Starting phenix.real_space_refine on Wed Feb 4 15:41:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps3_71821/02_2026/9ps3_71821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps3_71821/02_2026/9ps3_71821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ps3_71821/02_2026/9ps3_71821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps3_71821/02_2026/9ps3_71821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ps3_71821/02_2026/9ps3_71821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps3_71821/02_2026/9ps3_71821.map" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7545 2.51 5 N 1809 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 11322 Number of models: 1 Model: "" Number of chains: 3 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 Time building chain proxies: 2.50, per 1000 atoms: 0.22 Number of scatterers: 11322 At special positions: 0 Unit cell: (135.85, 126.35, 78.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1914 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=2.02 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 74 " distance=2.01 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 417.3 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: 72 helices and 6 sheets defined 84.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.521A pdb=" N VAL C 56 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N CYS C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 72 through 75 removed outlier: 3.707A pdb=" N HIS C 75 " --> pdb=" O PRO C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 82 through 90 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 removed outlier: 3.584A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 removed outlier: 3.723A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 143 through 161 Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 166 through 193 removed outlier: 3.899A pdb=" N ALA C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 5.108A 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: 4.422A 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 377 through 382 Processing helix chain 'C' and resid 389 through 409 Processing helix chain 'C' and resid 418 through 452 Processing helix chain 'C' and resid 454 through 482 removed outlier: 4.026A pdb=" N LEU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 482 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 515 removed outlier: 3.702A pdb=" N PHE C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 549 removed outlier: 3.682A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 554 through 577 removed outlier: 3.800A pdb=" N GLY C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.521A pdb=" N VAL A 56 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N CYS A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.703A pdb=" N HIS A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 82 through 90 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 removed outlier: 3.584A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.723A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 143 through 161 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 166 through 193 removed outlier: 3.899A pdb=" N ALA A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 5.108A 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: 4.423A 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 377 through 382 Processing helix chain 'A' and resid 389 through 409 Processing helix chain 'A' and resid 418 through 452 Processing helix chain 'A' and resid 454 through 482 removed outlier: 4.027A pdb=" N LEU A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 515 removed outlier: 3.701A pdb=" N PHE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 549 removed outlier: 3.682A pdb=" N VAL A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Proline residue: A 547 - end of helix Processing helix chain 'A' and resid 554 through 577 removed outlier: 3.799A pdb=" N GLY A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.521A pdb=" N VAL B 56 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N CYS B 57 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 72 through 75 removed outlier: 3.928A pdb=" N HIS B 75 " --> pdb=" O PRO B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 82 through 90 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 removed outlier: 3.583A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.723A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 143 through 161 Proline residue: B 152 - end of helix Processing helix chain 'B' and resid 166 through 193 removed outlier: 3.899A pdb=" N ALA B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 5.109A 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: 4.423A 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 377 through 382 Processing helix chain 'B' and resid 389 through 409 Processing helix chain 'B' and resid 418 through 452 Processing helix chain 'B' and resid 454 through 482 removed outlier: 3.793A pdb=" N LEU B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 3.701A pdb=" N PHE B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 496 " --> pdb=" O PHE B 492 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 549 removed outlier: 3.682A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 554 through 577 removed outlier: 3.800A 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 'A' and resid 195 through 196 Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA5, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AA6, first strand: chain 'B' and resid 224 through 226 879 hydrogen bonds defined for protein. 2619 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: 1.84 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: 1.21 - 1.33: 2472 1.33 - 1.45: 2573 1.45 - 1.57: 6499 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11610 Sorted by residual: bond pdb=" N GLY B 78 " pdb=" CA GLY B 78 " ideal model delta sigma weight residual 1.448 1.476 -0.027 1.00e-02 1.00e+04 7.47e+00 bond pdb=" N TYR C 90 " pdb=" CA TYR C 90 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.25e-02 6.40e+03 6.94e+00 bond pdb=" N TYR B 90 " pdb=" CA TYR B 90 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.25e-02 6.40e+03 6.84e+00 bond pdb=" N TYR A 90 " pdb=" CA TYR A 90 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.25e-02 6.40e+03 6.84e+00 bond pdb=" N ASP C 471 " pdb=" CA ASP C 471 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.52e+00 ... (remaining 11605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 15495 2.65 - 5.31: 318 5.31 - 7.96: 45 7.96 - 10.61: 9 10.61 - 13.26: 3 Bond angle restraints: 15870 Sorted by residual: angle pdb=" N TYR C 90 " pdb=" CA TYR C 90 " pdb=" C TYR C 90 " ideal model delta sigma weight residual 112.93 99.67 13.26 1.33e+00 5.65e-01 9.94e+01 angle pdb=" N TYR A 90 " pdb=" CA TYR A 90 " pdb=" C TYR A 90 " ideal model delta sigma weight residual 112.93 99.67 13.26 1.33e+00 5.65e-01 9.94e+01 angle pdb=" N TYR B 90 " pdb=" CA TYR B 90 " pdb=" C TYR B 90 " ideal model delta sigma weight residual 112.93 99.70 13.23 1.33e+00 5.65e-01 9.89e+01 angle pdb=" C ASP B 73 " pdb=" N CYS B 74 " pdb=" CA CYS B 74 " ideal model delta sigma weight residual 123.20 115.82 7.38 1.38e+00 5.25e-01 2.86e+01 angle pdb=" C PHE B 88 " pdb=" N CYS B 89 " pdb=" CA CYS B 89 " ideal model delta sigma weight residual 123.34 113.90 9.44 1.80e+00 3.09e-01 2.75e+01 ... (remaining 15865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 6049 16.61 - 33.22: 526 33.22 - 49.83: 97 49.83 - 66.44: 9 66.44 - 83.05: 12 Dihedral angle restraints: 6693 sinusoidal: 2478 harmonic: 4215 Sorted by residual: dihedral pdb=" CB CYS A 53 " pdb=" SG CYS A 53 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 176.05 -83.05 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS C 53 " pdb=" SG CYS C 53 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 176.04 -83.04 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 174.82 -81.82 1 1.00e+01 1.00e-02 8.23e+01 ... (remaining 6690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1667 0.080 - 0.159: 244 0.159 - 0.239: 15 0.239 - 0.318: 3 0.318 - 0.398: 3 Chirality restraints: 1932 Sorted by residual: chirality pdb=" CA CYS A 89 " pdb=" N CYS A 89 " pdb=" C CYS A 89 " pdb=" CB CYS A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA CYS C 89 " pdb=" N CYS C 89 " pdb=" C CYS C 89 " pdb=" CB CYS C 89 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA CYS B 89 " pdb=" N CYS B 89 " pdb=" C CYS B 89 " pdb=" CB CYS B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 1929 not shown) Planarity restraints: 1929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 123 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO A 124 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 123 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO C 124 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 123 " 0.036 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 124 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.030 5.00e-02 4.00e+02 ... (remaining 1926 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2463 2.78 - 3.31: 11089 3.31 - 3.84: 18511 3.84 - 4.37: 20754 4.37 - 4.90: 36723 Nonbonded interactions: 89540 Sorted by model distance: nonbonded pdb=" O TRP C 317 " pdb=" NZ LYS C 325 " model vdw 2.250 3.120 nonbonded pdb=" O TRP A 317 " pdb=" NZ LYS A 325 " model vdw 2.250 3.120 nonbonded pdb=" O TRP B 317 " pdb=" NZ LYS B 325 " model vdw 2.250 3.120 nonbonded pdb=" O PHE C 121 " pdb=" ND2 ASN C 125 " model vdw 2.254 3.120 nonbonded pdb=" O PHE B 121 " pdb=" ND2 ASN B 125 " model vdw 2.254 3.120 ... (remaining 89535 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: 2.180 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.990 Find NCS groups from input model: 0.140 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.009 0.085 11616 Z= 0.371 Angle : 0.976 13.263 15882 Z= 0.548 Chirality : 0.058 0.398 1932 Planarity : 0.007 0.054 1929 Dihedral : 13.290 77.421 3969 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.65 % Allowed : 1.06 % Favored : 98.29 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1452 helix: 0.21 (0.14), residues: 1143 sheet: None (None), residues: 0 loop : -2.52 (0.28), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 70 TYR 0.018 0.002 TYR B 237 PHE 0.019 0.003 PHE A 564 TRP 0.011 0.002 TRP A 529 HIS 0.009 0.002 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00881 (11610) covalent geometry : angle 0.96484 (15870) SS BOND : bond 0.00918 ( 6) SS BOND : angle 5.38862 ( 12) hydrogen bonds : bond 0.16142 ( 879) hydrogen bonds : angle 6.11436 ( 2619) *********************** 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 129 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.287 Fit side-chains REVERT: C 510 GLN cc_start: 0.8338 (tp40) cc_final: 0.8127 (tp40) REVERT: A 207 THR cc_start: 0.8648 (m) cc_final: 0.8436 (m) REVERT: B 50 MET cc_start: 0.5089 (pmm) cc_final: 0.4469 (pmm) REVERT: B 480 ARG cc_start: 0.6859 (mtm110) cc_final: 0.6528 (mtm110) REVERT: B 510 GLN cc_start: 0.8175 (tp40) cc_final: 0.7846 (tp40) outliers start: 8 outliers final: 2 residues processed: 128 average time/residue: 0.4775 time to fit residues: 66.7941 Evaluate side-chains 98 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 537 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.178461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124583 restraints weight = 11401.657| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.86 r_work: 0.3205 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11616 Z= 0.152 Angle : 0.660 8.729 15882 Z= 0.337 Chirality : 0.042 0.186 1932 Planarity : 0.005 0.045 1929 Dihedral : 5.158 37.979 1570 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.63 % Allowed : 7.72 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1452 helix: 1.27 (0.15), residues: 1137 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 224 TYR 0.015 0.002 TYR C 237 PHE 0.011 0.001 PHE A 564 TRP 0.010 0.001 TRP C 354 HIS 0.005 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00318 (11610) covalent geometry : angle 0.65553 (15870) SS BOND : bond 0.00299 ( 6) SS BOND : angle 2.85336 ( 12) hydrogen bonds : bond 0.06238 ( 879) hydrogen bonds : angle 4.47366 ( 2619) *********************** 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 137 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.422 Fit side-chains REVERT: C 59 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7679 (mp) REVERT: C 70 ARG cc_start: 0.6717 (mtm-85) cc_final: 0.6475 (ppt170) REVERT: A 70 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6828 (ppt170) REVERT: A 135 LEU cc_start: 0.8261 (mp) cc_final: 0.8013 (mp) REVERT: A 145 LEU cc_start: 0.7310 (mp) cc_final: 0.7034 (mm) REVERT: A 373 THR cc_start: 0.6753 (m) cc_final: 0.6542 (m) REVERT: B 50 MET cc_start: 0.5076 (pmm) cc_final: 0.4555 (pmm) REVERT: B 142 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7081 (p) REVERT: B 510 GLN cc_start: 0.8202 (tp40) cc_final: 0.7958 (tp40) REVERT: B 513 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6547 (ptp-170) outliers start: 20 outliers final: 8 residues processed: 131 average time/residue: 0.5490 time to fit residues: 78.1008 Evaluate side-chains 111 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 513 ARG Chi-restraints excluded: chain B residue 537 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 ASN C 362 GLN A 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128471 restraints weight = 11667.812| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.84 r_work: 0.3365 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11616 Z= 0.158 Angle : 0.657 8.510 15882 Z= 0.333 Chirality : 0.043 0.208 1932 Planarity : 0.005 0.043 1929 Dihedral : 4.966 41.925 1570 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 11.30 % Favored : 86.75 % 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: 1.29 (0.22), residues: 1452 helix: 1.53 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.67 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 224 TYR 0.014 0.001 TYR C 237 PHE 0.014 0.002 PHE B 88 TRP 0.009 0.001 TRP B 432 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00366 (11610) covalent geometry : angle 0.65141 (15870) SS BOND : bond 0.00194 ( 6) SS BOND : angle 3.07406 ( 12) hydrogen bonds : bond 0.06294 ( 879) hydrogen bonds : angle 4.26965 ( 2619) *********************** 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 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: C 70 ARG cc_start: 0.6714 (mtm-85) cc_final: 0.6413 (tmt170) REVERT: C 95 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6183 (pt) REVERT: C 518 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: A 95 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6233 (pt) REVERT: A 135 LEU cc_start: 0.8269 (mp) cc_final: 0.7983 (mp) REVERT: A 145 LEU cc_start: 0.6932 (mp) cc_final: 0.6675 (mm) REVERT: B 50 MET cc_start: 0.5326 (pmm) cc_final: 0.4685 (pmm) REVERT: B 59 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7532 (mp) outliers start: 24 outliers final: 9 residues processed: 132 average time/residue: 0.5257 time to fit residues: 75.6534 Evaluate side-chains 110 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 537 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124238 restraints weight = 11939.264| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.85 r_work: 0.3327 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11616 Z= 0.212 Angle : 0.745 11.121 15882 Z= 0.372 Chirality : 0.046 0.217 1932 Planarity : 0.005 0.051 1929 Dihedral : 5.215 51.281 1570 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.52 % Allowed : 14.15 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.15 (0.22), residues: 1452 helix: 1.40 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 224 TYR 0.016 0.002 TYR B 237 PHE 0.015 0.002 PHE A 564 TRP 0.008 0.001 TRP B 432 HIS 0.006 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00530 (11610) covalent geometry : angle 0.73844 (15870) SS BOND : bond 0.00465 ( 6) SS BOND : angle 3.68582 ( 12) hydrogen bonds : bond 0.07570 ( 879) hydrogen bonds : angle 4.36980 ( 2619) *********************** 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 138 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.353 Fit side-chains REVERT: C 70 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.6422 (tmt170) REVERT: A 135 LEU cc_start: 0.8279 (mp) cc_final: 0.7987 (mp) REVERT: B 50 MET cc_start: 0.5446 (pmm) cc_final: 0.4576 (pmm) REVERT: B 59 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7512 (mp) REVERT: B 70 ARG cc_start: 0.6736 (tmt170) cc_final: 0.6372 (tmm160) outliers start: 31 outliers final: 15 residues processed: 129 average time/residue: 0.4903 time to fit residues: 69.5451 Evaluate side-chains 109 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 537 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 GLN A 138 ASN B 138 ASN B 362 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125637 restraints weight = 11791.432| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.82 r_work: 0.3354 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11616 Z= 0.169 Angle : 0.681 9.884 15882 Z= 0.342 Chirality : 0.043 0.211 1932 Planarity : 0.005 0.062 1929 Dihedral : 5.137 51.615 1570 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.68 % Allowed : 15.20 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.38 (0.22), residues: 1452 helix: 1.57 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -1.58 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 224 TYR 0.014 0.002 TYR C 237 PHE 0.014 0.002 PHE B 88 TRP 0.009 0.001 TRP B 432 HIS 0.005 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00408 (11610) covalent geometry : angle 0.67472 (15870) SS BOND : bond 0.00243 ( 6) SS BOND : angle 3.29015 ( 12) hydrogen bonds : bond 0.06609 ( 879) hydrogen bonds : angle 4.25183 ( 2619) *********************** 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 130 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.510 Fit side-chains REVERT: C 50 MET cc_start: 0.4600 (pmm) cc_final: 0.4034 (pmm) REVERT: C 70 ARG cc_start: 0.6776 (mtm-85) cc_final: 0.6500 (tmt170) REVERT: A 50 MET cc_start: 0.4912 (pmm) cc_final: 0.4122 (pmm) REVERT: A 135 LEU cc_start: 0.8271 (mp) cc_final: 0.7962 (mp) REVERT: A 142 VAL cc_start: 0.7457 (t) cc_final: 0.6974 (p) REVERT: B 50 MET cc_start: 0.5360 (pmm) cc_final: 0.4702 (pmm) REVERT: B 59 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 85 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7008 (mtmt) REVERT: B 135 LEU cc_start: 0.8351 (mp) cc_final: 0.8135 (mt) outliers start: 33 outliers final: 14 residues processed: 122 average time/residue: 0.5151 time to fit residues: 68.8581 Evaluate side-chains 110 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 580 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125134 restraints weight = 11806.024| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.86 r_work: 0.3345 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11616 Z= 0.179 Angle : 0.690 10.739 15882 Z= 0.346 Chirality : 0.044 0.250 1932 Planarity : 0.005 0.063 1929 Dihedral : 5.149 54.707 1570 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.76 % Allowed : 15.37 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.34 (0.22), residues: 1452 helix: 1.52 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -1.53 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 224 TYR 0.014 0.002 TYR B 237 PHE 0.013 0.002 PHE B 88 TRP 0.009 0.001 TRP B 432 HIS 0.005 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00436 (11610) covalent geometry : angle 0.68388 (15870) SS BOND : bond 0.00329 ( 6) SS BOND : angle 3.33798 ( 12) hydrogen bonds : bond 0.06854 ( 879) hydrogen bonds : angle 4.25577 ( 2619) *********************** 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 129 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.445 Fit side-chains REVERT: C 50 MET cc_start: 0.4667 (pmm) cc_final: 0.4105 (pmm) REVERT: C 70 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.6639 (tmt170) REVERT: A 50 MET cc_start: 0.4949 (pmm) cc_final: 0.4202 (pmm) REVERT: A 135 LEU cc_start: 0.8246 (mp) cc_final: 0.7998 (mp) REVERT: A 142 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.6953 (p) REVERT: B 50 MET cc_start: 0.5270 (pmm) cc_final: 0.4549 (pmm) REVERT: B 59 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7548 (mp) REVERT: B 85 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7004 (mtmt) REVERT: B 135 LEU cc_start: 0.8374 (mp) cc_final: 0.8152 (mt) outliers start: 34 outliers final: 19 residues processed: 121 average time/residue: 0.4898 time to fit residues: 65.0854 Evaluate side-chains 110 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 537 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 138 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 127 optimal weight: 6.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128575 restraints weight = 11847.371| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.78 r_work: 0.3397 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11616 Z= 0.135 Angle : 0.617 8.702 15882 Z= 0.312 Chirality : 0.041 0.233 1932 Planarity : 0.005 0.069 1929 Dihedral : 4.914 49.978 1570 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.03 % Allowed : 16.42 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.72 (0.22), residues: 1452 helix: 1.88 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.63 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 224 TYR 0.014 0.001 TYR B 557 PHE 0.012 0.001 PHE A 88 TRP 0.011 0.001 TRP B 432 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00300 (11610) covalent geometry : angle 0.61188 (15870) SS BOND : bond 0.00089 ( 6) SS BOND : angle 2.84342 ( 12) hydrogen bonds : bond 0.05374 ( 879) hydrogen bonds : angle 4.08566 ( 2619) *********************** 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 121 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.300 Fit side-chains REVERT: C 50 MET cc_start: 0.4657 (pmm) cc_final: 0.4128 (pmm) REVERT: C 70 ARG cc_start: 0.6922 (mtm-85) cc_final: 0.6673 (tmt170) REVERT: C 224 ARG cc_start: 0.7681 (mtm110) cc_final: 0.6997 (mtp85) REVERT: C 373 THR cc_start: 0.6940 (m) cc_final: 0.6697 (p) REVERT: C 500 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6895 (mp) REVERT: A 50 MET cc_start: 0.4940 (pmm) cc_final: 0.4246 (pmm) REVERT: A 135 LEU cc_start: 0.8196 (mp) cc_final: 0.7922 (mp) REVERT: A 142 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.6782 (p) REVERT: B 50 MET cc_start: 0.5169 (pmm) cc_final: 0.4443 (pmm) REVERT: B 59 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7616 (mp) REVERT: B 85 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7069 (mtmt) REVERT: B 135 LEU cc_start: 0.8391 (mp) cc_final: 0.8175 (mt) REVERT: B 142 VAL cc_start: 0.7247 (OUTLIER) cc_final: 0.7041 (t) outliers start: 25 outliers final: 11 residues processed: 115 average time/residue: 0.5029 time to fit residues: 63.0359 Evaluate side-chains 107 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 537 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127867 restraints weight = 11825.370| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.77 r_work: 0.3388 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11616 Z= 0.142 Angle : 0.632 9.333 15882 Z= 0.318 Chirality : 0.043 0.299 1932 Planarity : 0.005 0.084 1929 Dihedral : 4.891 49.689 1570 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.87 % Allowed : 16.99 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.74 (0.22), residues: 1452 helix: 1.89 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.60 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 224 TYR 0.014 0.001 TYR C 557 PHE 0.012 0.001 PHE A 88 TRP 0.010 0.001 TRP B 432 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00326 (11610) covalent geometry : angle 0.62766 (15870) SS BOND : bond 0.00197 ( 6) SS BOND : angle 2.90404 ( 12) hydrogen bonds : bond 0.05657 ( 879) hydrogen bonds : angle 4.08221 ( 2619) *********************** 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 115 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.396 Fit side-chains REVERT: C 50 MET cc_start: 0.4672 (pmm) cc_final: 0.4160 (pmm) REVERT: C 70 ARG cc_start: 0.6921 (mtm-85) cc_final: 0.6673 (tmt170) REVERT: C 373 THR cc_start: 0.6933 (m) cc_final: 0.6693 (p) REVERT: A 50 MET cc_start: 0.4927 (pmm) cc_final: 0.4262 (pmm) REVERT: A 59 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7582 (mp) REVERT: A 135 LEU cc_start: 0.8193 (mp) cc_final: 0.7907 (mp) REVERT: A 142 VAL cc_start: 0.7356 (OUTLIER) cc_final: 0.6854 (p) REVERT: A 224 ARG cc_start: 0.7721 (mtm110) cc_final: 0.6802 (mtp180) REVERT: B 50 MET cc_start: 0.5099 (pmm) cc_final: 0.4358 (pmm) REVERT: B 59 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7636 (mp) REVERT: B 85 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7056 (mtmt) REVERT: B 135 LEU cc_start: 0.8382 (mp) cc_final: 0.8139 (mt) outliers start: 23 outliers final: 13 residues processed: 110 average time/residue: 0.4929 time to fit residues: 59.3378 Evaluate side-chains 107 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 537 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 120 optimal weight: 0.0670 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.179456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127570 restraints weight = 11820.318| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.78 r_work: 0.3385 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11616 Z= 0.145 Angle : 0.637 9.301 15882 Z= 0.319 Chirality : 0.042 0.268 1932 Planarity : 0.005 0.077 1929 Dihedral : 4.885 49.791 1570 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.20 % Allowed : 16.83 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.75 (0.22), residues: 1452 helix: 1.89 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 224 TYR 0.014 0.001 TYR C 557 PHE 0.012 0.001 PHE A 88 TRP 0.011 0.001 TRP B 432 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00338 (11610) covalent geometry : angle 0.63205 (15870) SS BOND : bond 0.00179 ( 6) SS BOND : angle 2.94125 ( 12) hydrogen bonds : bond 0.05764 ( 879) hydrogen bonds : angle 4.04955 ( 2619) *********************** 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 121 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.420 Fit side-chains REVERT: C 50 MET cc_start: 0.4759 (pmm) cc_final: 0.4248 (pmm) REVERT: C 70 ARG cc_start: 0.6912 (mtm-85) cc_final: 0.6600 (tmt170) REVERT: C 224 ARG cc_start: 0.7637 (mtm110) cc_final: 0.6961 (mtp85) REVERT: C 373 THR cc_start: 0.6916 (m) cc_final: 0.6676 (p) REVERT: A 50 MET cc_start: 0.4914 (pmm) cc_final: 0.4245 (pmm) REVERT: A 135 LEU cc_start: 0.8181 (mp) cc_final: 0.7884 (mp) REVERT: A 142 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.6856 (p) REVERT: B 50 MET cc_start: 0.5064 (pmm) cc_final: 0.4307 (pmm) REVERT: B 59 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 85 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7068 (mtmt) REVERT: B 135 LEU cc_start: 0.8379 (mp) cc_final: 0.8143 (mt) outliers start: 27 outliers final: 18 residues processed: 117 average time/residue: 0.4513 time to fit residues: 57.9420 Evaluate side-chains 111 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 537 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 136 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 124 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129677 restraints weight = 11816.150| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.79 r_work: 0.3392 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2364 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= 0.133 Angle : 0.614 8.725 15882 Z= 0.309 Chirality : 0.042 0.297 1932 Planarity : 0.005 0.081 1929 Dihedral : 4.797 48.287 1570 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.87 % Allowed : 16.99 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.89 (0.22), residues: 1452 helix: 1.99 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.54 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 224 TYR 0.014 0.001 TYR C 557 PHE 0.011 0.001 PHE A 88 TRP 0.012 0.001 TRP B 432 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00299 (11610) covalent geometry : angle 0.60966 (15870) SS BOND : bond 0.00127 ( 6) SS BOND : angle 2.78896 ( 12) hydrogen bonds : bond 0.05281 ( 879) hydrogen bonds : angle 4.00511 ( 2619) ********************** 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 120 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.415 Fit side-chains REVERT: C 50 MET cc_start: 0.4416 (pmm) cc_final: 0.4062 (pmm) REVERT: C 70 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.6638 (tmt170) REVERT: C 224 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7003 (ptp-110) REVERT: C 373 THR cc_start: 0.6904 (m) cc_final: 0.6667 (p) REVERT: C 500 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6855 (mp) REVERT: A 50 MET cc_start: 0.4900 (pmm) cc_final: 0.4220 (pmm) REVERT: A 135 LEU cc_start: 0.8192 (mp) cc_final: 0.7910 (mp) REVERT: A 145 LEU cc_start: 0.6787 (mp) cc_final: 0.6525 (mm) REVERT: A 224 ARG cc_start: 0.7709 (mtm110) cc_final: 0.6947 (ptm160) REVERT: B 59 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 85 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7060 (mtmt) REVERT: B 135 LEU cc_start: 0.8354 (mp) cc_final: 0.8109 (mt) REVERT: B 224 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7073 (ptp-170) outliers start: 23 outliers final: 18 residues processed: 118 average time/residue: 0.4636 time to fit residues: 59.9459 Evaluate side-chains 117 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 537 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128963 restraints weight = 11777.483| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.05 r_work: 0.3428 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2434 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= 0.129 Angle : 0.607 8.526 15882 Z= 0.304 Chirality : 0.041 0.287 1932 Planarity : 0.005 0.087 1929 Dihedral : 4.728 46.794 1570 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.71 % Allowed : 17.15 % Favored : 81.14 % 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: 1.95 (0.22), residues: 1452 helix: 1.99 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 224 TYR 0.014 0.001 TYR C 557 PHE 0.028 0.001 PHE A 473 TRP 0.012 0.001 TRP B 432 HIS 0.003 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00290 (11610) covalent geometry : angle 0.60226 (15870) SS BOND : bond 0.00119 ( 6) SS BOND : angle 2.73555 ( 12) hydrogen bonds : bond 0.05091 ( 879) hydrogen bonds : angle 3.97580 ( 2619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3944.53 seconds wall clock time: 67 minutes 50.14 seconds (4070.14 seconds total)