Starting phenix.real_space_refine on Wed Feb 4 15:51:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps1_71819/02_2026/9ps1_71819.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps1_71819/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ps1_71819/02_2026/9ps1_71819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps1_71819/02_2026/9ps1_71819.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ps1_71819/02_2026/9ps1_71819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps1_71819/02_2026/9ps1_71819.map" } 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): 0.01s 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: 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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.06, per 1000 atoms: 0.27 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: 0.92 Conformation dependent library (CDL) restraints added in 552.0 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: 0.30 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: 1.78 Time building geometry restraints manager: 1.25 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 2.510 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 covalent geometry : bond 0.00911 (11610) covalent geometry : angle 0.82037 (15870) SS BOND : bond 0.00581 ( 6) SS BOND : angle 3.08579 ( 12) hydrogen bonds : bond 0.15368 ( 860) hydrogen bonds : angle 6.94737 ( 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 : 0.463 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: 0.4669 time to fit residues: 65.8156 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 : 0.424 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3851 r_free = 0.3851 target = 0.153447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099208 restraints weight = 14004.893| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.19 r_work: 0.3123 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11616 Z= 0.131 Angle : 0.576 8.607 15882 Z= 0.292 Chirality : 0.040 0.142 1932 Planarity : 0.005 0.053 1929 Dihedral : 4.288 16.572 1566 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.89 % Allowed : 6.42 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.22), residues: 1452 helix: 1.69 (0.15), residues: 1127 sheet: None (None), residues: 0 loop : -0.98 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 352 TYR 0.015 0.001 TYR B 557 PHE 0.011 0.001 PHE C 492 TRP 0.012 0.001 TRP C 106 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00268 (11610) covalent geometry : angle 0.57260 (15870) SS BOND : bond 0.00430 ( 6) SS BOND : angle 2.18666 ( 12) hydrogen bonds : bond 0.05348 ( 860) hydrogen bonds : angle 4.19872 ( 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 140 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.452 Fit side-chains REVERT: B 224 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7178 (ttp-110) REVERT: A 70 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7597 (mtm110) outliers start: 11 outliers final: 3 residues processed: 137 average time/residue: 0.4513 time to fit residues: 68.6263 Evaluate side-chains 104 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3840 r_free = 0.3840 target = 0.152490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097764 restraints weight = 13993.799| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.18 r_work: 0.3103 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11616 Z= 0.137 Angle : 0.559 6.987 15882 Z= 0.282 Chirality : 0.040 0.128 1932 Planarity : 0.004 0.046 1929 Dihedral : 4.107 16.020 1566 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.79 % Allowed : 9.02 % Favored : 89.19 % 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: 2.08 (0.22), residues: 1452 helix: 1.97 (0.15), residues: 1129 sheet: None (None), residues: 0 loop : -0.75 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 352 TYR 0.015 0.001 TYR B 557 PHE 0.012 0.001 PHE A 488 TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00315 (11610) covalent geometry : angle 0.55661 (15870) SS BOND : bond 0.00110 ( 6) SS BOND : angle 1.88606 ( 12) hydrogen bonds : bond 0.05354 ( 860) hydrogen bonds : angle 4.00814 ( 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 130 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.448 Fit side-chains REVERT: B 224 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7173 (ttp-110) REVERT: A 70 ARG cc_start: 0.8013 (mmt180) cc_final: 0.7603 (mtm110) outliers start: 22 outliers final: 9 residues processed: 123 average time/residue: 0.4367 time to fit residues: 59.8221 Evaluate side-chains 110 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 130 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3796 r_free = 0.3796 target = 0.148789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.092999 restraints weight = 13620.249| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.05 r_work: 0.2955 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11616 Z= 0.130 Angle : 0.535 6.779 15882 Z= 0.270 Chirality : 0.039 0.127 1932 Planarity : 0.004 0.041 1929 Dihedral : 3.995 15.666 1566 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.36 % Allowed : 10.24 % Favored : 87.40 % 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: 2.26 (0.22), residues: 1452 helix: 2.13 (0.15), residues: 1119 sheet: None (None), residues: 0 loop : -0.71 (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 0.011 0.001 PHE C 147 TRP 0.009 0.001 TRP C 106 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00298 (11610) covalent geometry : angle 0.53381 (15870) SS BOND : bond 0.00112 ( 6) SS BOND : angle 1.63635 ( 12) hydrogen bonds : bond 0.05074 ( 860) hydrogen bonds : angle 3.88789 ( 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 139 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.365 Fit side-chains REVERT: B 224 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7566 (ttp-110) REVERT: A 70 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7640 (mtp180) REVERT: A 96 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6680 (tm) outliers start: 29 outliers final: 13 residues processed: 130 average time/residue: 0.3634 time to fit residues: 52.6591 Evaluate side-chains 114 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 569 ILE 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 199 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3904 r_free = 0.3904 target = 0.155315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103460 restraints weight = 14295.320| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.04 r_work: 0.3261 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1879 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= 0.119 Angle : 0.517 6.407 15882 Z= 0.260 Chirality : 0.039 0.130 1932 Planarity : 0.004 0.040 1929 Dihedral : 3.903 15.423 1566 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.03 % Allowed : 11.71 % Favored : 86.26 % 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: 2.44 (0.22), residues: 1452 helix: 2.27 (0.15), residues: 1119 sheet: None (None), residues: 0 loop : -0.67 (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 0.011 0.001 PHE C 147 TRP 0.012 0.001 TRP A 317 HIS 0.002 0.000 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00263 (11610) covalent geometry : angle 0.51581 (15870) SS BOND : bond 0.00167 ( 6) SS BOND : angle 1.49476 ( 12) hydrogen bonds : bond 0.04710 ( 860) hydrogen bonds : angle 3.80576 ( 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 132 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.450 Fit side-chains REVERT: B 224 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7537 (ttp-110) REVERT: C 70 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7246 (tmt170) REVERT: C 518 GLU cc_start: 0.8128 (pt0) cc_final: 0.7761 (pm20) REVERT: A 70 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7626 (mtp180) REVERT: A 309 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7402 (mp) REVERT: A 439 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8042 (mp0) outliers start: 25 outliers final: 11 residues processed: 124 average time/residue: 0.3930 time to fit residues: 54.1967 Evaluate side-chains 111 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 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 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 199 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 0.0010 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 GLN B 362 GLN B 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095981 restraints weight = 13896.871| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.95 r_work: 0.3061 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11616 Z= 0.145 Angle : 0.548 7.439 15882 Z= 0.273 Chirality : 0.040 0.134 1932 Planarity : 0.004 0.042 1929 Dihedral : 3.908 14.919 1566 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.03 % Allowed : 11.79 % Favored : 86.18 % 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: 2.41 (0.22), residues: 1452 helix: 2.21 (0.15), residues: 1129 sheet: None (None), residues: 0 loop : -0.62 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.016 0.002 TYR A 209 PHE 0.012 0.001 PHE A 217 TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00346 (11610) covalent geometry : angle 0.54626 (15870) SS BOND : bond 0.00093 ( 6) SS BOND : angle 1.54468 ( 12) hydrogen bonds : bond 0.05273 ( 860) hydrogen bonds : angle 3.86236 ( 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 135 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.354 Fit side-chains REVERT: B 224 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7502 (ttp-110) REVERT: B 528 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8320 (p) REVERT: A 70 ARG cc_start: 0.8056 (mmt180) cc_final: 0.7631 (mtp180) REVERT: A 96 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6526 (tm) REVERT: A 309 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7242 (mp) REVERT: A 439 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8142 (mp0) outliers start: 25 outliers final: 16 residues processed: 128 average time/residue: 0.4101 time to fit residues: 58.2990 Evaluate side-chains 119 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 LEU 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: 0.6980 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3852 r_free = 0.3852 target = 0.149977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095733 restraints weight = 14006.201| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.98 r_work: 0.3053 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11616 Z= 0.147 Angle : 0.552 7.390 15882 Z= 0.276 Chirality : 0.040 0.146 1932 Planarity : 0.004 0.042 1929 Dihedral : 3.940 16.555 1566 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.11 % Allowed : 12.03 % 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: 2.44 (0.22), residues: 1452 helix: 2.22 (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 352 TYR 0.019 0.002 TYR A 209 PHE 0.013 0.001 PHE C 406 TRP 0.009 0.001 TRP C 106 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00351 (11610) covalent geometry : angle 0.55002 (15870) SS BOND : bond 0.00092 ( 6) SS BOND : angle 1.83946 ( 12) hydrogen bonds : bond 0.05301 ( 860) hydrogen bonds : angle 3.86914 ( 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 130 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.472 Fit side-chains REVERT: B 224 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7416 (ttp-110) REVERT: B 528 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8230 (p) REVERT: C 196 MET cc_start: 0.9085 (ttm) cc_final: 0.8876 (ttp) REVERT: C 518 GLU cc_start: 0.8165 (pt0) cc_final: 0.7800 (pm20) REVERT: A 70 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7598 (mtp180) REVERT: A 96 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6394 (tm) REVERT: A 309 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7157 (mp) REVERT: A 439 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8016 (mp0) outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 0.4200 time to fit residues: 56.6881 Evaluate side-chains 119 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain C residue 460 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 199 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 GLN B 510 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 = 0.3890 r_free = 0.3890 target = 0.153327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099660 restraints weight = 13877.522| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.97 r_work: 0.3115 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2151 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= 0.107 Angle : 0.501 6.972 15882 Z= 0.252 Chirality : 0.038 0.122 1932 Planarity : 0.004 0.040 1929 Dihedral : 3.791 16.752 1566 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.63 % Allowed : 12.93 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.22), residues: 1452 helix: 2.42 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.016 0.001 TYR A 209 PHE 0.007 0.001 PHE B 551 TRP 0.010 0.001 TRP C 106 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00222 (11610) covalent geometry : angle 0.49850 (15870) SS BOND : bond 0.00058 ( 6) SS BOND : angle 1.71667 ( 12) hydrogen bonds : bond 0.04169 ( 860) hydrogen bonds : angle 3.70318 ( 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 129 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.417 Fit side-chains REVERT: B 224 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7511 (ttp-110) REVERT: B 528 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8201 (p) REVERT: C 379 TYR cc_start: 0.4271 (t80) cc_final: 0.3446 (m-10) REVERT: C 518 GLU cc_start: 0.8135 (pt0) cc_final: 0.7804 (pm20) REVERT: A 70 ARG cc_start: 0.7970 (mmt180) cc_final: 0.7493 (mtp180) REVERT: A 96 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6255 (tm) REVERT: A 309 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7240 (mp) REVERT: A 439 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8053 (mp0) outliers start: 20 outliers final: 11 residues processed: 124 average time/residue: 0.3909 time to fit residues: 53.8030 Evaluate side-chains 114 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 199 SER Chi-restraints excluded: chain A residue 309 LEU 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: 0.7980 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.152752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099035 restraints weight = 13826.683| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.96 r_work: 0.3103 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11616 Z= 0.112 Angle : 0.521 7.689 15882 Z= 0.257 Chirality : 0.039 0.194 1932 Planarity : 0.004 0.041 1929 Dihedral : 3.745 16.354 1566 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.46 % Allowed : 13.50 % Favored : 85.04 % 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: 2.72 (0.22), residues: 1452 helix: 2.42 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.021 0.001 TYR C 209 PHE 0.014 0.001 PHE C 406 TRP 0.015 0.001 TRP A 317 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00243 (11610) covalent geometry : angle 0.51880 (15870) SS BOND : bond 0.00067 ( 6) SS BOND : angle 1.62480 ( 12) hydrogen bonds : bond 0.04330 ( 860) hydrogen bonds : angle 3.70910 ( 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 125 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: B 528 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8225 (p) REVERT: C 379 TYR cc_start: 0.4288 (t80) cc_final: 0.3466 (m-10) REVERT: C 518 GLU cc_start: 0.8139 (pt0) cc_final: 0.7813 (pm20) REVERT: A 70 ARG cc_start: 0.7975 (mmt180) cc_final: 0.7476 (mtp180) REVERT: A 96 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6339 (tm) REVERT: A 439 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8042 (mp0) outliers start: 18 outliers final: 13 residues processed: 120 average time/residue: 0.3933 time to fit residues: 52.3382 Evaluate side-chains 117 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 131 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 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 309 LEU 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: 6.9990 chunk 121 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3880 r_free = 0.3880 target = 0.152464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098584 restraints weight = 13913.392| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.97 r_work: 0.3095 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11616 Z= 0.116 Angle : 0.524 7.979 15882 Z= 0.259 Chirality : 0.039 0.168 1932 Planarity : 0.004 0.041 1929 Dihedral : 3.732 16.454 1566 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.38 % Allowed : 13.66 % Favored : 84.96 % 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: 2.42 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -0.38 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.025 0.001 TYR A 209 PHE 0.017 0.001 PHE C 147 TRP 0.011 0.001 TRP A 317 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00259 (11610) covalent geometry : angle 0.52192 (15870) SS BOND : bond 0.00077 ( 6) SS BOND : angle 1.61603 ( 12) hydrogen bonds : bond 0.04452 ( 860) hydrogen bonds : angle 3.71169 ( 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 123 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.565 Fit side-chains REVERT: B 224 ARG cc_start: 0.8021 (ttp-110) cc_final: 0.7479 (ttp-110) REVERT: B 528 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8241 (p) REVERT: C 196 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8776 (tpp) REVERT: C 379 TYR cc_start: 0.4314 (t80) cc_final: 0.3489 (m-10) REVERT: C 518 GLU cc_start: 0.8138 (pt0) cc_final: 0.7811 (pm20) REVERT: A 70 ARG cc_start: 0.7970 (mmt180) cc_final: 0.7471 (mtp180) REVERT: A 96 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6338 (tm) REVERT: A 439 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8021 (mp0) outliers start: 17 outliers final: 13 residues processed: 118 average time/residue: 0.4033 time to fit residues: 52.7146 Evaluate side-chains 121 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain C residue 196 MET 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 580 ILE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 309 LEU 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: 0.3980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 120 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.154600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101170 restraints weight = 14047.203| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.98 r_work: 0.3134 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11616 Z= 0.102 Angle : 0.504 8.555 15882 Z= 0.248 Chirality : 0.038 0.163 1932 Planarity : 0.004 0.040 1929 Dihedral : 3.655 15.971 1566 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.46 % Allowed : 13.90 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.23), residues: 1452 helix: 2.51 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -0.32 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.026 0.001 TYR A 209 PHE 0.012 0.001 PHE C 406 TRP 0.011 0.001 TRP A 317 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00208 (11610) covalent geometry : angle 0.50227 (15870) SS BOND : bond 0.00045 ( 6) SS BOND : angle 1.51593 ( 12) hydrogen bonds : bond 0.03865 ( 860) hydrogen bonds : angle 3.63089 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4055.26 seconds wall clock time: 69 minutes 43.02 seconds (4183.02 seconds total)