Starting phenix.real_space_refine on Wed Feb 4 16:22:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lii_63118/02_2026/9lii_63118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lii_63118/02_2026/9lii_63118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lii_63118/02_2026/9lii_63118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lii_63118/02_2026/9lii_63118.map" model { file = "/net/cci-nas-00/data/ceres_data/9lii_63118/02_2026/9lii_63118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lii_63118/02_2026/9lii_63118.cif" } resolution = 3.06 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= -0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 7360 2.51 5 N 1948 2.21 5 O 2164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11514 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" 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: "A" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2194 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain: "D" 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: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2194 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Time building chain proxies: 2.81, per 1000 atoms: 0.24 Number of scatterers: 11514 At special positions: 0 Unit cell: (126.88, 119.6, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2164 8.00 N 1948 7.00 C 7360 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: 0.93 Conformation dependent library (CDL) restraints added in 750.4 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 21 sheets defined 46.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'C' and resid 6 through 16 removed outlier: 3.895A pdb=" N SER C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 removed outlier: 3.600A pdb=" N ASN C 26 " --> pdb=" O TYR C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.680A pdb=" N LEU C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 89 removed outlier: 4.407A pdb=" N SER C 79 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.607A pdb=" N TYR C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.551A pdb=" N ALA C 136 " --> pdb=" O THR C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.735A pdb=" N ASN C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 239 through 247 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 319 through 365 removed outlier: 3.706A pdb=" N LEU C 323 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 404 through 427 Processing helix chain 'C' and resid 429 through 438 Processing helix chain 'A' and resid 418 through 427 removed outlier: 4.105A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 4.068A pdb=" N LEU A 453 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.215A pdb=" N SER A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 583 removed outlier: 4.118A pdb=" N PHE A 581 " --> pdb=" O TRP A 577 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 654 through 662 removed outlier: 5.011A pdb=" N GLU A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 61 through 67 removed outlier: 3.647A pdb=" N GLY D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.586A pdb=" N LEU D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 89 removed outlier: 4.510A pdb=" N SER D 79 " --> pdb=" O HIS D 75 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 removed outlier: 3.535A pdb=" N TYR D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.516A pdb=" N GLY D 161 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 319 through 365 removed outlier: 3.611A pdb=" N LEU D 323 " --> pdb=" O ASN D 319 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 334 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 360 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.578A pdb=" N LYS D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 390 removed outlier: 4.125A pdb=" N SER D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 Processing helix chain 'D' and resid 399 through 403 removed outlier: 3.565A pdb=" N HIS D 402 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 Processing helix chain 'D' and resid 429 through 438 removed outlier: 3.517A pdb=" N ASP D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 removed outlier: 3.808A pdb=" N ASP B 425 " --> pdb=" O GLY B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 509 through 514 removed outlier: 3.607A pdb=" N LYS B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 559 through 564 removed outlier: 3.653A pdb=" N GLY B 564 " --> pdb=" O HIS B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 removed outlier: 4.177A pdb=" N SER B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 571 " --> pdb=" O TYR B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 3.660A pdb=" N GLU B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 615 removed outlier: 3.548A pdb=" N TYR B 611 " --> pdb=" O THR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 removed outlier: 3.542A pdb=" N SER B 631 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 632 " --> pdb=" O LEU B 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 628 through 632' Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 654 through 662 removed outlier: 4.041A pdb=" N PHE B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.684A pdb=" N GLN C 2 " --> pdb=" O TYR A 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'C' and resid 163 through 166 removed outlier: 3.515A pdb=" N THR C 171 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AA6, first strand: chain 'C' and resid 305 through 308 removed outlier: 4.167A pdb=" N ILE C 305 " --> pdb=" O TYR C 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 414 removed outlier: 6.710A pdb=" N LEU A 411 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET A 555 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU A 413 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 552 " --> pdb=" O ARG A 587 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 476 removed outlier: 6.941A pdb=" N GLU A 475 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 490 through 495 Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 508 Processing sheet with id=AB2, first strand: chain 'A' and resid 594 through 595 Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AB4, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AB5, first strand: chain 'D' and resid 163 through 165 Processing sheet with id=AB6, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 223 removed outlier: 3.704A pdb=" N LYS D 271 " --> pdb=" O ASP D 260 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 305 through 308 removed outlier: 4.402A pdb=" N ILE D 305 " --> pdb=" O TYR D 317 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 410 through 414 removed outlier: 6.171A pdb=" N LEU B 411 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET B 555 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU B 413 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 552 " --> pdb=" O ARG B 587 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 490 through 495 Processing sheet with id=AC2, first strand: chain 'B' and resid 505 through 508 Processing sheet with id=AC3, first strand: chain 'B' and resid 604 through 605 removed outlier: 3.784A pdb=" N ILE B 595 " --> pdb=" O ARG B 624 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 624 " --> pdb=" O ILE B 595 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3728 1.34 - 1.46: 1803 1.46 - 1.57: 6140 1.57 - 1.69: 1 1.69 - 1.81: 78 Bond restraints: 11750 Sorted by residual: bond pdb=" CA ILE D 145 " pdb=" CB ILE D 145 " ideal model delta sigma weight residual 1.534 1.555 -0.021 6.80e-03 2.16e+04 9.33e+00 bond pdb=" CB PRO D 96 " pdb=" CG PRO D 96 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.67e+00 bond pdb=" CB ASP C 49 " pdb=" CG ASP C 49 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.99e+00 bond pdb=" CG PRO A 578 " pdb=" CD PRO A 578 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.81e+00 bond pdb=" CB ASP D 239 " pdb=" CG ASP D 239 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.61e+00 ... (remaining 11745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 15298 1.63 - 3.26: 442 3.26 - 4.89: 63 4.89 - 6.52: 15 6.52 - 8.15: 8 Bond angle restraints: 15826 Sorted by residual: angle pdb=" CA PRO D 96 " pdb=" N PRO D 96 " pdb=" CD PRO D 96 " ideal model delta sigma weight residual 112.00 106.25 5.75 1.40e+00 5.10e-01 1.69e+01 angle pdb=" CA PRO A 578 " pdb=" N PRO A 578 " pdb=" CD PRO A 578 " ideal model delta sigma weight residual 112.00 107.15 4.85 1.40e+00 5.10e-01 1.20e+01 angle pdb=" C SER A 565 " pdb=" N ILE A 566 " pdb=" CA ILE A 566 " ideal model delta sigma weight residual 120.46 125.18 -4.72 1.37e+00 5.33e-01 1.19e+01 angle pdb=" C LEU C 48 " pdb=" N ASP C 49 " pdb=" CA ASP C 49 " ideal model delta sigma weight residual 121.14 115.46 5.68 1.75e+00 3.27e-01 1.05e+01 angle pdb=" N VAL B 426 " pdb=" CA VAL B 426 " pdb=" C VAL B 426 " ideal model delta sigma weight residual 113.53 110.64 2.89 9.80e-01 1.04e+00 8.71e+00 ... (remaining 15821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 6011 17.80 - 35.61: 845 35.61 - 53.41: 184 53.41 - 71.21: 37 71.21 - 89.01: 15 Dihedral angle restraints: 7092 sinusoidal: 2928 harmonic: 4164 Sorted by residual: dihedral pdb=" CA GLY C 366 " pdb=" C GLY C 366 " pdb=" N GLU C 367 " pdb=" CA GLU C 367 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ILE A 398 " pdb=" C ILE A 398 " pdb=" N LYS A 399 " pdb=" CA LYS A 399 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA TYR D 238 " pdb=" C TYR D 238 " pdb=" N ASP D 239 " pdb=" CA ASP D 239 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 7089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1405 0.054 - 0.107: 262 0.107 - 0.161: 42 0.161 - 0.215: 0 0.215 - 0.269: 3 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CG LEU B 431 " pdb=" CB LEU B 431 " pdb=" CD1 LEU B 431 " pdb=" CD2 LEU B 431 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CG LEU A 431 " pdb=" CB LEU A 431 " pdb=" CD1 LEU A 431 " pdb=" CD2 LEU A 431 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB THR C 346 " pdb=" CA THR C 346 " pdb=" OG1 THR C 346 " pdb=" CG2 THR C 346 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1709 not shown) Planarity restraints: 2026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 577 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 578 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 578 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 578 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 95 " 0.055 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO D 96 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 96 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 96 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 435 " 0.046 5.00e-02 4.00e+02 7.08e-02 8.01e+00 pdb=" N PRO A 436 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.039 5.00e-02 4.00e+02 ... (remaining 2023 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 184 2.65 - 3.21: 10814 3.21 - 3.77: 17821 3.77 - 4.34: 24499 4.34 - 4.90: 40219 Nonbonded interactions: 93537 Sorted by model distance: nonbonded pdb=" OH TYR D 278 " pdb=" OD2 ASP D 294 " model vdw 2.082 3.040 nonbonded pdb=" OH TYR D 135 " pdb=" OD1 ASN D 341 " model vdw 2.101 3.040 nonbonded pdb=" OE1 GLN B 602 " pdb=" NE1 TRP B 604 " model vdw 2.117 3.120 nonbonded pdb=" OG1 THR C 404 " pdb=" OD1 ASP C 406 " model vdw 2.123 3.040 nonbonded pdb=" O TRP C 91 " pdb=" OH TYR C 236 " model vdw 2.134 3.040 ... (remaining 93532 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: 0.01 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 0.096 11750 Z= 0.195 Angle : 0.678 8.149 15826 Z= 0.374 Chirality : 0.044 0.269 1712 Planarity : 0.005 0.128 2026 Dihedral : 17.109 89.012 4420 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.56 % Allowed : 24.27 % Favored : 75.16 % 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 are not related in a simple way. whole: -0.36 (0.22), residues: 1422 helix: 0.44 (0.22), residues: 556 sheet: -1.31 (0.38), residues: 178 loop : -0.37 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 46 TYR 0.022 0.002 TYR B 422 PHE 0.029 0.002 PHE B 588 TRP 0.033 0.002 TRP A 577 HIS 0.005 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00460 (11750) covalent geometry : angle 0.67806 (15826) hydrogen bonds : bond 0.17300 ( 462) hydrogen bonds : angle 6.62297 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: C 172 TYR cc_start: 0.7884 (t80) cc_final: 0.7525 (t80) REVERT: A 610 GLU cc_start: 0.8085 (tp30) cc_final: 0.7648 (mt-10) REVERT: D 394 LYS cc_start: 0.7238 (mmtp) cc_final: 0.6602 (mtmt) REVERT: D 403 MET cc_start: 0.4717 (mtm) cc_final: 0.3603 (mmm) REVERT: B 422 TYR cc_start: 0.8421 (m-80) cc_final: 0.7458 (m-80) REVERT: B 661 MET cc_start: 0.6791 (ppp) cc_final: 0.6509 (ppp) outliers start: 7 outliers final: 5 residues processed: 188 average time/residue: 0.0955 time to fit residues: 26.1805 Evaluate side-chains 174 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 12 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.213043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.155082 restraints weight = 14620.409| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.89 r_work: 0.3782 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11750 Z= 0.126 Angle : 0.570 7.747 15826 Z= 0.299 Chirality : 0.042 0.158 1712 Planarity : 0.004 0.070 2026 Dihedral : 5.052 44.232 1562 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.18 % Allowed : 22.74 % Favored : 75.08 % 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 are not related in a simple way. whole: -0.14 (0.22), residues: 1422 helix: 0.63 (0.22), residues: 574 sheet: -1.37 (0.41), residues: 154 loop : -0.28 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 6 TYR 0.018 0.001 TYR A 435 PHE 0.011 0.001 PHE B 483 TRP 0.018 0.001 TRP A 577 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00290 (11750) covalent geometry : angle 0.57010 (15826) hydrogen bonds : bond 0.03652 ( 462) hydrogen bonds : angle 5.07541 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 172 TYR cc_start: 0.7605 (t80) cc_final: 0.6998 (t80) REVERT: C 238 TYR cc_start: 0.8326 (m-80) cc_final: 0.8121 (m-10) REVERT: C 350 PHE cc_start: 0.7673 (t80) cc_final: 0.7239 (t80) REVERT: C 354 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: A 555 MET cc_start: 0.7973 (ttm) cc_final: 0.7763 (ttm) REVERT: A 610 GLU cc_start: 0.8041 (tp30) cc_final: 0.7801 (tp30) REVERT: A 660 GLU cc_start: 0.7976 (mp0) cc_final: 0.7690 (mp0) REVERT: D 218 ARG cc_start: 0.7729 (mtt90) cc_final: 0.7492 (mtp85) REVERT: D 394 LYS cc_start: 0.7298 (mmtp) cc_final: 0.6493 (mtmt) REVERT: B 422 TYR cc_start: 0.8314 (m-80) cc_final: 0.7287 (m-80) REVERT: B 431 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6618 (pp) REVERT: B 447 MET cc_start: 0.5678 (tmm) cc_final: 0.5430 (tmt) REVERT: B 616 ASP cc_start: 0.6624 (m-30) cc_final: 0.6365 (p0) outliers start: 27 outliers final: 15 residues processed: 204 average time/residue: 0.0816 time to fit residues: 25.0038 Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.211447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.154234 restraints weight = 14735.403| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.86 r_work: 0.3767 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11750 Z= 0.124 Angle : 0.529 7.622 15826 Z= 0.277 Chirality : 0.041 0.154 1712 Planarity : 0.004 0.056 2026 Dihedral : 4.816 44.066 1554 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.39 % Allowed : 22.02 % Favored : 74.60 % 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 are not related in a simple way. whole: -0.06 (0.22), residues: 1422 helix: 0.74 (0.22), residues: 576 sheet: -1.35 (0.44), residues: 134 loop : -0.32 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 218 TYR 0.015 0.001 TYR D 135 PHE 0.009 0.001 PHE C 359 TRP 0.020 0.001 TRP A 577 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00294 (11750) covalent geometry : angle 0.52918 (15826) hydrogen bonds : bond 0.03398 ( 462) hydrogen bonds : angle 4.79892 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.293 Fit side-chains REVERT: C 172 TYR cc_start: 0.7768 (t80) cc_final: 0.7061 (t80) REVERT: C 238 TYR cc_start: 0.8384 (m-80) cc_final: 0.8158 (m-10) REVERT: C 354 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: C 429 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7097 (p0) REVERT: C 438 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7716 (tt) REVERT: A 555 MET cc_start: 0.8028 (ttm) cc_final: 0.7797 (ttm) REVERT: A 660 GLU cc_start: 0.7962 (mp0) cc_final: 0.7544 (mp0) REVERT: D 394 LYS cc_start: 0.7252 (mmtp) cc_final: 0.6456 (mtmt) REVERT: B 422 TYR cc_start: 0.8373 (m-80) cc_final: 0.7410 (m-80) REVERT: B 431 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6893 (pp) REVERT: B 432 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7785 (m-70) REVERT: B 616 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6374 (p0) REVERT: B 661 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6276 (ppp) outliers start: 42 outliers final: 19 residues processed: 214 average time/residue: 0.0723 time to fit residues: 24.0102 Evaluate side-chains 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 28 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 136 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.211679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.154737 restraints weight = 14820.170| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.85 r_work: 0.3781 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11750 Z= 0.109 Angle : 0.516 7.963 15826 Z= 0.269 Chirality : 0.041 0.151 1712 Planarity : 0.004 0.047 2026 Dihedral : 4.749 44.467 1554 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.74 % Allowed : 22.98 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.22), residues: 1422 helix: 0.82 (0.22), residues: 588 sheet: -1.22 (0.45), residues: 134 loop : -0.32 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 427 TYR 0.021 0.001 TYR D 135 PHE 0.024 0.001 PHE B 588 TRP 0.020 0.001 TRP A 577 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00252 (11750) covalent geometry : angle 0.51641 (15826) hydrogen bonds : bond 0.03052 ( 462) hydrogen bonds : angle 4.59363 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.423 Fit side-chains REVERT: C 19 TYR cc_start: 0.7834 (t80) cc_final: 0.7609 (t80) REVERT: C 187 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7133 (mt0) REVERT: C 238 TYR cc_start: 0.8421 (m-80) cc_final: 0.8206 (m-10) REVERT: C 354 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: C 429 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7087 (p0) REVERT: C 438 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 428 ASP cc_start: 0.7629 (t70) cc_final: 0.7228 (t0) REVERT: A 555 MET cc_start: 0.8043 (ttm) cc_final: 0.7801 (ttm) REVERT: A 566 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7600 (pt) REVERT: A 660 GLU cc_start: 0.7917 (mp0) cc_final: 0.7467 (mp0) REVERT: D 394 LYS cc_start: 0.7281 (mmtp) cc_final: 0.6469 (mtmt) REVERT: B 422 TYR cc_start: 0.8360 (m-80) cc_final: 0.7463 (m-80) REVERT: B 431 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6948 (pp) REVERT: B 616 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.6396 (p0) REVERT: B 661 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6253 (ppp) outliers start: 34 outliers final: 16 residues processed: 203 average time/residue: 0.0825 time to fit residues: 25.4294 Evaluate side-chains 187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 0.0030 chunk 131 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.210843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.153388 restraints weight = 14756.243| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.91 r_work: 0.3778 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11750 Z= 0.119 Angle : 0.513 8.014 15826 Z= 0.267 Chirality : 0.041 0.160 1712 Planarity : 0.003 0.047 2026 Dihedral : 4.718 44.335 1554 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.39 % Allowed : 22.66 % Favored : 73.95 % 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 are not related in a simple way. whole: -0.01 (0.22), residues: 1422 helix: 0.83 (0.22), residues: 588 sheet: -1.74 (0.41), residues: 146 loop : -0.21 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 218 TYR 0.023 0.001 TYR D 135 PHE 0.025 0.001 PHE B 588 TRP 0.018 0.001 TRP A 577 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00281 (11750) covalent geometry : angle 0.51326 (15826) hydrogen bonds : bond 0.02993 ( 462) hydrogen bonds : angle 4.53929 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.374 Fit side-chains REVERT: C 19 TYR cc_start: 0.7826 (t80) cc_final: 0.7603 (t80) REVERT: C 187 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7116 (mt0) REVERT: C 238 TYR cc_start: 0.8377 (m-80) cc_final: 0.8145 (m-10) REVERT: C 304 ASN cc_start: 0.8285 (t0) cc_final: 0.8068 (t0) REVERT: C 354 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: C 429 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7153 (p0) REVERT: C 438 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7652 (tt) REVERT: A 428 ASP cc_start: 0.7611 (t70) cc_final: 0.7205 (t0) REVERT: A 555 MET cc_start: 0.8066 (ttm) cc_final: 0.7815 (ttm) REVERT: A 566 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7503 (pt) REVERT: A 660 GLU cc_start: 0.7946 (mp0) cc_final: 0.7594 (mp0) REVERT: D 394 LYS cc_start: 0.7346 (mmtp) cc_final: 0.6522 (mtmt) REVERT: B 422 TYR cc_start: 0.8265 (m-80) cc_final: 0.7307 (m-80) REVERT: B 431 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6846 (pp) REVERT: B 616 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6418 (p0) REVERT: B 661 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6272 (ppp) outliers start: 42 outliers final: 25 residues processed: 201 average time/residue: 0.0729 time to fit residues: 22.5552 Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 HIS ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.202573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.144865 restraints weight = 14617.537| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.77 r_work: 0.3634 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11750 Z= 0.196 Angle : 0.597 8.357 15826 Z= 0.309 Chirality : 0.044 0.183 1712 Planarity : 0.004 0.044 2026 Dihedral : 4.990 46.383 1554 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.71 % Allowed : 22.34 % Favored : 73.95 % 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 are not related in a simple way. whole: -0.22 (0.22), residues: 1422 helix: 0.55 (0.21), residues: 592 sheet: -1.53 (0.43), residues: 134 loop : -0.36 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 587 TYR 0.025 0.002 TYR D 135 PHE 0.028 0.002 PHE B 588 TRP 0.019 0.001 TRP A 577 HIS 0.007 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00482 (11750) covalent geometry : angle 0.59652 (15826) hydrogen bonds : bond 0.03424 ( 462) hydrogen bonds : angle 4.66826 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.397 Fit side-chains REVERT: C 19 TYR cc_start: 0.8078 (t80) cc_final: 0.7826 (t80) REVERT: C 187 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: C 238 TYR cc_start: 0.8501 (m-80) cc_final: 0.8212 (m-10) REVERT: C 429 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7425 (p0) REVERT: C 438 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7922 (tt) REVERT: A 555 MET cc_start: 0.8150 (ttm) cc_final: 0.7890 (ttm) REVERT: A 566 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7681 (pt) REVERT: A 660 GLU cc_start: 0.7832 (mp0) cc_final: 0.7440 (mp0) REVERT: D 27 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.6036 (mtt180) REVERT: D 135 TYR cc_start: 0.7461 (m-10) cc_final: 0.7238 (m-80) REVERT: D 186 LEU cc_start: 0.6696 (tp) cc_final: 0.6456 (tt) REVERT: D 394 LYS cc_start: 0.7540 (mmtp) cc_final: 0.6750 (mtmt) REVERT: B 422 TYR cc_start: 0.8384 (m-80) cc_final: 0.7505 (m-80) REVERT: B 431 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7143 (pp) REVERT: B 600 LYS cc_start: 0.7683 (mmtt) cc_final: 0.6518 (tptp) REVERT: B 661 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6306 (ppp) outliers start: 46 outliers final: 26 residues processed: 203 average time/residue: 0.0695 time to fit residues: 21.6690 Evaluate side-chains 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 138 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 107 optimal weight: 0.0770 chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 144 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.207226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149278 restraints weight = 14579.892| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.85 r_work: 0.3706 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11750 Z= 0.113 Angle : 0.541 9.917 15826 Z= 0.282 Chirality : 0.041 0.169 1712 Planarity : 0.004 0.048 2026 Dihedral : 4.881 48.567 1554 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.26 % Allowed : 24.11 % Favored : 73.63 % 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 are not related in a simple way. whole: -0.02 (0.22), residues: 1422 helix: 0.73 (0.21), residues: 590 sheet: -1.47 (0.43), residues: 134 loop : -0.24 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 218 TYR 0.027 0.001 TYR A 646 PHE 0.023 0.001 PHE B 588 TRP 0.011 0.001 TRP A 577 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00260 (11750) covalent geometry : angle 0.54096 (15826) hydrogen bonds : bond 0.02903 ( 462) hydrogen bonds : angle 4.52811 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 19 TYR cc_start: 0.8028 (t80) cc_final: 0.7813 (t80) REVERT: C 92 ASN cc_start: 0.8203 (t0) cc_final: 0.7975 (t0) REVERT: C 218 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7189 (mtt90) REVERT: C 238 TYR cc_start: 0.8403 (m-80) cc_final: 0.8134 (m-10) REVERT: C 429 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7111 (p0) REVERT: C 438 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7739 (tt) REVERT: A 428 ASP cc_start: 0.7626 (t70) cc_final: 0.7231 (t0) REVERT: A 566 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7635 (pt) REVERT: A 660 GLU cc_start: 0.7835 (mp0) cc_final: 0.7411 (mp0) REVERT: D 186 LEU cc_start: 0.6533 (tp) cc_final: 0.6307 (tt) REVERT: D 229 MET cc_start: 0.6659 (ptt) cc_final: 0.6368 (ptm) REVERT: D 300 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7545 (mmt90) REVERT: B 431 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7006 (pp) REVERT: B 587 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7953 (mtt180) REVERT: B 600 LYS cc_start: 0.7497 (mmtt) cc_final: 0.6370 (tptp) REVERT: B 661 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6401 (ppp) outliers start: 28 outliers final: 16 residues processed: 187 average time/residue: 0.0716 time to fit residues: 20.4057 Evaluate side-chains 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 0.0670 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.206991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150614 restraints weight = 14495.050| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.79 r_work: 0.3689 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11750 Z= 0.105 Angle : 0.537 9.397 15826 Z= 0.279 Chirality : 0.041 0.177 1712 Planarity : 0.003 0.048 2026 Dihedral : 4.815 48.880 1554 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.34 % Allowed : 24.60 % Favored : 73.06 % 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 are not related in a simple way. whole: -0.00 (0.22), residues: 1422 helix: 0.76 (0.22), residues: 594 sheet: -1.49 (0.43), residues: 134 loop : -0.24 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 218 TYR 0.017 0.001 TYR A 646 PHE 0.022 0.001 PHE B 588 TRP 0.015 0.001 TRP A 577 HIS 0.002 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00241 (11750) covalent geometry : angle 0.53656 (15826) hydrogen bonds : bond 0.02795 ( 462) hydrogen bonds : angle 4.44356 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 ASN cc_start: 0.8184 (t0) cc_final: 0.7957 (t0) REVERT: C 218 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7158 (mtt90) REVERT: C 238 TYR cc_start: 0.8343 (m-80) cc_final: 0.8122 (m-10) REVERT: C 429 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7101 (p0) REVERT: C 438 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7760 (tt) REVERT: A 396 LYS cc_start: 0.6000 (pttp) cc_final: 0.5789 (mtmm) REVERT: A 428 ASP cc_start: 0.7658 (t70) cc_final: 0.7348 (t0) REVERT: A 566 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7592 (pt) REVERT: A 660 GLU cc_start: 0.7763 (mp0) cc_final: 0.7323 (mp0) REVERT: D 186 LEU cc_start: 0.6609 (tp) cc_final: 0.6332 (tt) REVERT: B 431 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7087 (pp) REVERT: B 445 TRP cc_start: 0.6900 (t-100) cc_final: 0.6505 (t-100) REVERT: B 555 MET cc_start: 0.6596 (mtp) cc_final: 0.6239 (mtp) REVERT: B 600 LYS cc_start: 0.7468 (mmtt) cc_final: 0.6371 (tptp) REVERT: B 661 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6425 (ppp) outliers start: 29 outliers final: 18 residues processed: 179 average time/residue: 0.0850 time to fit residues: 22.8949 Evaluate side-chains 173 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.202355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144933 restraints weight = 14384.156| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.74 r_work: 0.3660 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11750 Z= 0.203 Angle : 0.612 9.220 15826 Z= 0.317 Chirality : 0.044 0.188 1712 Planarity : 0.004 0.045 2026 Dihedral : 5.065 50.012 1554 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.18 % Allowed : 24.68 % Favored : 73.15 % 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 are not related in a simple way. whole: -0.16 (0.22), residues: 1422 helix: 0.56 (0.21), residues: 592 sheet: -1.50 (0.44), residues: 134 loop : -0.27 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 218 TYR 0.020 0.002 TYR C 19 PHE 0.027 0.002 PHE B 588 TRP 0.018 0.001 TRP A 577 HIS 0.005 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00503 (11750) covalent geometry : angle 0.61183 (15826) hydrogen bonds : bond 0.03230 ( 462) hydrogen bonds : angle 4.61489 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: C 218 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7305 (mtt90) REVERT: C 238 TYR cc_start: 0.8484 (m-80) cc_final: 0.8099 (m-10) REVERT: C 429 ASP cc_start: 0.7801 (p0) cc_final: 0.7192 (p0) REVERT: C 438 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 428 ASP cc_start: 0.7814 (t70) cc_final: 0.7339 (t0) REVERT: A 566 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7652 (pt) REVERT: A 660 GLU cc_start: 0.7717 (mp0) cc_final: 0.7383 (mp0) REVERT: D 211 ILE cc_start: 0.8100 (mm) cc_final: 0.7666 (tt) REVERT: D 297 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6449 (mp) REVERT: B 422 TYR cc_start: 0.8361 (m-80) cc_final: 0.7503 (m-80) REVERT: B 431 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7070 (pp) REVERT: B 445 TRP cc_start: 0.7034 (t-100) cc_final: 0.6597 (t-100) REVERT: B 555 MET cc_start: 0.7166 (mtp) cc_final: 0.6874 (mtp) REVERT: B 600 LYS cc_start: 0.7415 (mmtt) cc_final: 0.6293 (tptp) REVERT: B 601 LYS cc_start: 0.7637 (ptpp) cc_final: 0.7334 (mtmm) REVERT: B 661 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6455 (ppp) outliers start: 27 outliers final: 21 residues processed: 178 average time/residue: 0.0804 time to fit residues: 22.1713 Evaluate side-chains 178 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 107 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 120 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.206084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148271 restraints weight = 14623.337| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.84 r_work: 0.3666 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11750 Z= 0.118 Angle : 0.563 9.701 15826 Z= 0.291 Chirality : 0.042 0.178 1712 Planarity : 0.004 0.048 2026 Dihedral : 4.996 52.774 1554 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.18 % Allowed : 25.16 % Favored : 72.66 % 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 are not related in a simple way. whole: -0.06 (0.22), residues: 1422 helix: 0.67 (0.21), residues: 592 sheet: -1.39 (0.42), residues: 154 loop : -0.21 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 585 TYR 0.019 0.001 TYR A 646 PHE 0.025 0.002 PHE A 474 TRP 0.017 0.001 TRP A 577 HIS 0.003 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00277 (11750) covalent geometry : angle 0.56303 (15826) hydrogen bonds : bond 0.02835 ( 462) hydrogen bonds : angle 4.54551 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: C 218 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7340 (mtt90) REVERT: C 238 TYR cc_start: 0.8407 (m-80) cc_final: 0.8107 (m-10) REVERT: C 429 ASP cc_start: 0.7802 (p0) cc_final: 0.7178 (p0) REVERT: C 438 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7844 (tt) REVERT: A 498 ASP cc_start: 0.4999 (m-30) cc_final: 0.3538 (m-30) REVERT: A 566 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7681 (pt) REVERT: A 660 GLU cc_start: 0.7686 (mp0) cc_final: 0.7364 (mp0) REVERT: D 211 ILE cc_start: 0.8193 (mm) cc_final: 0.7794 (tt) REVERT: D 297 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6336 (mp) REVERT: D 403 MET cc_start: 0.6266 (mtm) cc_final: 0.4382 (mmm) REVERT: B 431 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7197 (pp) REVERT: B 445 TRP cc_start: 0.6916 (t-100) cc_final: 0.6541 (t-100) REVERT: B 555 MET cc_start: 0.6971 (mtp) cc_final: 0.6660 (mtp) REVERT: B 600 LYS cc_start: 0.7354 (mmtt) cc_final: 0.6224 (tptp) REVERT: B 661 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6451 (ppp) outliers start: 27 outliers final: 19 residues processed: 167 average time/residue: 0.0858 time to fit residues: 21.6426 Evaluate side-chains 171 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 263 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 115 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.205959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.152955 restraints weight = 14613.381| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.03 r_work: 0.3663 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 11750 Z= 0.171 Angle : 0.845 59.136 15826 Z= 0.482 Chirality : 0.042 0.165 1712 Planarity : 0.004 0.048 2026 Dihedral : 4.808 36.809 1552 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.50 % Allowed : 25.00 % Favored : 72.50 % Cbeta Deviations : 0.07 % 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 are not related in a simple way. whole: -0.07 (0.22), residues: 1422 helix: 0.67 (0.21), residues: 592 sheet: -1.40 (0.42), residues: 154 loop : -0.22 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 585 TYR 0.017 0.001 TYR A 646 PHE 0.022 0.002 PHE A 474 TRP 0.015 0.001 TRP A 577 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00372 (11750) covalent geometry : angle 0.84494 (15826) hydrogen bonds : bond 0.02841 ( 462) hydrogen bonds : angle 4.55491 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2812.61 seconds wall clock time: 48 minutes 59.07 seconds (2939.07 seconds total)