Starting phenix.real_space_refine on Fri Jul 3 02:44:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps1_71819/07_2026/9ps1_71819.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps1_71819/07_2026/9ps1_71819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ps1_71819/07_2026/9ps1_71819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps1_71819/07_2026/9ps1_71819.map" model { file = "/net/cci-nas-00/data/ceres_data/9ps1_71819/07_2026/9ps1_71819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps1_71819/07_2026/9ps1_71819.cif" } resolution = 2.6 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= 0.181 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 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11325 Number of models: 1 Model: "" Number of chains: 6 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: 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.91, per 1000 atoms: 0.26 Number of scatterers: 11325 At special positions: 0 Unit cell: (133.386, 121.088, 86.086, 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 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 B 53 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 74 " distance=2.03 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=2.04 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: 1.00 Conformation dependent library (CDL) restraints added in 616.7 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: 67 helices and 9 sheets defined 82.9% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.531A pdb=" N VAL B 56 " --> pdb=" O CYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 95 through 121 Processing helix chain 'B' and resid 121 through 134 removed outlier: 3.772A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 161 removed outlier: 4.472A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Proline residue: B 152 - end of helix Processing helix chain 'B' and resid 166 through 193 removed outlier: 3.620A pdb=" N ILE B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.642A 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 319 removed outlier: 3.861A pdb=" N THR B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) 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: 3.981A 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 390 through 409 Processing helix chain 'B' and resid 419 through 451 removed outlier: 3.869A pdb=" N PHE B 423 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 removed outlier: 4.395A pdb=" N LEU B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 459' Processing helix chain 'B' and resid 461 through 481 removed outlier: 5.232A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 3.510A pdb=" N ALA B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE B 496 " --> pdb=" O PHE B 492 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 549 removed outlier: 3.527A 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: 3.664A pdb=" N GLY B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 59 removed outlier: 4.127A pdb=" N CYS C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 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 131 removed outlier: 3.735A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 136 through 162 removed outlier: 3.752A pdb=" N ALA C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Proline residue: C 152 - end of helix removed outlier: 3.539A pdb=" N SER C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 193 removed outlier: 4.005A pdb=" N ALA C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.505A 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: 4.016A 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 removed outlier: 4.091A pdb=" N ILE C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 382' 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 418 through 452 removed outlier: 4.108A pdb=" N ALA C 422 " --> pdb=" O HIS C 418 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 481 removed outlier: 3.745A pdb=" N LEU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 515 removed outlier: 4.660A pdb=" N ILE C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.726A pdb=" N GLY C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 removed outlier: 4.203A pdb=" N CYS A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 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 removed outlier: 3.516A pdb=" N PHE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.893A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 161 removed outlier: 3.783A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.229A 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: 3.852A pdb=" N ALA A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.570A 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 removed outlier: 3.776A pdb=" N THR A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) 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: 3.973A 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 removed outlier: 3.669A pdb=" N ILE A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 382' Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 419 through 452 removed outlier: 3.899A pdb=" N PHE A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 481 removed outlier: 3.694A pdb=" N LEU A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 515 removed outlier: 4.714A pdb=" N ILE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 549 removed outlier: 3.546A 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: 3.640A pdb=" N GLY A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA3, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.698A pdb=" N LEU B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AA5, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'C' and resid 383 through 384 Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA8, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain 'A' and resid 383 through 384 removed outlier: 4.259A pdb=" N LEU A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2535 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: 1.95 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3309 1.34 - 1.45: 2031 1.45 - 1.57: 6204 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11610 Sorted by residual: bond pdb=" CB ASN C 498 " pdb=" CG ASN C 498 " ideal model delta sigma weight residual 1.516 1.451 0.065 2.50e-02 1.60e+03 6.73e+00 bond pdb=" N TYR A 109 " pdb=" CA TYR A 109 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.25e-02 6.40e+03 5.66e+00 bond pdb=" N PHE A 111 " pdb=" CA PHE A 111 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.39e+00 bond pdb=" N LEU A 110 " pdb=" CA LEU A 110 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.30e+00 bond pdb=" N ASP B 153 " pdb=" CA ASP B 153 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.24e+00 ... (remaining 11605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 15391 2.10 - 4.19: 391 4.19 - 6.29: 73 6.29 - 8.38: 11 8.38 - 10.48: 4 Bond angle restraints: 15870 Sorted by residual: angle pdb=" N ILE A 381 " pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 113.07 108.19 4.88 1.36e+00 5.41e-01 1.29e+01 angle pdb=" C THR B 182 " pdb=" N THR B 183 " pdb=" CA THR B 183 " ideal model delta sigma weight residual 122.42 117.63 4.79 1.55e+00 4.16e-01 9.57e+00 angle pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " pdb=" CG ASP B 153 " ideal model delta sigma weight residual 112.60 115.68 -3.08 1.00e+00 1.00e+00 9.50e+00 angle pdb=" CA LEU A 305 " pdb=" CB LEU A 305 " pdb=" CG LEU A 305 " ideal model delta sigma weight residual 116.30 126.78 -10.48 3.50e+00 8.16e-02 8.96e+00 angle pdb=" N SER C 554 " pdb=" CA SER C 554 " pdb=" C SER C 554 " ideal model delta sigma weight residual 108.34 112.20 -3.86 1.31e+00 5.83e-01 8.66e+00 ... (remaining 15865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 6053 16.84 - 33.67: 534 33.67 - 50.51: 79 50.51 - 67.34: 19 67.34 - 84.18: 8 Dihedral angle restraints: 6693 sinusoidal: 2478 harmonic: 4215 Sorted by residual: dihedral pdb=" CB CYS A 65 " pdb=" SG CYS A 65 " pdb=" SG CYS A 89 " pdb=" CB CYS A 89 " ideal model delta sinusoidal sigma weight residual -86.00 -160.90 74.90 1 1.00e+01 1.00e-02 7.10e+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 93.00 133.65 -40.65 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA GLY B 78 " pdb=" C GLY B 78 " pdb=" N GLY B 79 " pdb=" CA GLY B 79 " ideal model delta harmonic sigma weight residual 180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 6690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1547 0.063 - 0.125: 360 0.125 - 0.188: 22 0.188 - 0.251: 2 0.251 - 0.314: 1 Chirality restraints: 1932 Sorted by residual: chirality pdb=" CG LEU A 559 " pdb=" CB LEU A 559 " pdb=" CD1 LEU A 559 " pdb=" CD2 LEU A 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA GLU B 439 " pdb=" N GLU B 439 " pdb=" C GLU B 439 " pdb=" CB GLU B 439 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE A 225 " pdb=" CA ILE A 225 " pdb=" CG1 ILE A 225 " pdb=" CG2 ILE A 225 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1929 not shown) Planarity restraints: 1929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 522 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.67e+00 pdb=" N PRO B 523 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 523 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 523 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 123 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 124 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 440 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C VAL B 440 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL B 440 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 441 " -0.013 2.00e-02 2.50e+03 ... (remaining 1926 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2065 2.76 - 3.29: 11360 3.29 - 3.83: 18334 3.83 - 4.36: 21316 4.36 - 4.90: 37144 Nonbonded interactions: 90219 Sorted by model distance: nonbonded pdb=" O TRP C 317 " pdb=" NZ LYS C 325 " model vdw 2.221 3.120 nonbonded pdb=" OD1 ASP B 471 " pdb="CA CA B 601 " model vdw 2.242 3.250 nonbonded pdb=" O THR A 341 " pdb=" OG SER A 366 " model vdw 2.250 3.040 nonbonded pdb=" O TRP B 317 " pdb=" NZ LYS B 325 " model vdw 2.277 3.120 nonbonded pdb=" O VAL B 159 " pdb=" OG SER B 162 " model vdw 2.284 3.040 ... (remaining 90214 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 0.072 11616 Z= 0.366 Angle : 0.824 10.476 15882 Z= 0.431 Chirality : 0.051 0.314 1932 Planarity : 0.007 0.069 1929 Dihedral : 13.126 84.180 3969 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.24 % Allowed : 0.81 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1452 helix: 0.38 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 200 TYR 0.027 0.003 TYR A 209 PHE 0.025 0.003 PHE C 147 TRP 0.013 0.002 TRP A 106 HIS 0.012 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.37 (11610) covalent geometry : angle 0.82037 / 0.43 (15870) SS BOND : bond 0.00581 / 0.32 ( 6) SS BOND : angle 3.08579 / 1.64 ( 12) hydrogen bonds : bond 0.15368 / 10.12 ( 860) hydrogen bonds : angle 6.94737 / 5.12 ( 2535) *********************** 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 128 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.399 Fit side-chains REVERT: B 224 ARG cc_start: 0.7726 (ttp-110) cc_final: 0.7302 (ttp-110) REVERT: B 251 TYR cc_start: 0.8398 (t80) cc_final: 0.8018 (t80) REVERT: C 249 TRP cc_start: 0.6635 (t-100) cc_final: 0.5925 (t60) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.4719 time to fit residues: 66.6320 Evaluate side-chains 106 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 510 GLN A 353 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099240 restraints weight = 14014.487| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.18 r_work: 0.3120 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11616 Z= 0.138 Angle : 0.580 8.535 15882 Z= 0.296 Chirality : 0.040 0.138 1932 Planarity : 0.005 0.053 1929 Dihedral : 4.322 16.476 1566 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.89 % Allowed : 6.34 % Favored : 92.76 % 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: 1.57 (0.22), residues: 1452 helix: 1.64 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.01 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 352 TYR 0.015 0.001 TYR B 557 PHE 0.011 0.001 PHE C 155 TRP 0.011 0.001 TRP C 106 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (11610) covalent geometry : angle 0.57629 / 0.29 (15870) SS BOND : bond 0.00139 / 0.06 ( 6) SS BOND : angle 2.30773 / 1.36 ( 12) hydrogen bonds : bond 0.05532 / 3.66 ( 860) hydrogen bonds : angle 4.27199 / 3.10 ( 2535) *********************** 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 132 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.550 Fit side-chains REVERT: B 224 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7220 (ttp-110) outliers start: 11 outliers final: 3 residues processed: 129 average time/residue: 0.4190 time to fit residues: 60.1923 Evaluate side-chains 103 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 509 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN 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 = 0.3857 r_free = 0.3857 target = 0.154065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099546 restraints weight = 14015.680| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.19 r_work: 0.3129 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11616 Z= 0.123 Angle : 0.538 6.553 15882 Z= 0.272 Chirality : 0.039 0.166 1932 Planarity : 0.004 0.045 1929 Dihedral : 4.080 16.416 1566 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.71 % Allowed : 8.05 % Favored : 90.24 % 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: 2.12 (0.22), residues: 1452 helix: 2.03 (0.15), residues: 1119 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 352 TYR 0.015 0.001 TYR B 557 PHE 0.009 0.001 PHE A 488 TRP 0.008 0.001 TRP A 106 HIS 0.002 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11610) covalent geometry : angle 0.53592 / 0.27 (15870) SS BOND : bond 0.00289 / 0.10 ( 6) SS BOND : angle 1.96530 / 1.13 ( 12) hydrogen bonds : bond 0.04956 / 3.31 ( 860) hydrogen bonds : angle 3.98470 / 2.88 ( 2535) *********************** 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 138 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.440 Fit side-chains REVERT: B 224 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7152 (ttp-110) REVERT: A 70 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7577 (mtm110) REVERT: A 471 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7627 (m-30) outliers start: 21 outliers final: 6 residues processed: 130 average time/residue: 0.3919 time to fit residues: 56.7907 Evaluate side-chains 107 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 320 GLN B 362 GLN B 510 GLN C 353 ASN C 362 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095798 restraints weight = 13632.739| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.05 r_work: 0.2995 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11616 Z= 0.115 Angle : 0.512 6.417 15882 Z= 0.258 Chirality : 0.039 0.123 1932 Planarity : 0.004 0.041 1929 Dihedral : 3.898 15.485 1566 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 10.33 % Favored : 87.72 % 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: 2.45 (0.22), residues: 1452 helix: 2.27 (0.15), residues: 1119 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 513 TYR 0.014 0.001 TYR B 557 PHE 0.010 0.001 PHE C 144 TRP 0.012 0.001 TRP A 317 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (11610) covalent geometry : angle 0.51058 / 0.26 (15870) SS BOND : bond 0.00080 / 0.04 ( 6) SS BOND : angle 1.58955 / 0.92 ( 12) hydrogen bonds : bond 0.04496 / 3.01 ( 860) hydrogen bonds : angle 3.79198 / 2.74 ( 2535) *********************** 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: 24 poor density : 114 time to evaluate : 0.396 Fit side-chains REVERT: B 224 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7562 (ttp-110) REVERT: C 70 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7201 (tmt170) REVERT: A 70 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7628 (mtp180) REVERT: A 96 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6560 (tm) REVERT: A 346 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7356 (t70) REVERT: A 439 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8178 (mp0) REVERT: A 495 ILE cc_start: 0.8709 (mt) cc_final: 0.8493 (mm) outliers start: 24 outliers final: 11 residues processed: 129 average time/residue: 0.3905 time to fit residues: 56.0276 Evaluate side-chains 116 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103563 restraints weight = 14274.101| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.05 r_work: 0.3262 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11616 Z= 0.127 Angle : 0.526 6.843 15882 Z= 0.263 Chirality : 0.039 0.135 1932 Planarity : 0.004 0.039 1929 Dihedral : 3.879 15.093 1566 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.11 % Allowed : 11.79 % Favored : 86.10 % 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: 2.50 (0.22), residues: 1452 helix: 2.29 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 513 TYR 0.014 0.001 TYR A 237 PHE 0.011 0.001 PHE C 147 TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11610) covalent geometry : angle 0.52503 / 0.26 (15870) SS BOND : bond 0.00099 / 0.05 ( 6) SS BOND : angle 1.51515 / 0.87 ( 12) hydrogen bonds : bond 0.04858 / 3.25 ( 860) hydrogen bonds : angle 3.80214 / 2.75 ( 2535) *********************** 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 136 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.361 Fit side-chains REVERT: B 224 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7532 (ttp-110) REVERT: C 70 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7245 (tmt170) REVERT: C 518 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: A 70 ARG cc_start: 0.8094 (mmt180) cc_final: 0.7623 (mtp180) REVERT: A 96 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6349 (tm) REVERT: A 309 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7365 (mp) REVERT: A 346 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7407 (t70) REVERT: A 439 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8037 (mp0) REVERT: A 495 ILE cc_start: 0.8692 (mt) cc_final: 0.8449 (mm) outliers start: 26 outliers final: 14 residues processed: 124 average time/residue: 0.3618 time to fit residues: 49.9601 Evaluate side-chains 119 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN B 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095750 restraints weight = 13913.501| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.96 r_work: 0.3050 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11616 Z= 0.160 Angle : 0.564 7.327 15882 Z= 0.282 Chirality : 0.041 0.147 1932 Planarity : 0.004 0.040 1929 Dihedral : 3.948 16.862 1566 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.52 % Allowed : 11.38 % Favored : 86.10 % 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: 2.39 (0.22), residues: 1452 helix: 2.19 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -0.61 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.017 0.002 TYR A 209 PHE 0.013 0.001 PHE A 217 TRP 0.009 0.001 TRP C 106 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (11610) covalent geometry : angle 0.56122 / 0.28 (15870) SS BOND : bond 0.00292 / 0.11 ( 6) SS BOND : angle 1.92838 / 1.08 ( 12) hydrogen bonds : bond 0.05574 / 3.72 ( 860) hydrogen bonds : angle 3.90607 / 2.83 ( 2535) *********************** 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: 31 poor density : 109 time to evaluate : 0.278 Fit side-chains REVERT: B 224 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7589 (ttp-110) REVERT: B 528 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8258 (p) REVERT: C 518 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: A 70 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7601 (mtp180) REVERT: A 96 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6329 (tm) REVERT: A 309 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7130 (mp) REVERT: A 346 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7395 (t70) outliers start: 31 outliers final: 17 residues processed: 128 average time/residue: 0.3556 time to fit residues: 50.8077 Evaluate side-chains 125 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN C 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096254 restraints weight = 14005.452| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.97 r_work: 0.3059 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11616 Z= 0.148 Angle : 0.554 7.213 15882 Z= 0.276 Chirality : 0.040 0.147 1932 Planarity : 0.004 0.042 1929 Dihedral : 3.947 17.206 1566 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.20 % Allowed : 11.95 % Favored : 85.85 % 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: 2.42 (0.22), residues: 1452 helix: 2.21 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 54 TYR 0.019 0.002 TYR A 209 PHE 0.013 0.001 PHE A 217 TRP 0.012 0.001 TRP A 317 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11610) covalent geometry : angle 0.55161 / 0.28 (15870) SS BOND : bond 0.00107 / 0.05 ( 6) SS BOND : angle 1.81446 / 1.00 ( 12) hydrogen bonds : bond 0.05338 / 3.57 ( 860) hydrogen bonds : angle 3.88637 / 2.81 ( 2535) *********************** 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 136 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.510 Fit side-chains REVERT: B 224 ARG cc_start: 0.8030 (ttp-110) cc_final: 0.7415 (ttp-110) REVERT: B 528 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8232 (p) REVERT: C 379 TYR cc_start: 0.4281 (t80) cc_final: 0.3393 (m-10) REVERT: C 518 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: A 70 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7553 (mtp180) REVERT: A 96 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6354 (tm) REVERT: A 309 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7161 (mp) REVERT: A 346 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7457 (t70) REVERT: A 439 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8017 (mp0) outliers start: 27 outliers final: 16 residues processed: 125 average time/residue: 0.3773 time to fit residues: 52.8870 Evaluate side-chains 122 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 0.0040 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 86 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN B 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100698 restraints weight = 13840.079| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.97 r_work: 0.3130 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11616 Z= 0.106 Angle : 0.499 7.044 15882 Z= 0.250 Chirality : 0.038 0.123 1932 Planarity : 0.004 0.040 1929 Dihedral : 3.789 16.161 1566 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.95 % Allowed : 12.44 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.22), residues: 1452 helix: 2.43 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -0.43 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.017 0.001 TYR C 209 PHE 0.013 0.001 PHE C 406 TRP 0.010 0.001 TRP C 106 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (11610) covalent geometry : angle 0.49746 / 0.25 (15870) SS BOND : bond 0.00055 / 0.03 ( 6) SS BOND : angle 1.69695 / 0.94 ( 12) hydrogen bonds : bond 0.04093 / 2.75 ( 860) hydrogen bonds : angle 3.70528 / 2.67 ( 2535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.287 Fit side-chains REVERT: B 224 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7561 (ttp-110) REVERT: B 528 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8194 (p) REVERT: C 379 TYR cc_start: 0.4309 (t80) cc_final: 0.3477 (m-10) REVERT: C 518 GLU cc_start: 0.8112 (pt0) cc_final: 0.7745 (pm20) REVERT: A 70 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7527 (mtp180) REVERT: A 96 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6336 (tp) REVERT: A 309 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7225 (mp) REVERT: A 439 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8028 (mp0) REVERT: A 471 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7843 (m-30) outliers start: 24 outliers final: 13 residues processed: 126 average time/residue: 0.3903 time to fit residues: 54.9251 Evaluate side-chains 119 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.151630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097776 restraints weight = 13799.525| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.96 r_work: 0.3083 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11616 Z= 0.133 Angle : 0.546 8.248 15882 Z= 0.269 Chirality : 0.040 0.246 1932 Planarity : 0.004 0.042 1929 Dihedral : 3.809 16.295 1566 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.79 % Allowed : 13.01 % Favored : 85.20 % 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: 2.62 (0.22), residues: 1452 helix: 2.35 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -0.44 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.024 0.002 TYR C 209 PHE 0.011 0.001 PHE A 217 TRP 0.008 0.001 TRP A 317 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (11610) covalent geometry : angle 0.54394 / 0.27 (15870) SS BOND : bond 0.00105 / 0.05 ( 6) SS BOND : angle 1.71533 / 0.95 ( 12) hydrogen bonds : bond 0.04913 / 3.29 ( 860) hydrogen bonds : angle 3.79331 / 2.74 ( 2535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.315 Fit side-chains REVERT: B 224 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7445 (ttp-110) REVERT: B 528 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8254 (p) REVERT: C 379 TYR cc_start: 0.4309 (t80) cc_final: 0.3456 (m-10) REVERT: C 518 GLU cc_start: 0.8214 (pt0) cc_final: 0.7854 (pm20) REVERT: A 70 ARG cc_start: 0.7962 (mmt180) cc_final: 0.7503 (mtp180) REVERT: A 96 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6310 (tm) REVERT: A 309 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7202 (mp) REVERT: A 439 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8056 (mp0) outliers start: 22 outliers final: 14 residues processed: 125 average time/residue: 0.3473 time to fit residues: 48.6060 Evaluate side-chains 121 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN B 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100270 restraints weight = 13891.277| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.97 r_work: 0.3120 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11616 Z= 0.109 Angle : 0.510 7.746 15882 Z= 0.253 Chirality : 0.039 0.166 1932 Planarity : 0.004 0.041 1929 Dihedral : 3.732 15.710 1566 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 13.33 % Favored : 85.20 % 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: 2.77 (0.22), residues: 1452 helix: 2.45 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.022 0.001 TYR A 209 PHE 0.012 0.001 PHE C 406 TRP 0.010 0.001 TRP C 106 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (11610) covalent geometry : angle 0.50868 / 0.25 (15870) SS BOND : bond 0.00072 / 0.03 ( 6) SS BOND : angle 1.57701 / 0.88 ( 12) hydrogen bonds : bond 0.04205 / 2.82 ( 860) hydrogen bonds : angle 3.70509 / 2.67 ( 2535) ********************** 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 128 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.400 Fit side-chains REVERT: B 224 ARG cc_start: 0.8030 (ttp-110) cc_final: 0.7504 (ttp-110) REVERT: B 528 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8207 (p) REVERT: C 379 TYR cc_start: 0.4339 (t80) cc_final: 0.3508 (m-10) REVERT: C 518 GLU cc_start: 0.8107 (pt0) cc_final: 0.7751 (pm20) REVERT: A 70 ARG cc_start: 0.7947 (mmt180) cc_final: 0.7464 (mtp180) REVERT: A 96 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6382 (tm) REVERT: A 309 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7265 (mp) REVERT: A 439 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8032 (mp0) REVERT: A 471 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7865 (m-30) outliers start: 18 outliers final: 11 residues processed: 120 average time/residue: 0.3690 time to fit residues: 49.4125 Evaluate side-chains 120 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 120 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100359 restraints weight = 14022.158| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.98 r_work: 0.3124 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11616 Z= 0.108 Angle : 0.516 9.885 15882 Z= 0.254 Chirality : 0.039 0.165 1932 Planarity : 0.004 0.042 1929 Dihedral : 3.689 15.349 1566 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.22 % Allowed : 13.90 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.23), residues: 1452 helix: 2.46 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -0.30 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.029 0.001 TYR A 209 PHE 0.009 0.001 PHE A 426 TRP 0.008 0.001 TRP C 106 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (11610) covalent geometry : angle 0.51426 / 0.25 (15870) SS BOND : bond 0.00061 / 0.03 ( 6) SS BOND : angle 1.57204 / 0.88 ( 12) hydrogen bonds : bond 0.04183 / 2.80 ( 860) hydrogen bonds : angle 3.68077 / 2.65 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3763.46 seconds wall clock time: 64 minutes 40.61 seconds (3880.61 seconds total)