Starting phenix.real_space_refine on Wed Feb 4 16:02:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps2_71820/02_2026/9ps2_71820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps2_71820/02_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_71820/02_2026/9ps2_71820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps2_71820/02_2026/9ps2_71820.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ps2_71820/02_2026/9ps2_71820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps2_71820/02_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-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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: 2.81, 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: 0.78 Conformation dependent library (CDL) restraints added in 431.3 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: 0.40 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: 1.59 Time building geometry restraints manager: 1.00 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: 0.01 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: 2.630 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.680 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 covalent geometry : bond 0.00718 (11610) covalent geometry : angle 0.87833 (15870) SS BOND : bond 0.00886 ( 6) SS BOND : angle 3.86636 ( 12) hydrogen bonds : bond 0.13360 ( 895) hydrogen bonds : angle 5.30152 ( 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 : 0.265 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: 0.5121 time to fit residues: 76.8381 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 : 0.389 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4134 r_free = 0.4134 target = 0.174082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108905 restraints weight = 10692.200| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.63 r_work: 0.3208 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1210 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= 0.144 Angle : 0.618 16.090 15882 Z= 0.309 Chirality : 0.041 0.131 1932 Planarity : 0.004 0.035 1929 Dihedral : 4.473 54.714 1571 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.95 % Allowed : 14.88 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.21), residues: 1452 helix: 2.00 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.74 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 356 TYR 0.014 0.002 TYR B 557 PHE 0.027 0.002 PHE C 564 TRP 0.013 0.001 TRP A 106 HIS 0.009 0.002 HIS C 581 Details of bonding type rmsd covalent geometry : bond 0.00285 (11610) covalent geometry : angle 0.61674 (15870) SS BOND : bond 0.00920 ( 6) SS BOND : angle 1.64921 ( 12) hydrogen bonds : bond 0.06161 ( 895) hydrogen bonds : angle 4.34137 ( 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 153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: C 537 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 320 GLN cc_start: 0.6486 (OUTLIER) cc_final: 0.5856 (mp10) REVERT: A 373 THR cc_start: 0.7770 (t) cc_final: 0.7547 (p) REVERT: B 522 GLU cc_start: 0.6279 (tp30) cc_final: 0.5863 (mt-10) outliers start: 24 outliers final: 1 residues processed: 145 average time/residue: 0.5044 time to fit residues: 79.7084 Evaluate side-chains 116 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 0.6980 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: 2.9990 chunk 78 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4105 r_free = 0.4105 target = 0.171360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105611 restraints weight = 10672.276| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.63 r_work: 0.3163 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11616 Z= 0.158 Angle : 0.632 14.728 15882 Z= 0.318 Chirality : 0.043 0.147 1932 Planarity : 0.004 0.034 1929 Dihedral : 4.153 18.594 1566 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.01 % Allowed : 14.07 % 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: 2.25 (0.21), residues: 1452 helix: 2.07 (0.15), residues: 1137 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.015 0.002 TYR C 565 PHE 0.018 0.002 PHE C 564 TRP 0.014 0.001 TRP A 106 HIS 0.010 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00338 (11610) covalent geometry : angle 0.63038 (15870) SS BOND : bond 0.00598 ( 6) SS BOND : angle 1.67573 ( 12) hydrogen bonds : bond 0.06840 ( 895) hydrogen bonds : angle 4.35599 ( 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 155 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.353 Fit side-chains REVERT: C 337 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6820 (mm) REVERT: C 537 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8304 (mm) REVERT: A 320 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.6076 (mp10) REVERT: A 337 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6918 (mm) REVERT: B 101 THR cc_start: 0.8074 (m) cc_final: 0.7748 (p) REVERT: B 337 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6926 (mm) outliers start: 37 outliers final: 14 residues processed: 146 average time/residue: 0.4830 time to fit residues: 77.3364 Evaluate side-chains 135 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 110 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4131 r_free = 0.4131 target = 0.173788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108814 restraints weight = 10668.773| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.62 r_work: 0.3211 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11616 Z= 0.128 Angle : 0.565 13.294 15882 Z= 0.284 Chirality : 0.040 0.128 1932 Planarity : 0.004 0.034 1929 Dihedral : 4.027 16.189 1566 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.03 % Allowed : 15.28 % Favored : 82.68 % 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: 2.53 (0.21), residues: 1452 helix: 2.24 (0.15), residues: 1137 sheet: None (None), residues: 0 loop : -0.43 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.015 0.001 TYR B 557 PHE 0.018 0.001 PHE C 564 TRP 0.012 0.001 TRP A 106 HIS 0.005 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00246 (11610) covalent geometry : angle 0.56419 (15870) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.35311 ( 12) hydrogen bonds : bond 0.05611 ( 895) hydrogen bonds : angle 4.13832 ( 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 153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.437 Fit side-chains REVERT: C 69 LYS cc_start: 0.7958 (mttp) cc_final: 0.7271 (mtmm) REVERT: C 337 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6802 (mm) REVERT: C 513 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.7001 (mtm-85) REVERT: A 337 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6870 (mm) REVERT: B 101 THR cc_start: 0.8070 (m) cc_final: 0.7743 (p) REVERT: B 337 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7000 (mm) outliers start: 25 outliers final: 7 residues processed: 143 average time/residue: 0.4616 time to fit residues: 72.3208 Evaluate side-chains 124 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 460 LEU Chi-restraints excluded: chain B residue 580 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4140 r_free = 0.4140 target = 0.174725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110025 restraints weight = 10703.729| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.62 r_work: 0.3226 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11616 Z= 0.120 Angle : 0.551 13.322 15882 Z= 0.274 Chirality : 0.039 0.153 1932 Planarity : 0.004 0.033 1929 Dihedral : 4.025 20.851 1566 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.63 % Allowed : 16.34 % Favored : 82.03 % 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: 2.34 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.32 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.015 0.001 TYR B 557 PHE 0.015 0.001 PHE C 564 TRP 0.011 0.001 TRP A 106 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00227 (11610) covalent geometry : angle 0.54897 (15870) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.77609 ( 12) hydrogen bonds : bond 0.05222 ( 895) hydrogen bonds : angle 4.04121 ( 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 141 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.353 Fit side-chains REVERT: C 69 LYS cc_start: 0.7918 (mttp) cc_final: 0.7203 (mtmt) REVERT: C 337 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6765 (mm) REVERT: C 513 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.7039 (mtm-85) REVERT: A 337 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6852 (mm) REVERT: B 69 LYS cc_start: 0.8030 (mttt) cc_final: 0.7486 (mtmt) REVERT: B 101 THR cc_start: 0.8030 (m) cc_final: 0.7702 (p) REVERT: B 331 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7581 (mtmt) REVERT: B 337 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6959 (mm) REVERT: B 520 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8073 (mmmt) outliers start: 20 outliers final: 8 residues processed: 135 average time/residue: 0.4722 time to fit residues: 69.3869 Evaluate side-chains 124 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 460 LEU 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 460 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4145 r_free = 0.4145 target = 0.175230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110580 restraints weight = 10725.707| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.62 r_work: 0.3232 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2043 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= 0.118 Angle : 0.542 12.980 15882 Z= 0.270 Chirality : 0.039 0.187 1932 Planarity : 0.004 0.032 1929 Dihedral : 4.029 23.688 1566 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.79 % Allowed : 16.34 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.78 (0.22), residues: 1452 helix: 2.40 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.30 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 54 TYR 0.015 0.001 TYR B 557 PHE 0.014 0.001 PHE C 564 TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00221 (11610) covalent geometry : angle 0.54021 (15870) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.67508 ( 12) hydrogen bonds : bond 0.05088 ( 895) hydrogen bonds : angle 4.00288 ( 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 140 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.424 Fit side-chains REVERT: C 337 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6751 (mm) REVERT: C 513 ARG cc_start: 0.7316 (ttp-110) cc_final: 0.7038 (mtm-85) REVERT: A 337 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6767 (mm) REVERT: B 69 LYS cc_start: 0.8009 (mttt) cc_final: 0.7463 (mtmt) REVERT: B 331 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7534 (mtmt) REVERT: B 337 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6952 (mm) outliers start: 22 outliers final: 12 residues processed: 138 average time/residue: 0.4745 time to fit residues: 71.7747 Evaluate side-chains 126 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 393 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 460 LEU 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 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: 0.7980 chunk 121 optimal weight: 3.9990 chunk 99 optimal weight: 0.0170 chunk 132 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 8 optimal weight: 0.0370 chunk 141 optimal weight: 0.0470 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4173 r_free = 0.4173 target = 0.178002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114641 restraints weight = 10886.974| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.63 r_work: 0.3290 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 11616 Z= 0.107 Angle : 0.515 11.116 15882 Z= 0.256 Chirality : 0.038 0.163 1932 Planarity : 0.003 0.032 1929 Dihedral : 3.900 23.876 1566 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.54 % Allowed : 16.67 % Favored : 81.79 % 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: 2.95 (0.22), residues: 1452 helix: 2.57 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -0.28 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.016 0.001 TYR C 557 PHE 0.016 0.001 PHE A 147 TRP 0.011 0.001 TRP A 106 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00195 (11610) covalent geometry : angle 0.51363 (15870) SS BOND : bond 0.00170 ( 6) SS BOND : angle 1.44158 ( 12) hydrogen bonds : bond 0.04287 ( 895) hydrogen bonds : angle 3.86643 ( 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 150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.410 Fit side-chains REVERT: C 69 LYS cc_start: 0.7831 (mttp) cc_final: 0.7183 (mtmt) REVERT: C 337 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6659 (mm) REVERT: C 513 ARG cc_start: 0.7293 (ttp-110) cc_final: 0.7082 (mtm-85) REVERT: A 337 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6714 (mm) REVERT: B 69 LYS cc_start: 0.7989 (mttt) cc_final: 0.7443 (mtmt) REVERT: B 101 THR cc_start: 0.8060 (m) cc_final: 0.7727 (p) REVERT: B 331 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7520 (mtmt) REVERT: B 337 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6906 (mm) REVERT: B 520 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8101 (mmmt) outliers start: 19 outliers final: 8 residues processed: 148 average time/residue: 0.4714 time to fit residues: 76.1585 Evaluate side-chains 129 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 393 VAL 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: 0.0370 chunk 84 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4152 r_free = 0.4152 target = 0.175994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111597 restraints weight = 10665.882| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.62 r_work: 0.3248 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 11616 Z= 0.114 Angle : 0.530 12.224 15882 Z= 0.265 Chirality : 0.039 0.167 1932 Planarity : 0.003 0.031 1929 Dihedral : 3.922 25.362 1566 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.30 % Allowed : 16.83 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.93 (0.22), residues: 1452 helix: 2.50 (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 0.015 0.001 TYR B 557 PHE 0.017 0.001 PHE C 147 TRP 0.009 0.001 TRP A 106 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00215 (11610) covalent geometry : angle 0.52925 (15870) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.36010 ( 12) hydrogen bonds : bond 0.04864 ( 895) hydrogen bonds : angle 3.93975 ( 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 133 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.436 Fit side-chains REVERT: C 69 LYS cc_start: 0.7821 (mttp) cc_final: 0.7182 (mtmt) REVERT: C 337 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6722 (mm) REVERT: C 513 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.7049 (mtm-85) REVERT: A 337 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6712 (mm) REVERT: B 69 LYS cc_start: 0.7972 (mttt) cc_final: 0.7423 (mtmt) REVERT: B 337 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6908 (mm) outliers start: 16 outliers final: 9 residues processed: 129 average time/residue: 0.5112 time to fit residues: 71.7420 Evaluate side-chains 123 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 393 VAL Chi-restraints excluded: chain B residue 394 VAL 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: 1.9990 chunk 83 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.174670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109588 restraints weight = 10585.409| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.61 r_work: 0.3217 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11616 Z= 0.123 Angle : 0.548 13.059 15882 Z= 0.274 Chirality : 0.040 0.166 1932 Planarity : 0.004 0.034 1929 Dihedral : 3.969 24.352 1566 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.38 % Allowed : 16.67 % Favored : 81.95 % 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: 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 0.014 0.001 TYR C 557 PHE 0.019 0.001 PHE C 147 TRP 0.009 0.001 TRP A 106 HIS 0.005 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00238 (11610) covalent geometry : angle 0.54578 (15870) SS BOND : bond 0.00339 ( 6) SS BOND : angle 1.70589 ( 12) hydrogen bonds : bond 0.05343 ( 895) hydrogen bonds : angle 4.02936 ( 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 127 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.361 Fit side-chains REVERT: C 69 LYS cc_start: 0.7859 (mttp) cc_final: 0.7227 (mtmt) REVERT: C 337 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6753 (mm) REVERT: C 513 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6990 (mtm-85) REVERT: A 337 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6811 (mm) REVERT: B 69 LYS cc_start: 0.7989 (mttt) cc_final: 0.7443 (mtmt) REVERT: B 337 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6963 (mm) REVERT: B 520 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8064 (mmmt) outliers start: 17 outliers final: 9 residues processed: 122 average time/residue: 0.4898 time to fit residues: 64.9116 Evaluate side-chains 118 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4101 r_free = 0.4101 target = 0.171185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105253 restraints weight = 10509.197| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.60 r_work: 0.3154 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11616 Z= 0.166 Angle : 0.627 15.875 15882 Z= 0.316 Chirality : 0.043 0.165 1932 Planarity : 0.004 0.036 1929 Dihedral : 4.189 25.414 1566 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.06 % Allowed : 16.99 % Favored : 81.95 % 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: 2.55 (0.21), residues: 1452 helix: 2.22 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.33 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 224 TYR 0.016 0.002 TYR B 565 PHE 0.020 0.002 PHE C 147 TRP 0.010 0.001 TRP A 249 HIS 0.009 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00357 (11610) covalent geometry : angle 0.62362 (15870) SS BOND : bond 0.00479 ( 6) SS BOND : angle 2.33998 ( 12) hydrogen bonds : bond 0.06862 ( 895) hydrogen bonds : angle 4.31857 ( 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: 13 poor density : 113 time to evaluate : 0.433 Fit side-chains REVERT: C 307 GLN cc_start: 0.6685 (tt0) cc_final: 0.6335 (tp40) REVERT: C 337 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6839 (mm) REVERT: A 337 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6998 (mm) REVERT: B 69 LYS cc_start: 0.8040 (mttt) cc_final: 0.7468 (mtmt) REVERT: B 337 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7010 (mm) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.4960 time to fit residues: 66.3532 Evaluate side-chains 123 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 580 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 310 ASN B 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.173818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108624 restraints weight = 10594.635| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.61 r_work: 0.3209 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2219 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= 0.127 Angle : 0.582 13.902 15882 Z= 0.291 Chirality : 0.040 0.243 1932 Planarity : 0.004 0.032 1929 Dihedral : 4.163 26.603 1566 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.06 % Allowed : 16.83 % 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: 2.69 (0.22), residues: 1452 helix: 2.32 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -0.29 (0.34), residues: 309 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 0.020 0.001 PHE C 147 TRP 0.011 0.001 TRP A 106 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00239 (11610) covalent geometry : angle 0.57309 (15870) SS BOND : bond 0.00666 ( 6) SS BOND : angle 3.64624 ( 12) hydrogen bonds : bond 0.05564 ( 895) hydrogen bonds : angle 4.11580 ( 2610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5378.36 seconds wall clock time: 91 minutes 44.04 seconds (5504.04 seconds total)