Starting phenix.real_space_refine on Fri Jul 3 02:52:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps2_71820/07_2026/9ps2_71820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps2_71820/07_2026/9ps2_71820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ps2_71820/07_2026/9ps2_71820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps2_71820/07_2026/9ps2_71820.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ps2_71820/07_2026/9ps2_71820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps2_71820/07_2026/9ps2_71820.map" } resolution = 2.15 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= -0.001 sd= 0.219 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 54 5.16 5 C 7545 2.51 5 N 1809 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11395 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3774 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 21, 'TRANS': 466} Chain breaks: 1 Chain: "A" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3774 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 21, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3774 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 21, 'TRANS': 466} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 2.85, per 1000 atoms: 0.25 Number of scatterers: 11395 At special positions: 0 Unit cell: (132.44, 132.44, 75.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 54 16.00 O 1984 8.00 N 1809 7.00 C 7545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 89 " distance=2.04 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: 0.92 Conformation dependent library (CDL) restraints added in 574.5 milliseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 9 sheets defined 84.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 60 through 71 removed outlier: 4.613A pdb=" N CYS C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.861A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 162 removed outlier: 3.902A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 166 through 193 removed outlier: 3.931A pdb=" N ALA C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 223 Processing helix chain 'C' and resid 227 through 254 Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 313 through 320 Processing helix chain 'C' and resid 321 through 342 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 3.816A pdb=" N VAL C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 375 through 381 removed outlier: 6.126A pdb=" N TYR C 379 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 387 No H-bonds generated for 'chain 'C' and resid 385 through 387' Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 419 through 452 Processing helix chain 'C' and resid 454 through 481 removed outlier: 3.863A pdb=" N LEU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 515 removed outlier: 3.612A pdb=" N PHE C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 549 Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 554 through 577 removed outlier: 3.592A pdb=" N GLY C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.565A pdb=" N VAL A 56 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N CYS A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 71 removed outlier: 4.614A pdb=" N CYS A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 121 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.861A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.903A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 166 through 193 removed outlier: 3.932A pdb=" N ALA A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 223 Processing helix chain 'A' and resid 227 through 254 Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 313 through 320 Processing helix chain 'A' and resid 321 through 342 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 374 removed outlier: 3.817A pdb=" N VAL A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 375 through 381 removed outlier: 6.564A pdb=" N TYR A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 419 through 452 Processing helix chain 'A' and resid 454 through 481 removed outlier: 3.863A pdb=" N LEU A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 515 removed outlier: 3.612A pdb=" N PHE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 549 Proline residue: A 547 - end of helix Processing helix chain 'A' and resid 554 through 577 removed outlier: 3.592A pdb=" N GLY A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 59 Processing helix chain 'B' and resid 60 through 71 removed outlier: 4.614A pdb=" N CYS B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 121 Processing helix chain 'B' and resid 121 through 132 removed outlier: 3.861A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 162 removed outlier: 3.903A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Proline residue: B 152 - end of helix Processing helix chain 'B' and resid 166 through 193 removed outlier: 3.931A pdb=" N ALA B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 227 through 254 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 313 through 320 Processing helix chain 'B' and resid 321 through 342 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 355 through 374 removed outlier: 3.817A pdb=" N VAL B 364 " --> pdb=" O CYS B 360 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 375 through 381 removed outlier: 5.848A pdb=" N TYR B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 387 No H-bonds generated for 'chain 'B' and resid 385 through 387' Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 419 through 452 Processing helix chain 'B' and resid 454 through 481 removed outlier: 3.863A pdb=" N LEU B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 3.612A pdb=" N PHE B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 496 " --> pdb=" O PHE B 492 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 549 Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 554 through 577 removed outlier: 3.593A pdb=" N GLY B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AA2, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AA3, first strand: chain 'C' and resid 383 through 384 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'A' and resid 383 through 384 Processing sheet with id=AA7, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 384 895 hydrogen bonds defined for protein. 2610 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: 2.06 Time building geometry restraints manager: 1.24 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: 3423 1.34 - 1.47: 2920 1.47 - 1.59: 5201 1.59 - 1.71: 0 1.71 - 1.84: 66 Bond restraints: 11610 Sorted by residual: bond pdb=" N LEU C 135 " pdb=" CA LEU C 135 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.22e-02 6.72e+03 8.96e+00 bond pdb=" N VAL B 329 " pdb=" CA VAL B 329 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.85e+00 bond pdb=" N VAL C 56 " pdb=" CA VAL C 56 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.85e+00 bond pdb=" N VAL C 329 " pdb=" CA VAL C 329 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.78e+00 bond pdb=" N SER C 136 " pdb=" CA SER C 136 " ideal model delta sigma weight residual 1.453 1.494 -0.040 1.37e-02 5.33e+03 8.74e+00 ... (remaining 11605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 14904 1.65 - 3.29: 764 3.29 - 4.94: 153 4.94 - 6.59: 34 6.59 - 8.23: 15 Bond angle restraints: 15870 Sorted by residual: angle pdb=" N LEU C 133 " pdb=" CA LEU C 133 " pdb=" C LEU C 133 " ideal model delta sigma weight residual 112.59 118.57 -5.98 1.22e+00 6.72e-01 2.40e+01 angle pdb=" N PHE B 91 " pdb=" CA PHE B 91 " pdb=" C PHE B 91 " ideal model delta sigma weight residual 110.31 116.92 -6.61 1.38e+00 5.25e-01 2.30e+01 angle pdb=" N THR C 373 " pdb=" CA THR C 373 " pdb=" C THR C 373 " ideal model delta sigma weight residual 113.72 107.51 6.21 1.30e+00 5.92e-01 2.28e+01 angle pdb=" N LYS C 134 " pdb=" CA LYS C 134 " pdb=" C LYS C 134 " ideal model delta sigma weight residual 111.56 118.34 -6.78 1.43e+00 4.89e-01 2.25e+01 angle pdb=" N LEU C 135 " pdb=" CA LEU C 135 " pdb=" CB LEU C 135 " ideal model delta sigma weight residual 109.97 116.81 -6.84 1.47e+00 4.63e-01 2.17e+01 ... (remaining 15865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5929 17.13 - 34.27: 576 34.27 - 51.40: 144 51.40 - 68.53: 32 68.53 - 85.67: 12 Dihedral angle restraints: 6693 sinusoidal: 2478 harmonic: 4215 Sorted by residual: dihedral pdb=" CA VAL A 142 " pdb=" C VAL A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA VAL C 142 " pdb=" C VAL C 142 " pdb=" N THR C 143 " pdb=" CA THR C 143 " ideal model delta harmonic sigma weight residual 180.00 -159.86 -20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA VAL B 142 " pdb=" C VAL B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta harmonic sigma weight residual -180.00 -159.86 -20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1516 0.064 - 0.128: 363 0.128 - 0.192: 44 0.192 - 0.256: 8 0.256 - 0.320: 1 Chirality restraints: 1932 Sorted by residual: chirality pdb=" CG LEU B 537 " pdb=" CB LEU B 537 " pdb=" CD1 LEU B 537 " pdb=" CD2 LEU B 537 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA LEU C 135 " pdb=" N LEU C 135 " pdb=" C LEU C 135 " pdb=" CB LEU C 135 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL C 519 " pdb=" N VAL C 519 " pdb=" C VAL C 519 " pdb=" CB VAL C 519 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1929 not shown) Planarity restraints: 1929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 51 " 0.028 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C ALA B 51 " -0.092 2.00e-02 2.50e+03 pdb=" O ALA B 51 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP B 52 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 513 " 0.266 9.50e-02 1.11e+02 1.19e-01 8.75e+00 pdb=" NE ARG C 513 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 513 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 513 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 513 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 581 " -0.019 2.00e-02 2.50e+03 2.18e-02 7.10e+00 pdb=" CG HIS A 581 " 0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A 581 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS A 581 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS A 581 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 581 " -0.008 2.00e-02 2.50e+03 ... (remaining 1926 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1283 2.74 - 3.28: 11423 3.28 - 3.82: 19368 3.82 - 4.36: 21912 4.36 - 4.90: 37655 Nonbonded interactions: 91641 Sorted by model distance: nonbonded pdb=" CB ASP C 524 " pdb=" O HOH C 705 " model vdw 2.203 3.440 nonbonded pdb=" O TRP B 317 " pdb=" NZ LYS B 325 " model vdw 2.237 3.120 nonbonded pdb=" O TRP C 317 " pdb=" NZ LYS C 325 " model vdw 2.237 3.120 nonbonded pdb=" O TRP A 317 " pdb=" NZ LYS A 325 " model vdw 2.237 3.120 nonbonded pdb=" O PRO A 311 " pdb=" NZ LYS A 328 " model vdw 2.257 3.120 ... (remaining 91636 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 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: 0.040 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 11616 Z= 0.366 Angle : 0.884 9.103 15882 Z= 0.529 Chirality : 0.056 0.320 1932 Planarity : 0.006 0.119 1929 Dihedral : 15.156 85.669 3969 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.63 % Allowed : 15.12 % Favored : 83.25 % 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: 1.25 (0.21), residues: 1452 helix: 1.41 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 224 TYR 0.018 0.002 TYR A 565 PHE 0.027 0.003 PHE A 147 TRP 0.016 0.002 TRP A 106 HIS 0.025 0.003 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.37 (11610) covalent geometry : angle 0.87833 / 0.53 (15870) SS BOND : bond 0.00886 / 0.41 ( 6) SS BOND : angle 3.86636 / 2.09 ( 12) hydrogen bonds : bond 0.13360 / 8.71 ( 895) hydrogen bonds : angle 5.30152 / 3.88 ( 2610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: C 69 LYS cc_start: 0.8062 (mttt) cc_final: 0.7684 (mtmt) REVERT: A 53 CYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6269 (t) REVERT: A 373 THR cc_start: 0.8014 (t) cc_final: 0.7736 (p) outliers start: 20 outliers final: 2 residues processed: 139 average time/residue: 0.5369 time to fit residues: 80.8461 Evaluate side-chains 112 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 136 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 75 HIS A 75 HIS A 310 ASN A 375 GLN B 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.174340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109260 restraints weight = 10757.553| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.63 r_work: 0.3215 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11616 Z= 0.145 Angle : 0.616 15.702 15882 Z= 0.309 Chirality : 0.041 0.131 1932 Planarity : 0.004 0.035 1929 Dihedral : 4.490 54.495 1571 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.87 % Allowed : 14.88 % Favored : 83.25 % 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: 2.14 (0.21), residues: 1452 helix: 1.99 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.014 0.002 TYR A 557 PHE 0.028 0.002 PHE C 564 TRP 0.013 0.001 TRP A 106 HIS 0.008 0.001 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (11610) covalent geometry : angle 0.61449 / 0.31 (15870) SS BOND : bond 0.01477 / 0.99 ( 6) SS BOND : angle 1.50203 / 0.90 ( 12) hydrogen bonds : bond 0.06244 / 4.17 ( 895) hydrogen bonds : angle 4.36799 / 3.20 ( 2610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: C 69 LYS cc_start: 0.7780 (mttt) cc_final: 0.7268 (mtmm) REVERT: C 537 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 320 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.5842 (mp10) REVERT: A 373 THR cc_start: 0.7795 (t) cc_final: 0.7577 (p) REVERT: B 522 GLU cc_start: 0.6284 (tp30) cc_final: 0.5878 (mt-10) outliers start: 23 outliers final: 1 residues processed: 142 average time/residue: 0.4820 time to fit residues: 74.7739 Evaluate side-chains 115 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 320 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN A 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.172115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106439 restraints weight = 10720.882| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.63 r_work: 0.3173 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11616 Z= 0.154 Angle : 0.621 14.346 15882 Z= 0.313 Chirality : 0.042 0.146 1932 Planarity : 0.004 0.034 1929 Dihedral : 4.140 18.521 1566 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.09 % Allowed : 13.98 % Favored : 82.93 % 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: 2.29 (0.21), residues: 1452 helix: 2.10 (0.15), residues: 1137 sheet: None (None), residues: 0 loop : -0.62 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 224 TYR 0.015 0.002 TYR C 565 PHE 0.019 0.002 PHE C 564 TRP 0.014 0.001 TRP A 106 HIS 0.010 0.002 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (11610) covalent geometry : angle 0.62020 / 0.31 (15870) SS BOND : bond 0.00545 / 0.35 ( 6) SS BOND : angle 1.49267 / 0.91 ( 12) hydrogen bonds : bond 0.06635 / 4.42 ( 895) hydrogen bonds : angle 4.32681 / 3.17 ( 2610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.405 Fit side-chains REVERT: C 69 LYS cc_start: 0.7893 (mttt) cc_final: 0.7523 (mttp) REVERT: C 337 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6789 (mm) REVERT: C 537 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8303 (mm) REVERT: A 320 GLN cc_start: 0.6260 (OUTLIER) cc_final: 0.6024 (mp10) REVERT: A 337 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6879 (mm) REVERT: B 91 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.5270 (t80) REVERT: B 101 THR cc_start: 0.8056 (m) cc_final: 0.7727 (p) REVERT: B 337 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6968 (mm) outliers start: 38 outliers final: 14 residues processed: 151 average time/residue: 0.4143 time to fit residues: 68.9545 Evaluate side-chains 136 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 580 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 0.0020 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.174701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110124 restraints weight = 10753.497| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.63 r_work: 0.3227 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11616 Z= 0.126 Angle : 0.556 13.197 15882 Z= 0.280 Chirality : 0.039 0.126 1932 Planarity : 0.004 0.035 1929 Dihedral : 4.013 17.133 1566 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.71 % Allowed : 15.85 % Favored : 82.44 % 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: 2.58 (0.21), residues: 1452 helix: 2.27 (0.15), residues: 1137 sheet: None (None), residues: 0 loop : -0.40 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 224 TYR 0.016 0.001 TYR B 557 PHE 0.017 0.001 PHE C 564 TRP 0.012 0.001 TRP A 106 HIS 0.004 0.001 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (11610) covalent geometry : angle 0.55504 / 0.28 (15870) SS BOND : bond 0.00977 / 0.50 ( 6) SS BOND : angle 1.50364 / 0.82 ( 12) hydrogen bonds : bond 0.05418 / 3.62 ( 895) hydrogen bonds : angle 4.11480 / 3.01 ( 2610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.394 Fit side-chains REVERT: C 69 LYS cc_start: 0.7745 (mttt) cc_final: 0.7382 (mttp) REVERT: C 337 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6788 (mm) REVERT: C 513 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.7006 (mtm-85) REVERT: A 85 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7768 (mttt) REVERT: A 337 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6782 (mm) REVERT: B 90 TYR cc_start: 0.7022 (t80) cc_final: 0.6762 (t80) REVERT: B 91 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.5319 (t80) REVERT: B 101 THR cc_start: 0.8066 (m) cc_final: 0.7739 (p) REVERT: B 337 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6969 (mm) REVERT: B 375 GLN cc_start: 0.7858 (tp40) cc_final: 0.7604 (mm110) outliers start: 21 outliers final: 5 residues processed: 148 average time/residue: 0.4157 time to fit residues: 67.9898 Evaluate side-chains 125 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 104 optimal weight: 0.0010 chunk 142 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN A 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.176393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112185 restraints weight = 10818.531| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.64 r_work: 0.3261 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11616 Z= 0.115 Angle : 0.528 12.445 15882 Z= 0.265 Chirality : 0.039 0.147 1932 Planarity : 0.004 0.033 1929 Dihedral : 3.902 16.944 1566 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.54 % Allowed : 16.34 % Favored : 82.11 % 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: 2.80 (0.22), residues: 1452 helix: 2.40 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.23 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.016 0.001 TYR B 557 PHE 0.015 0.001 PHE C 564 TRP 0.010 0.001 TRP A 106 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.12 (11610) covalent geometry : angle 0.52696 / 0.26 (15870) SS BOND : bond 0.00231 / 0.13 ( 6) SS BOND : angle 1.12043 / 0.60 ( 12) hydrogen bonds : bond 0.04881 / 3.26 ( 895) hydrogen bonds : angle 3.97949 / 2.91 ( 2610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.355 Fit side-chains REVERT: C 69 LYS cc_start: 0.7738 (mttt) cc_final: 0.7381 (mttp) REVERT: C 337 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6710 (mm) REVERT: C 513 ARG cc_start: 0.7292 (ttp-110) cc_final: 0.7056 (mtm-85) REVERT: A 337 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6738 (mm) REVERT: B 69 LYS cc_start: 0.7994 (mttt) cc_final: 0.7449 (mtmt) REVERT: B 90 TYR cc_start: 0.7263 (t80) cc_final: 0.7000 (t80) REVERT: B 101 THR cc_start: 0.8041 (m) cc_final: 0.7723 (p) REVERT: B 337 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6938 (mm) REVERT: B 375 GLN cc_start: 0.7825 (tp40) cc_final: 0.7576 (mm110) REVERT: B 520 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8013 (mmmt) outliers start: 19 outliers final: 6 residues processed: 143 average time/residue: 0.4673 time to fit residues: 73.3884 Evaluate side-chains 126 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN A 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.173858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108699 restraints weight = 10740.823| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.62 r_work: 0.3204 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11616 Z= 0.133 Angle : 0.579 14.055 15882 Z= 0.288 Chirality : 0.040 0.165 1932 Planarity : 0.004 0.033 1929 Dihedral : 4.044 21.555 1566 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.11 % Allowed : 16.18 % Favored : 81.71 % 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: 2.74 (0.21), residues: 1452 helix: 2.35 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.21 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.013 0.001 TYR C 557 PHE 0.014 0.001 PHE C 147 TRP 0.010 0.001 TRP A 106 HIS 0.007 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (11610) covalent geometry : angle 0.57548 / 0.29 (15870) SS BOND : bond 0.00330 / 0.17 ( 6) SS BOND : angle 2.29573 / 1.03 ( 12) hydrogen bonds : bond 0.05722 / 3.83 ( 895) hydrogen bonds : angle 4.10855 / 3.01 ( 2610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.370 Fit side-chains REVERT: C 69 LYS cc_start: 0.7772 (mttt) cc_final: 0.7388 (mtmt) REVERT: C 337 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6762 (mm) REVERT: C 513 ARG cc_start: 0.7301 (ttp-110) cc_final: 0.7017 (mtm-85) REVERT: A 337 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6852 (mm) REVERT: B 69 LYS cc_start: 0.8006 (mttt) cc_final: 0.7456 (mtmt) REVERT: B 337 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6956 (mm) REVERT: B 375 GLN cc_start: 0.7887 (tp40) cc_final: 0.7629 (mm110) outliers start: 26 outliers final: 15 residues processed: 137 average time/residue: 0.4771 time to fit residues: 71.5517 Evaluate side-chains 128 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 580 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 127 optimal weight: 0.5980 chunk 8 optimal weight: 0.0770 chunk 141 optimal weight: 0.0970 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN A 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113003 restraints weight = 10921.828| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.65 r_work: 0.3272 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11616 Z= 0.113 Angle : 0.530 11.764 15882 Z= 0.263 Chirality : 0.039 0.187 1932 Planarity : 0.003 0.031 1929 Dihedral : 3.988 24.605 1566 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.63 % Allowed : 16.67 % Favored : 81.71 % 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: 2.89 (0.22), residues: 1452 helix: 2.47 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.22 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.016 0.001 TYR B 557 PHE 0.015 0.001 PHE C 147 TRP 0.011 0.001 TRP A 106 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (11610) covalent geometry : angle 0.52759 / 0.26 (15870) SS BOND : bond 0.00240 / 0.12 ( 6) SS BOND : angle 1.87399 / 0.88 ( 12) hydrogen bonds : bond 0.04685 / 3.13 ( 895) hydrogen bonds : angle 3.95033 / 2.89 ( 2610) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.401 Fit side-chains REVERT: C 69 LYS cc_start: 0.7762 (mttt) cc_final: 0.7377 (mtmt) REVERT: C 337 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6693 (mm) REVERT: C 513 ARG cc_start: 0.7284 (ttp-110) cc_final: 0.7036 (mtm-85) REVERT: A 337 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6713 (mm) REVERT: B 69 LYS cc_start: 0.8019 (mttt) cc_final: 0.7475 (mtmt) REVERT: B 90 TYR cc_start: 0.7393 (t80) cc_final: 0.7147 (t80) REVERT: B 337 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6913 (mm) REVERT: B 375 GLN cc_start: 0.7796 (tp40) cc_final: 0.7547 (mm110) REVERT: B 520 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8062 (mmmt) outliers start: 20 outliers final: 7 residues processed: 146 average time/residue: 0.4450 time to fit residues: 71.3507 Evaluate side-chains 128 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 chunk 111 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN A 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.176259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111999 restraints weight = 10745.947| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.62 r_work: 0.3255 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11616 Z= 0.116 Angle : 0.544 12.491 15882 Z= 0.269 Chirality : 0.039 0.166 1932 Planarity : 0.004 0.032 1929 Dihedral : 3.965 24.831 1566 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.06 % Allowed : 17.32 % Favored : 81.63 % 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: 2.88 (0.22), residues: 1452 helix: 2.46 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.20 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.016 0.001 TYR B 557 PHE 0.016 0.001 PHE C 147 TRP 0.010 0.001 TRP A 106 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (11610) covalent geometry : angle 0.54162 / 0.27 (15870) SS BOND : bond 0.00249 / 0.13 ( 6) SS BOND : angle 1.81858 / 0.91 ( 12) hydrogen bonds : bond 0.04898 / 3.28 ( 895) hydrogen bonds : angle 3.96442 / 2.90 ( 2610) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.412 Fit side-chains REVERT: C 69 LYS cc_start: 0.7719 (mttt) cc_final: 0.7325 (mtmt) REVERT: C 337 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6677 (mm) REVERT: C 513 ARG cc_start: 0.7275 (ttp-110) cc_final: 0.7014 (mtm-85) REVERT: A 337 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6700 (mm) REVERT: B 69 LYS cc_start: 0.7991 (mttt) cc_final: 0.7449 (mtmt) REVERT: B 337 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6896 (mm) REVERT: B 375 GLN cc_start: 0.7790 (tp40) cc_final: 0.7538 (mm110) outliers start: 13 outliers final: 6 residues processed: 133 average time/residue: 0.4854 time to fit residues: 70.4492 Evaluate side-chains 124 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.175942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111400 restraints weight = 10710.551| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.62 r_work: 0.3247 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11616 Z= 0.118 Angle : 0.543 12.319 15882 Z= 0.270 Chirality : 0.039 0.196 1932 Planarity : 0.004 0.033 1929 Dihedral : 3.977 26.426 1566 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.22 % Allowed : 17.15 % Favored : 81.63 % 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: 2.82 (0.22), residues: 1452 helix: 2.42 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 224 TYR 0.015 0.001 TYR B 557 PHE 0.018 0.001 PHE C 147 TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (11610) covalent geometry : angle 0.54147 / 0.27 (15870) SS BOND : bond 0.00282 / 0.15 ( 6) SS BOND : angle 1.69657 / 0.88 ( 12) hydrogen bonds : bond 0.05029 / 3.36 ( 895) hydrogen bonds : angle 3.98563 / 2.91 ( 2610) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.403 Fit side-chains REVERT: C 69 LYS cc_start: 0.7729 (mttt) cc_final: 0.7323 (mtmt) REVERT: C 337 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6739 (mm) REVERT: C 513 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.7004 (mtm-85) REVERT: A 337 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6787 (mm) REVERT: B 69 LYS cc_start: 0.7987 (mttt) cc_final: 0.7438 (mtmt) REVERT: B 337 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6911 (mm) REVERT: B 375 GLN cc_start: 0.7772 (tp40) cc_final: 0.7515 (mm110) REVERT: B 520 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8070 (mmmt) outliers start: 15 outliers final: 9 residues processed: 130 average time/residue: 0.4881 time to fit residues: 69.4591 Evaluate side-chains 125 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.170853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104667 restraints weight = 10517.266| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.61 r_work: 0.3150 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11616 Z= 0.188 Angle : 0.677 16.584 15882 Z= 0.342 Chirality : 0.045 0.241 1932 Planarity : 0.004 0.036 1929 Dihedral : 4.368 28.627 1566 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.30 % Allowed : 17.07 % Favored : 81.63 % 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: 2.43 (0.21), residues: 1452 helix: 2.14 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.37 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 224 TYR 0.017 0.002 TYR C 565 PHE 0.021 0.002 PHE C 147 TRP 0.011 0.002 TRP A 249 HIS 0.010 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (11610) covalent geometry : angle 0.67075 / 0.34 (15870) SS BOND : bond 0.00777 / 0.48 ( 6) SS BOND : angle 3.52552 / 1.95 ( 12) hydrogen bonds : bond 0.07271 / 4.85 ( 895) hydrogen bonds : angle 4.38374 / 3.21 ( 2610) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.402 Fit side-chains REVERT: C 69 LYS cc_start: 0.7863 (mttt) cc_final: 0.7436 (mtmt) REVERT: C 337 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6859 (mm) REVERT: A 337 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7025 (mm) REVERT: B 69 LYS cc_start: 0.8026 (mttt) cc_final: 0.7464 (mtmt) REVERT: B 337 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7059 (mm) REVERT: B 375 GLN cc_start: 0.7909 (tp40) cc_final: 0.7640 (mm110) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 0.5169 time to fit residues: 67.3955 Evaluate side-chains 119 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.174521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109706 restraints weight = 10683.153| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.61 r_work: 0.3220 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11616 Z= 0.125 Angle : 0.574 13.372 15882 Z= 0.286 Chirality : 0.040 0.166 1932 Planarity : 0.004 0.032 1929 Dihedral : 4.183 26.506 1566 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.89 % Allowed : 17.64 % Favored : 81.46 % 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: 2.70 (0.22), residues: 1452 helix: 2.33 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 224 TYR 0.017 0.001 TYR B 557 PHE 0.021 0.001 PHE C 147 TRP 0.012 0.001 TRP A 106 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (11610) covalent geometry : angle 0.56659 / 0.28 (15870) SS BOND : bond 0.00477 / 0.27 ( 6) SS BOND : angle 3.30467 / 1.92 ( 12) hydrogen bonds : bond 0.05396 / 3.60 ( 895) hydrogen bonds : angle 4.10292 / 3.00 ( 2610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5433.00 seconds wall clock time: 92 minutes 57.09 seconds (5577.09 seconds total)