Starting phenix.real_space_refine on Sat Aug 23 09:57:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yo7_39437/08_2025/8yo7_39437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yo7_39437/08_2025/8yo7_39437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yo7_39437/08_2025/8yo7_39437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yo7_39437/08_2025/8yo7_39437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yo7_39437/08_2025/8yo7_39437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yo7_39437/08_2025/8yo7_39437.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.003 sd= 0.087 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: 6 Type Number sf(0) Gaussians P 38 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 7170 2.51 5 N 1935 2.21 5 O 2210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11395 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1715 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1715 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 244 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "X" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "Y" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 145 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ASW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ASW': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.13, per 1000 atoms: 0.27 Number of scatterers: 11395 At special positions: 0 Unit cell: (97.76, 116.48, 122.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 38 15.00 Mg 2 11.99 O 2210 8.00 N 1935 7.00 C 7170 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 - 3.00 Amino acid : True - 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: 0.90 Conformation dependent library (CDL) restraints added in 570.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 13 sheets defined 47.3% alpha, 9.8% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.889A pdb=" N ASP A 70 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.269A pdb=" N ASP A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 123 through 130 removed outlier: 3.647A pdb=" N TYR A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.922A pdb=" N LEU A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 178 through 190 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 319 through 365 removed outlier: 3.531A pdb=" N LEU A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.871A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 3.673A pdb=" N GLU A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 15 Processing helix chain 'B' and resid 15 through 26 removed outlier: 3.939A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.746A pdb=" N ARG B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.811A pdb=" N ASN B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 161' Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 247 through 254 removed outlier: 4.024A pdb=" N LEU B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 319 through 366 removed outlier: 3.718A pdb=" N THR B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.608A pdb=" N LYS B 384 " --> pdb=" O GLU B 380 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.890A pdb=" N SER B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.720A pdb=" N LYS B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 440 removed outlier: 3.608A pdb=" N GLU B 433 " --> pdb=" O ASP B 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.531A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP C 425 " --> pdb=" O GLY C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 453 removed outlier: 3.985A pdb=" N LEU C 453 " --> pdb=" O TYR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 494 through 504 Processing helix chain 'C' and resid 507 through 512 removed outlier: 3.926A pdb=" N GLU C 511 " --> pdb=" O PRO C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 544 removed outlier: 3.666A pdb=" N TYR C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 561 removed outlier: 3.555A pdb=" N LEU C 561 " --> pdb=" O LEU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 572 Processing helix chain 'C' and resid 595 through 605 removed outlier: 3.796A pdb=" N ARG C 599 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN C 605 " --> pdb=" O GLU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 removed outlier: 4.637A pdb=" N ASP D 425 " --> pdb=" O GLY D 421 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 426 " --> pdb=" O TYR D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 455 through 465 removed outlier: 5.002A pdb=" N ILE D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 494 removed outlier: 3.599A pdb=" N LEU D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D 494 " --> pdb=" O ASP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 504 Processing helix chain 'D' and resid 505 through 510 removed outlier: 6.394A pdb=" N GLU D 508 " --> pdb=" O ASN D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.815A pdb=" N TYR D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 561 removed outlier: 3.702A pdb=" N LEU D 561 " --> pdb=" O LEU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 587 through 593 Processing helix chain 'D' and resid 595 through 603 removed outlier: 4.329A pdb=" N ARG D 599 " --> pdb=" O ASN D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 6.242A pdb=" N GLN A 2 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL D 577 " --> pdb=" O GLN A 2 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN A 4 " --> pdb=" O VAL D 577 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LYS D 579 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG A 6 " --> pdb=" O LYS D 579 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 578 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE D 515 " --> pdb=" O VAL D 578 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 481 " --> pdb=" O ARG D 516 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL D 518 " --> pdb=" O ILE D 481 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE D 483 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU D 411 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR D 410 " --> pdb=" O GLY D 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 231 Processing sheet with id=AA6, first strand: chain 'A' and resid 306 through 308 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7 removed outlier: 6.155A pdb=" N GLN B 2 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL C 577 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B 4 " --> pdb=" O VAL C 577 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS C 579 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG B 6 " --> pdb=" O LYS C 579 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 515 " --> pdb=" O VAL C 578 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE C 481 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 518 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 483 " --> pdb=" O VAL C 518 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR C 435 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE C 412 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165 Processing sheet with id=AB1, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.910A pdb=" N GLU B 207 " --> pdb=" O ARG B 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.452A pdb=" N THR B 220 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 306 through 308 Processing sheet with id=AB4, first strand: chain 'D' and resid 530 through 534 removed outlier: 3.536A pdb=" N ILE D 524 " --> pdb=" O ARG D 553 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2957 1.33 - 1.45: 2447 1.45 - 1.58: 6161 1.58 - 1.70: 75 1.70 - 1.82: 74 Bond restraints: 11714 Sorted by residual: bond pdb=" O10 ASW E 101 " pdb=" S7 ASW E 101 " ideal model delta sigma weight residual 1.453 1.653 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" O10 ASW F 101 " pdb=" S7 ASW F 101 " ideal model delta sigma weight residual 1.453 1.653 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" O9 ASW E 101 " pdb=" S7 ASW E 101 " ideal model delta sigma weight residual 1.453 1.653 -0.200 2.00e-02 2.50e+03 9.98e+01 bond pdb=" O9 ASW F 101 " pdb=" S7 ASW F 101 " ideal model delta sigma weight residual 1.453 1.652 -0.199 2.00e-02 2.50e+03 9.91e+01 bond pdb=" N GLU D 415 " pdb=" CA GLU D 415 " ideal model delta sigma weight residual 1.462 1.381 0.081 1.35e-02 5.49e+03 3.56e+01 ... (remaining 11709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 15620 2.02 - 4.04: 292 4.04 - 6.07: 28 6.07 - 8.09: 10 8.09 - 10.11: 5 Bond angle restraints: 15955 Sorted by residual: angle pdb=" C THR D 414 " pdb=" N GLU D 415 " pdb=" CA GLU D 415 " ideal model delta sigma weight residual 122.85 115.41 7.44 1.39e+00 5.18e-01 2.86e+01 angle pdb=" N GLY A 255 " pdb=" CA GLY A 255 " pdb=" C GLY A 255 " ideal model delta sigma weight residual 115.36 109.13 6.23 1.33e+00 5.65e-01 2.20e+01 angle pdb=" C ILE D 555 " pdb=" CA ILE D 555 " pdb=" CB ILE D 555 " ideal model delta sigma weight residual 111.31 105.21 6.10 1.40e+00 5.10e-01 1.90e+01 angle pdb=" N LYS D 556 " pdb=" CA LYS D 556 " pdb=" CB LYS D 556 " ideal model delta sigma weight residual 110.13 104.54 5.59 1.48e+00 4.57e-01 1.43e+01 angle pdb=" CA ASP A 249 " pdb=" C ASP A 249 " pdb=" N PRO A 250 " ideal model delta sigma weight residual 120.77 117.31 3.46 9.70e-01 1.06e+00 1.28e+01 ... (remaining 15950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 6517 35.72 - 71.43: 391 71.43 - 107.15: 19 107.15 - 142.86: 2 142.86 - 178.58: 1 Dihedral angle restraints: 6930 sinusoidal: 3112 harmonic: 3818 Sorted by residual: dihedral pdb=" CA PHE A 36 " pdb=" C PHE A 36 " pdb=" N LYS A 37 " pdb=" CA LYS A 37 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLU D 457 " pdb=" C GLU D 457 " pdb=" N LEU D 458 " pdb=" CA LEU D 458 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" C5 ASW F 101 " pdb=" N6 ASW F 101 " pdb=" S7 ASW F 101 " pdb=" O10 ASW F 101 " ideal model delta sinusoidal sigma weight residual -174.31 -41.28 -133.03 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 6927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1681 0.108 - 0.217: 34 0.217 - 0.325: 2 0.325 - 0.433: 0 0.433 - 0.541: 1 Chirality restraints: 1718 Sorted by residual: chirality pdb=" P DA E 10 " pdb=" OP1 DA E 10 " pdb=" OP2 DA E 10 " pdb=" O5' DA E 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CB ILE C 523 " pdb=" CA ILE C 523 " pdb=" CG1 ILE C 523 " pdb=" CG2 ILE C 523 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL B 396 " pdb=" CA VAL B 396 " pdb=" CG1 VAL B 396 " pdb=" CG2 VAL B 396 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1715 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 414 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C THR D 414 " -0.041 2.00e-02 2.50e+03 pdb=" O THR D 414 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU D 415 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 416 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C GLY D 416 " -0.033 2.00e-02 2.50e+03 pdb=" O GLY D 416 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP D 417 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 602 " -0.003 2.00e-02 2.50e+03 1.16e-02 3.37e+00 pdb=" CG TRP C 602 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 602 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 602 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 602 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 602 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 602 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 602 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 602 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 602 " 0.000 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 7 2.26 - 2.92: 4753 2.92 - 3.58: 16381 3.58 - 4.24: 27120 4.24 - 4.90: 45478 Nonbonded interactions: 93739 Sorted by model distance: nonbonded pdb=" OH TYR B 117 " pdb=" P DA F 10 " model vdw 1.597 3.400 nonbonded pdb=" OH TYR A 117 " pdb=" P DA E 10 " model vdw 1.627 3.400 nonbonded pdb=" OD2 ASP C 488 " pdb="MG MG C 701 " model vdw 2.122 2.170 nonbonded pdb=" OH TYR B 73 " pdb=" OP2 DA Y 8 " model vdw 2.201 3.040 nonbonded pdb=" O ASP D 490 " pdb=" OG SER D 494 " model vdw 2.216 3.040 ... (remaining 93734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 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: 1.160 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.005 0.200 11714 Z= 0.283 Angle : 0.650 10.110 15955 Z= 0.355 Chirality : 0.044 0.541 1718 Planarity : 0.003 0.039 1904 Dihedral : 20.571 178.579 4482 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.06 % Allowed : 31.95 % Favored : 66.99 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.23), residues: 1302 helix: 0.07 (0.23), residues: 528 sheet: -1.24 (0.46), residues: 140 loop : -0.77 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 438 TYR 0.019 0.001 TYR B 424 PHE 0.027 0.001 PHE B 359 TRP 0.026 0.002 TRP C 602 HIS 0.003 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00546 (11714) covalent geometry : angle 0.65013 (15955) hydrogen bonds : bond 0.15216 ( 463) hydrogen bonds : angle 6.51107 ( 1282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 351 ARG cc_start: 0.7519 (mmp80) cc_final: 0.6952 (mmp80) REVERT: B 403 MET cc_start: 0.5046 (ppp) cc_final: 0.4038 (ppp) REVERT: D 415 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7082 (tt0) outliers start: 12 outliers final: 8 residues processed: 197 average time/residue: 0.1155 time to fit residues: 32.3824 Evaluate side-chains 182 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 319 ASN D 397 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.178024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136838 restraints weight = 14365.138| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.99 r_work: 0.3279 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11714 Z= 0.169 Angle : 0.576 7.987 15955 Z= 0.310 Chirality : 0.042 0.213 1718 Planarity : 0.004 0.041 1904 Dihedral : 16.548 179.204 1882 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.16 % Allowed : 27.96 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.23), residues: 1302 helix: 0.13 (0.23), residues: 544 sheet: -1.49 (0.40), residues: 172 loop : -0.79 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 438 TYR 0.014 0.001 TYR D 435 PHE 0.012 0.001 PHE A 295 TRP 0.010 0.001 TRP C 445 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00384 (11714) covalent geometry : angle 0.57599 (15955) hydrogen bonds : bond 0.04467 ( 463) hydrogen bonds : angle 5.19943 ( 1282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6463 (ttp-170) REVERT: A 351 ARG cc_start: 0.8030 (mmt90) cc_final: 0.7813 (mmt90) REVERT: A 423 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 140 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: B 351 ARG cc_start: 0.8205 (mmp80) cc_final: 0.7834 (mmp80) REVERT: D 415 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7023 (tt0) outliers start: 47 outliers final: 29 residues processed: 217 average time/residue: 0.1117 time to fit residues: 34.7261 Evaluate side-chains 206 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137781 restraints weight = 14475.427| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.99 r_work: 0.3297 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11714 Z= 0.139 Angle : 0.553 12.004 15955 Z= 0.294 Chirality : 0.041 0.206 1718 Planarity : 0.004 0.040 1904 Dihedral : 16.393 177.999 1871 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.51 % Allowed : 27.96 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.23), residues: 1302 helix: 0.11 (0.23), residues: 550 sheet: -1.43 (0.37), residues: 190 loop : -0.73 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 567 TYR 0.015 0.001 TYR A 221 PHE 0.021 0.001 PHE A 350 TRP 0.011 0.001 TRP C 602 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00314 (11714) covalent geometry : angle 0.55252 (15955) hydrogen bonds : bond 0.03949 ( 463) hydrogen bonds : angle 4.95560 ( 1282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 423 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7987 (mm-30) REVERT: B 23 THR cc_start: 0.8563 (p) cc_final: 0.8087 (t) REVERT: B 86 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 140 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: B 351 ARG cc_start: 0.8315 (mmp80) cc_final: 0.7861 (mmp80) REVERT: B 403 MET cc_start: 0.6203 (ppp) cc_final: 0.5957 (ppp) REVERT: D 415 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: D 590 MET cc_start: 0.8534 (tmm) cc_final: 0.8330 (tmm) outliers start: 51 outliers final: 32 residues processed: 211 average time/residue: 0.1008 time to fit residues: 30.5089 Evaluate side-chains 210 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.180663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139569 restraints weight = 14431.546| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.67 r_work: 0.3345 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11714 Z= 0.113 Angle : 0.527 8.079 15955 Z= 0.282 Chirality : 0.040 0.220 1718 Planarity : 0.003 0.041 1904 Dihedral : 16.337 176.679 1871 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.16 % Allowed : 28.23 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.23), residues: 1302 helix: 0.26 (0.23), residues: 548 sheet: -1.35 (0.36), residues: 200 loop : -0.74 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 438 TYR 0.014 0.001 TYR B 424 PHE 0.021 0.001 PHE A 350 TRP 0.020 0.001 TRP C 602 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00249 (11714) covalent geometry : angle 0.52739 (15955) hydrogen bonds : bond 0.03577 ( 463) hydrogen bonds : angle 4.75051 ( 1282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8292 (tptp) cc_final: 0.8041 (tptt) REVERT: B 86 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7579 (mp) REVERT: B 140 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: B 351 ARG cc_start: 0.8346 (mmp80) cc_final: 0.7852 (mmp80) REVERT: B 398 MET cc_start: -0.1018 (OUTLIER) cc_final: -0.1268 (pmm) REVERT: B 403 MET cc_start: 0.6189 (ppp) cc_final: 0.5888 (ppp) REVERT: C 408 ASP cc_start: 0.7600 (p0) cc_final: 0.7368 (p0) REVERT: D 415 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: D 447 MET cc_start: 0.7768 (ptp) cc_final: 0.7304 (ptp) REVERT: D 567 ARG cc_start: 0.7223 (ttm-80) cc_final: 0.6885 (tpp-160) outliers start: 47 outliers final: 31 residues processed: 228 average time/residue: 0.0972 time to fit residues: 32.0138 Evaluate side-chains 213 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS C 571 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.177670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136368 restraints weight = 14398.063| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 4.10 r_work: 0.3274 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11714 Z= 0.165 Angle : 0.553 8.017 15955 Z= 0.295 Chirality : 0.042 0.235 1718 Planarity : 0.004 0.040 1904 Dihedral : 16.448 177.602 1871 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.60 % Allowed : 28.76 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.23), residues: 1302 helix: 0.24 (0.22), residues: 546 sheet: -1.43 (0.36), residues: 190 loop : -0.73 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 438 TYR 0.014 0.001 TYR A 221 PHE 0.022 0.001 PHE A 350 TRP 0.013 0.001 TRP D 584 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00379 (11714) covalent geometry : angle 0.55319 (15955) hydrogen bonds : bond 0.03912 ( 463) hydrogen bonds : angle 4.79432 ( 1282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8211 (tptp) cc_final: 0.7951 (tptt) REVERT: A 351 ARG cc_start: 0.8026 (mmt90) cc_final: 0.7396 (mmm160) REVERT: A 413 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: A 423 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8288 (mm-30) REVERT: B 86 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 140 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: B 351 ARG cc_start: 0.8341 (mmp80) cc_final: 0.8021 (mmp80) REVERT: B 403 MET cc_start: 0.6604 (ppp) cc_final: 0.6295 (ppp) REVERT: C 408 ASP cc_start: 0.7795 (p0) cc_final: 0.7523 (p0) REVERT: D 415 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: D 447 MET cc_start: 0.7912 (ptp) cc_final: 0.7500 (ptp) REVERT: D 567 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.6893 (tpp-160) outliers start: 52 outliers final: 37 residues processed: 210 average time/residue: 0.0998 time to fit residues: 30.0761 Evaluate side-chains 219 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 44 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.180938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140351 restraints weight = 14352.827| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.71 r_work: 0.3327 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11714 Z= 0.113 Angle : 0.529 7.825 15955 Z= 0.282 Chirality : 0.040 0.203 1718 Planarity : 0.003 0.043 1904 Dihedral : 16.350 176.097 1871 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.60 % Allowed : 28.23 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.23), residues: 1302 helix: 0.39 (0.23), residues: 546 sheet: -1.50 (0.35), residues: 200 loop : -0.71 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 275 TYR 0.016 0.001 TYR B 424 PHE 0.022 0.001 PHE A 256 TRP 0.013 0.001 TRP C 584 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00252 (11714) covalent geometry : angle 0.52897 (15955) hydrogen bonds : bond 0.03490 ( 463) hydrogen bonds : angle 4.66556 ( 1282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8196 (tptp) cc_final: 0.7938 (tptt) REVERT: A 292 MET cc_start: 0.7791 (mmt) cc_final: 0.7396 (mmp) REVERT: A 413 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: A 423 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8272 (mm-30) REVERT: B 86 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 140 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: B 240 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7512 (mmm-85) REVERT: B 343 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7162 (mm) REVERT: B 351 ARG cc_start: 0.8323 (mmp80) cc_final: 0.7975 (mmp80) REVERT: B 393 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7436 (t70) REVERT: B 398 MET cc_start: -0.0675 (OUTLIER) cc_final: -0.1074 (pmm) REVERT: B 403 MET cc_start: 0.6397 (ppp) cc_final: 0.6107 (ppp) REVERT: C 408 ASP cc_start: 0.7809 (p0) cc_final: 0.7573 (p0) REVERT: D 415 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: D 447 MET cc_start: 0.7882 (ptp) cc_final: 0.7466 (ptp) REVERT: D 567 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.6870 (tpp-160) REVERT: D 583 ASN cc_start: 0.7119 (p0) cc_final: 0.6888 (p0) outliers start: 52 outliers final: 37 residues processed: 219 average time/residue: 0.0990 time to fit residues: 31.1864 Evaluate side-chains 222 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 0.7980 chunk 105 optimal weight: 0.0060 chunk 87 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.180595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142540 restraints weight = 14336.191| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.85 r_work: 0.3315 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11714 Z= 0.122 Angle : 0.531 8.900 15955 Z= 0.281 Chirality : 0.040 0.191 1718 Planarity : 0.003 0.039 1904 Dihedral : 16.350 176.126 1871 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.78 % Allowed : 28.50 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.23), residues: 1302 helix: 0.43 (0.23), residues: 546 sheet: -1.52 (0.36), residues: 190 loop : -0.65 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 438 TYR 0.008 0.001 TYR A 334 PHE 0.023 0.001 PHE B 359 TRP 0.009 0.001 TRP D 584 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00275 (11714) covalent geometry : angle 0.53056 (15955) hydrogen bonds : bond 0.03495 ( 463) hydrogen bonds : angle 4.59837 ( 1282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8185 (tptp) cc_final: 0.7934 (tptt) REVERT: A 351 ARG cc_start: 0.7980 (mmt90) cc_final: 0.7470 (mmm160) REVERT: A 413 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 423 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8316 (mm-30) REVERT: B 86 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7615 (mp) REVERT: B 140 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: B 240 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7543 (mmm-85) REVERT: B 343 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7220 (mm) REVERT: B 351 ARG cc_start: 0.8339 (mmp80) cc_final: 0.7930 (mmp80) REVERT: B 398 MET cc_start: -0.0594 (OUTLIER) cc_final: -0.1023 (pmm) REVERT: B 403 MET cc_start: 0.6335 (ppp) cc_final: 0.6093 (ppp) REVERT: C 408 ASP cc_start: 0.7831 (p0) cc_final: 0.7631 (p0) REVERT: D 415 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: D 534 PHE cc_start: 0.7900 (m-80) cc_final: 0.7666 (m-80) REVERT: D 567 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.6931 (tpp-160) outliers start: 54 outliers final: 35 residues processed: 215 average time/residue: 0.0999 time to fit residues: 30.8942 Evaluate side-chains 218 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 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 402 HIS B 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.181603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143684 restraints weight = 14287.101| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.79 r_work: 0.3325 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11714 Z= 0.117 Angle : 0.533 8.266 15955 Z= 0.282 Chirality : 0.040 0.183 1718 Planarity : 0.003 0.039 1904 Dihedral : 16.315 175.742 1867 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.16 % Allowed : 29.12 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.23), residues: 1302 helix: 0.48 (0.23), residues: 546 sheet: -1.16 (0.37), residues: 176 loop : -0.74 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 438 TYR 0.019 0.001 TYR B 424 PHE 0.025 0.001 PHE A 350 TRP 0.011 0.001 TRP D 584 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00262 (11714) covalent geometry : angle 0.53251 (15955) hydrogen bonds : bond 0.03387 ( 463) hydrogen bonds : angle 4.56809 ( 1282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8173 (tptp) cc_final: 0.7930 (tptt) REVERT: A 351 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7757 (mmt90) REVERT: A 413 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: A 423 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 86 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 140 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7077 (mp10) REVERT: B 240 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: B 343 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7218 (mm) REVERT: B 351 ARG cc_start: 0.8331 (mmp80) cc_final: 0.7943 (mmp80) REVERT: B 393 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7423 (t70) REVERT: B 403 MET cc_start: 0.6300 (ppp) cc_final: 0.6085 (ppp) REVERT: D 415 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: D 534 PHE cc_start: 0.7873 (m-80) cc_final: 0.7632 (m-80) REVERT: D 567 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.7036 (tpp-160) outliers start: 47 outliers final: 34 residues processed: 209 average time/residue: 0.0992 time to fit residues: 29.9691 Evaluate side-chains 215 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 0.0050 chunk 11 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.181816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143766 restraints weight = 14196.535| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.82 r_work: 0.3338 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11714 Z= 0.116 Angle : 0.532 9.472 15955 Z= 0.283 Chirality : 0.040 0.226 1718 Planarity : 0.003 0.039 1904 Dihedral : 16.280 175.547 1867 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.07 % Allowed : 29.73 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.23), residues: 1302 helix: 0.50 (0.23), residues: 548 sheet: -1.48 (0.34), residues: 200 loop : -0.73 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 438 TYR 0.014 0.001 TYR C 535 PHE 0.026 0.001 PHE B 359 TRP 0.012 0.001 TRP C 602 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00261 (11714) covalent geometry : angle 0.53225 (15955) hydrogen bonds : bond 0.03354 ( 463) hydrogen bonds : angle 4.54479 ( 1282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8170 (tptp) cc_final: 0.7935 (tptt) REVERT: A 292 MET cc_start: 0.7737 (mmt) cc_final: 0.7513 (mmt) REVERT: A 351 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7729 (mmt90) REVERT: A 413 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: A 423 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 86 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 140 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: B 240 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7502 (mmm-85) REVERT: B 343 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7255 (mm) REVERT: B 351 ARG cc_start: 0.8350 (mmp80) cc_final: 0.7960 (mmp80) REVERT: B 393 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7418 (t70) REVERT: B 403 MET cc_start: 0.6269 (ppp) cc_final: 0.6065 (ppp) REVERT: D 415 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: D 534 PHE cc_start: 0.7836 (m-80) cc_final: 0.7607 (m-80) REVERT: D 567 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.7076 (tpp-160) outliers start: 46 outliers final: 35 residues processed: 210 average time/residue: 0.1041 time to fit residues: 31.2927 Evaluate side-chains 218 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.0020 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.181647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140607 restraints weight = 14433.034| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.68 r_work: 0.3353 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11714 Z= 0.122 Angle : 0.553 12.099 15955 Z= 0.291 Chirality : 0.041 0.223 1718 Planarity : 0.003 0.039 1904 Dihedral : 16.257 175.628 1867 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.98 % Allowed : 29.29 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.23), residues: 1302 helix: 0.45 (0.23), residues: 548 sheet: -1.44 (0.34), residues: 200 loop : -0.75 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.020 0.001 TYR B 424 PHE 0.027 0.001 PHE B 359 TRP 0.013 0.001 TRP D 584 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00274 (11714) covalent geometry : angle 0.55320 (15955) hydrogen bonds : bond 0.03401 ( 463) hydrogen bonds : angle 4.52453 ( 1282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8235 (tptp) cc_final: 0.7999 (tptt) REVERT: A 351 ARG cc_start: 0.7961 (mmt90) cc_final: 0.7707 (mmt90) REVERT: A 413 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: A 423 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8297 (mm-30) REVERT: B 86 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7552 (mp) REVERT: B 140 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: B 240 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7471 (mmm-85) REVERT: B 343 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7237 (mm) REVERT: B 351 ARG cc_start: 0.8355 (mmp80) cc_final: 0.7959 (mmp80) REVERT: B 393 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7410 (t70) REVERT: D 415 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: D 534 PHE cc_start: 0.7815 (m-80) cc_final: 0.7582 (m-80) REVERT: D 567 ARG cc_start: 0.7370 (ttm-80) cc_final: 0.7060 (tpp-160) outliers start: 45 outliers final: 35 residues processed: 205 average time/residue: 0.0976 time to fit residues: 29.1802 Evaluate side-chains 215 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 85 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.181869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140506 restraints weight = 14341.174| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.71 r_work: 0.3353 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11714 Z= 0.123 Angle : 0.565 11.725 15955 Z= 0.296 Chirality : 0.041 0.223 1718 Planarity : 0.003 0.038 1904 Dihedral : 16.230 175.592 1867 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.54 % Allowed : 30.09 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.23), residues: 1302 helix: 0.44 (0.23), residues: 548 sheet: -1.42 (0.34), residues: 200 loop : -0.74 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 240 TYR 0.008 0.001 TYR A 334 PHE 0.028 0.001 PHE B 359 TRP 0.013 0.001 TRP D 584 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00277 (11714) covalent geometry : angle 0.56543 (15955) hydrogen bonds : bond 0.03385 ( 463) hydrogen bonds : angle 4.50242 ( 1282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2752.64 seconds wall clock time: 47 minutes 59.78 seconds (2879.78 seconds total)