 275 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6267 (tmt170) outliers start: 22 outliers final: 11 residues processed: 169 average time/residue: 0.2730 time to fit residues: 64.6829 Evaluate side-chains 162 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 89 optimal weight: 0.0670 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN B 100 ASN B 396 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN D 57 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12266 Z= 0.179 Angle : 0.543 6.430 16505 Z= 0.275 Chirality : 0.042 0.145 1812 Planarity : 0.003 0.038 2105 Dihedral : 7.766 166.193 1622 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.09 % Allowed : 11.95 % Favored : 85.96 % 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: -2.09 (0.21), residues: 1461 helix: -0.39 (0.24), residues: 494 sheet: -1.93 (0.29), residues: 301 loop : -1.82 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 157 HIS 0.003 0.001 HIS A 625 PHE 0.012 0.001 PHE A 32 TYR 0.009 0.001 TYR A 373 ARG 0.006 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.5725 (OUTLIER) cc_final: 0.5512 (pm20) REVERT: A 372 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 577 LYS cc_start: 0.7585 (ptmm) cc_final: 0.7193 (ptpp) REVERT: A 629 ASN cc_start: 0.8702 (t0) cc_final: 0.8267 (t0) REVERT: B 200 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6931 (tm-30) REVERT: B 418 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5754 (mp0) REVERT: B 424 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8099 (tm-30) REVERT: B 471 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6461 (mt-10) REVERT: B 553 MET cc_start: 0.9151 (tmm) cc_final: 0.8728 (tmm) REVERT: B 573 LYS cc_start: 0.8716 (tppt) cc_final: 0.8480 (tppt) REVERT: B 629 ASN cc_start: 0.8836 (t0) cc_final: 0.8446 (t0) REVERT: C 47 PHE cc_start: 0.6614 (m-80) cc_final: 0.6321 (m-80) REVERT: E 275 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6168 (tmt170) outliers start: 28 outliers final: 19 residues processed: 174 average time/residue: 0.2708 time to fit residues: 66.7573 Evaluate side-chains 173 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 0.0970 chunk 105 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.0170 chunk 126 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN B 100 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN C 84 GLN D 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12266 Z= 0.131 Angle : 0.517 9.494 16505 Z= 0.259 Chirality : 0.041 0.147 1812 Planarity : 0.003 0.039 2105 Dihedral : 7.346 169.000 1619 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.87 % Allowed : 12.25 % Favored : 85.88 % 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: -1.86 (0.21), residues: 1461 helix: -0.19 (0.24), residues: 493 sheet: -1.75 (0.29), residues: 305 loop : -1.71 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 157 HIS 0.002 0.001 HIS A 625 PHE 0.008 0.001 PHE A 32 TYR 0.009 0.001 TYR A 305 ARG 0.006 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 529 ASP cc_start: 0.6878 (t0) cc_final: 0.6613 (t0) REVERT: A 577 LYS cc_start: 0.7282 (ptmm) cc_final: 0.7006 (ptpp) REVERT: A 629 ASN cc_start: 0.8649 (t0) cc_final: 0.8207 (t0) REVERT: B 25 MET cc_start: 0.6807 (tpp) cc_final: 0.6532 (mmm) REVERT: B 118 GLN cc_start: 0.7326 (pm20) cc_final: 0.7059 (pm20) REVERT: B 200 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6902 (tm-30) REVERT: B 418 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5521 (mp0) REVERT: B 424 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 553 MET cc_start: 0.9145 (tmm) cc_final: 0.8714 (tmm) REVERT: B 573 LYS cc_start: 0.8718 (tppt) cc_final: 0.8482 (tppt) REVERT: B 617 MET cc_start: 0.6978 (mpp) cc_final: 0.6735 (mpp) REVERT: B 629 ASN cc_start: 0.8762 (t0) cc_final: 0.8501 (t0) REVERT: C 47 PHE cc_start: 0.6574 (m-80) cc_final: 0.6305 (m-80) outliers start: 25 outliers final: 15 residues processed: 182 average time/residue: 0.2695 time to fit residues: 69.4511 Evaluate side-chains 170 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 74 optimal weight: 0.1980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 640 GLN B 100 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12266 Z= 0.329 Angle : 0.607 7.266 16505 Z= 0.308 Chirality : 0.044 0.151 1812 Planarity : 0.004 0.040 2105 Dihedral : 6.622 111.161 1615 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.61 % Allowed : 12.55 % Favored : 84.84 % 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: -2.02 (0.21), residues: 1461 helix: -0.38 (0.24), residues: 491 sheet: -1.81 (0.29), residues: 301 loop : -1.77 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 157 HIS 0.007 0.001 HIS B 149 PHE 0.014 0.002 PHE A 32 TYR 0.012 0.002 TYR B 216 ARG 0.006 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6478 (mt-10) REVERT: A 372 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 629 ASN cc_start: 0.8721 (t0) cc_final: 0.8204 (t0) REVERT: B 118 GLN cc_start: 0.7197 (pm20) cc_final: 0.6955 (pm20) REVERT: B 200 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7016 (tm-30) REVERT: B 418 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5861 (mp0) REVERT: B 424 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8133 (tm-30) REVERT: B 453 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: B 553 MET cc_start: 0.9153 (tmm) cc_final: 0.8696 (tmm) REVERT: B 554 GLU cc_start: 0.9520 (tp30) cc_final: 0.9286 (tp30) REVERT: B 560 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6521 (t80) REVERT: B 573 LYS cc_start: 0.8709 (tppt) cc_final: 0.8459 (tppt) REVERT: B 617 MET cc_start: 0.7045 (mpp) cc_final: 0.6730 (mpp) REVERT: B 629 ASN cc_start: 0.8833 (t0) cc_final: 0.8476 (t0) REVERT: C 10 ASP cc_start: 0.7198 (p0) cc_final: 0.6709 (t70) REVERT: C 47 PHE cc_start: 0.6660 (m-80) cc_final: 0.6401 (m-80) REVERT: E 275 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6285 (tmt170) outliers start: 35 outliers final: 24 residues processed: 182 average time/residue: 0.2755 time to fit residues: 70.1392 Evaluate side-chains 184 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 397 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12266 Z= 0.165 Angle : 0.541 9.538 16505 Z= 0.270 Chirality : 0.041 0.140 1812 Planarity : 0.003 0.037 2105 Dihedral : 5.748 98.357 1615 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.32 % Allowed : 13.82 % Favored : 83.87 % 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: -1.82 (0.22), residues: 1461 helix: -0.24 (0.24), residues: 490 sheet: -1.63 (0.29), residues: 305 loop : -1.66 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 157 HIS 0.004 0.001 HIS A 625 PHE 0.013 0.001 PHE C 16 TYR 0.019 0.001 TYR C 9 ARG 0.006 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7568 (p) REVERT: A 372 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 529 ASP cc_start: 0.6927 (t0) cc_final: 0.6680 (t0) REVERT: A 629 ASN cc_start: 0.8703 (t0) cc_final: 0.8230 (t0) REVERT: B 200 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6979 (tm-30) REVERT: B 418 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5695 (mp0) REVERT: B 424 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 453 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: B 553 MET cc_start: 0.9148 (tmm) cc_final: 0.8690 (tmm) REVERT: B 554 GLU cc_start: 0.9494 (tp30) cc_final: 0.9245 (tp30) REVERT: B 560 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6581 (t80) REVERT: B 617 MET cc_start: 0.7046 (mpp) cc_final: 0.6732 (mpp) REVERT: B 629 ASN cc_start: 0.8816 (t0) cc_final: 0.8489 (t0) REVERT: C 47 PHE cc_start: 0.6633 (m-80) cc_final: 0.6347 (m-80) REVERT: E 275 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6294 (tmt170) outliers start: 31 outliers final: 20 residues processed: 178 average time/residue: 0.2751 time to fit residues: 69.1847 Evaluate side-chains 176 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12266 Z= 0.176 Angle : 0.556 10.091 16505 Z= 0.275 Chirality : 0.042 0.139 1812 Planarity : 0.003 0.038 2105 Dihedral : 5.549 94.245 1615 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.54 % Allowed : 13.59 % Favored : 83.87 % 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: -1.67 (0.22), residues: 1461 helix: -0.11 (0.24), residues: 482 sheet: -1.52 (0.29), residues: 317 loop : -1.57 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 157 HIS 0.003 0.001 HIS A 625 PHE 0.009 0.001 PHE A 32 TYR 0.011 0.001 TYR C 9 ARG 0.006 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 550 LYS cc_start: 0.7867 (mptt) cc_final: 0.7519 (mmtt) REVERT: A 629 ASN cc_start: 0.8657 (t0) cc_final: 0.8185 (t0) REVERT: A 639 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6748 (ttp-170) REVERT: B 200 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6961 (tm-30) REVERT: B 418 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5638 (mp0) REVERT: B 424 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 453 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: B 553 MET cc_start: 0.9136 (tmm) cc_final: 0.8665 (tmm) REVERT: B 554 GLU cc_start: 0.9511 (tp30) cc_final: 0.9277 (tp30) REVERT: B 560 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6536 (t80) REVERT: B 573 LYS cc_start: 0.8780 (tppt) cc_final: 0.8106 (ttpp) REVERT: B 617 MET cc_start: 0.7065 (mpp) cc_final: 0.6775 (mpp) REVERT: B 629 ASN cc_start: 0.8815 (t0) cc_final: 0.8493 (t0) REVERT: C 47 PHE cc_start: 0.6525 (m-80) cc_final: 0.6221 (m-80) REVERT: E 275 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.6276 (tmt170) outliers start: 34 outliers final: 24 residues processed: 176 average time/residue: 0.2639 time to fit residues: 65.3694 Evaluate side-chains 182 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.0040 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 57 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12266 Z= 0.195 Angle : 0.562 8.012 16505 Z= 0.279 Chirality : 0.042 0.139 1812 Planarity : 0.003 0.037 2105 Dihedral : 5.550 94.917 1615 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.24 % Allowed : 13.74 % Favored : 84.02 % 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: -1.70 (0.22), residues: 1461 helix: -0.20 (0.24), residues: 489 sheet: -1.49 (0.29), residues: 317 loop : -1.57 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 157 HIS 0.004 0.001 HIS A 625 PHE 0.010 0.001 PHE A 32 TYR 0.014 0.001 TYR C 9 ARG 0.007 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7537 (p) REVERT: A 372 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 629 ASN cc_start: 0.8654 (t0) cc_final: 0.8174 (t0) REVERT: B 200 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 418 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5670 (mp0) REVERT: B 424 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 453 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: B 553 MET cc_start: 0.9135 (tmm) cc_final: 0.8663 (tmm) REVERT: B 554 GLU cc_start: 0.9509 (tp30) cc_final: 0.9271 (tp30) REVERT: B 560 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6546 (t80) REVERT: B 573 LYS cc_start: 0.8748 (tppt) cc_final: 0.8072 (ttpp) REVERT: B 602 MET cc_start: 0.7120 (tpt) cc_final: 0.6889 (tpp) REVERT: B 606 MET cc_start: 0.7937 (tpp) cc_final: 0.7356 (mpp) REVERT: B 617 MET cc_start: 0.7145 (mpp) cc_final: 0.6845 (mpp) REVERT: B 629 ASN cc_start: 0.8827 (t0) cc_final: 0.8483 (t0) REVERT: C 47 PHE cc_start: 0.6551 (m-80) cc_final: 0.6239 (m-80) REVERT: C 81 GLU cc_start: 0.7268 (mp0) cc_final: 0.7001 (mp0) REVERT: C 104 ASN cc_start: 0.8101 (m-40) cc_final: 0.7840 (m-40) REVERT: E 275 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6347 (tmt170) outliers start: 30 outliers final: 23 residues processed: 174 average time/residue: 0.2677 time to fit residues: 65.2491 Evaluate side-chains 179 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12266 Z= 0.308 Angle : 0.617 8.614 16505 Z= 0.309 Chirality : 0.044 0.205 1812 Planarity : 0.003 0.037 2105 Dihedral : 5.743 93.819 1615 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.24 % Allowed : 14.04 % Favored : 83.72 % 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: -1.83 (0.22), residues: 1461 helix: -0.30 (0.24), residues: 489 sheet: -1.59 (0.29), residues: 313 loop : -1.63 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 157 HIS 0.006 0.001 HIS B 149 PHE 0.013 0.002 PHE C 16 TYR 0.028 0.002 TYR B 305 ARG 0.007 0.000 ARG A 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 629 ASN cc_start: 0.8639 (t0) cc_final: 0.8186 (t0) REVERT: B 200 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7055 (tm-30) REVERT: B 418 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5707 (mp0) REVERT: B 424 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 453 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: B 553 MET cc_start: 0.9125 (tmm) cc_final: 0.8646 (tmm) REVERT: B 554 GLU cc_start: 0.9513 (tp30) cc_final: 0.9280 (tp30) REVERT: B 560 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6535 (t80) REVERT: B 573 LYS cc_start: 0.8744 (tppt) cc_final: 0.8058 (ttpp) REVERT: B 602 MET cc_start: 0.7248 (tpt) cc_final: 0.6922 (tpp) REVERT: B 606 MET cc_start: 0.7951 (tpp) cc_final: 0.7373 (mpp) REVERT: B 629 ASN cc_start: 0.8837 (t0) cc_final: 0.8480 (t0) REVERT: C 47 PHE cc_start: 0.6604 (m-80) cc_final: 0.6273 (m-80) REVERT: C 81 GLU cc_start: 0.7333 (mp0) cc_final: 0.7066 (mp0) REVERT: E 275 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6369 (tmt170) outliers start: 30 outliers final: 24 residues processed: 167 average time/residue: 0.2530 time to fit residues: 59.7517 Evaluate side-chains 173 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123917 restraints weight = 14185.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128348 restraints weight = 9484.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132344 restraints weight = 5852.287| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12266 Z= 0.246 Angle : 0.596 10.070 16505 Z= 0.297 Chirality : 0.043 0.156 1812 Planarity : 0.003 0.037 2105 Dihedral : 5.741 94.878 1615 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.17 % Allowed : 14.26 % Favored : 83.57 % 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: -1.79 (0.22), residues: 1461 helix: -0.28 (0.24), residues: 491 sheet: -1.56 (0.29), residues: 313 loop : -1.62 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.005 0.001 HIS B 149 PHE 0.016 0.001 PHE C 16 TYR 0.027 0.001 TYR B 305 ARG 0.007 0.000 ARG A 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.11 seconds wall clock time: 44 minutes 49.73 seconds (2689.73 seconds total)