Starting phenix.real_space_refine on Fri Aug 22 19:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6o_37330/08_2025/8w6o_37330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6o_37330/08_2025/8w6o_37330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6o_37330/08_2025/8w6o_37330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6o_37330/08_2025/8w6o_37330.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6o_37330/08_2025/8w6o_37330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6o_37330/08_2025/8w6o_37330.cif" } resolution = 2.9 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= -0.004 sd= 0.143 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 S 50 5.16 5 Na 4 4.78 5 C 4823 2.51 5 N 1076 2.21 5 O 1194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7147 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3497 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 27, 'TRANS': 420} Chain breaks: 5 Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3590 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 28, 'TRANS': 430} Chain breaks: 5 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' NA': 2, 'CLR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' NA': 2, 'CLR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.66, per 1000 atoms: 0.23 Number of scatterers: 7147 At special positions: 0 Unit cell: (82.612, 94.569, 78.264, 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) S 50 16.00 Na 4 11.00 O 1194 8.00 N 1076 7.00 C 4823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.43 Conformation dependent library (CDL) restraints added in 440.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 1 sheets defined 73.3% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.815A pdb=" N VAL A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.664A pdb=" N CYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 Proline residue: A 67 - end of helix removed outlier: 3.607A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 102 removed outlier: 3.677A pdb=" N SER A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.690A pdb=" N THR A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.847A pdb=" N MET A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 233 through 252 removed outlier: 4.079A pdb=" N ARG A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.534A pdb=" N PHE A 265 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 308 removed outlier: 3.590A pdb=" N PHE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.581A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.559A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 removed outlier: 3.628A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 423 through 431 removed outlier: 3.548A pdb=" N PHE A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.012A pdb=" N ILE A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.867A pdb=" N TRP A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.670A pdb=" N GLY A 466 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.534A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 485 " --> pdb=" O VAL A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.613A pdb=" N ILE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix removed outlier: 3.681A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.643A pdb=" N ILE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 533 through 539 removed outlier: 3.569A pdb=" N ALA A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 572 removed outlier: 3.576A pdb=" N MET A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.528A pdb=" N PHE A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 removed outlier: 3.929A pdb=" N VAL B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 51 removed outlier: 3.507A pdb=" N GLU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.615A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.935A pdb=" N ARG B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 135 removed outlier: 3.893A pdb=" N LEU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 160 removed outlier: 3.734A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 233 through 252 removed outlier: 4.109A pdb=" N ARG B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 238 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.574A pdb=" N PHE B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 308 removed outlier: 3.598A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.562A pdb=" N ILE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 362 removed outlier: 3.558A pdb=" N VAL B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.802A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 433 through 452 removed outlier: 4.059A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 4.101A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.706A pdb=" N GLY B 466 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 467 " --> pdb=" O PRO B 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 463 through 467' Processing helix chain 'B' and resid 469 through 485 Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.585A pdb=" N ILE B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix Processing helix chain 'B' and resid 511 through 523 removed outlier: 3.684A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 516 " --> pdb=" O PRO B 512 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.554A pdb=" N LEU B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 removed outlier: 3.553A pdb=" N ALA B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 572 removed outlier: 4.225A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.503A pdb=" N PHE B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.726A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1113 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: 0.95 Time building geometry restraints manager: 0.62 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: 1935 1.34 - 1.46: 1350 1.46 - 1.57: 3982 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 7349 Sorted by residual: bond pdb=" C PRO B 534 " pdb=" N PRO B 535 " ideal model delta sigma weight residual 1.334 1.367 -0.033 1.51e-02 4.39e+03 4.66e+00 bond pdb=" C PRO A 534 " pdb=" N PRO A 535 " ideal model delta sigma weight residual 1.334 1.364 -0.030 1.51e-02 4.39e+03 4.02e+00 bond pdb=" C LEU A 26 " pdb=" N PRO A 27 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.66e+00 bond pdb=" C LEU B 24 " pdb=" N PRO B 25 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.59e+00 bond pdb=" C LEU A 24 " pdb=" N PRO A 25 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.53e+00 ... (remaining 7344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9619 2.14 - 4.28: 334 4.28 - 6.42: 66 6.42 - 8.55: 31 8.55 - 10.69: 10 Bond angle restraints: 10060 Sorted by residual: angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 111.81 107.36 4.45 8.60e-01 1.35e+00 2.68e+01 angle pdb=" N GLU A 36 " pdb=" CA GLU A 36 " pdb=" C GLU A 36 " ideal model delta sigma weight residual 114.56 108.13 6.43 1.27e+00 6.20e-01 2.56e+01 angle pdb=" N TYR B 379 " pdb=" CA TYR B 379 " pdb=" C TYR B 379 " ideal model delta sigma weight residual 109.81 119.72 -9.91 2.21e+00 2.05e-01 2.01e+01 angle pdb=" N PRO A 534 " pdb=" CA PRO A 534 " pdb=" C PRO A 534 " ideal model delta sigma weight residual 110.70 116.05 -5.35 1.22e+00 6.72e-01 1.92e+01 angle pdb=" C VAL A 118 " pdb=" N ASN A 119 " pdb=" CA ASN A 119 " ideal model delta sigma weight residual 121.80 132.49 -10.69 2.44e+00 1.68e-01 1.92e+01 ... (remaining 10055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3968 17.83 - 35.66: 328 35.66 - 53.48: 47 53.48 - 71.31: 6 71.31 - 89.14: 3 Dihedral angle restraints: 4352 sinusoidal: 1718 harmonic: 2634 Sorted by residual: dihedral pdb=" CA ASN B 119 " pdb=" C ASN B 119 " pdb=" N PRO B 120 " pdb=" CA PRO B 120 " ideal model delta harmonic sigma weight residual 180.00 136.33 43.67 0 5.00e+00 4.00e-02 7.63e+01 dihedral pdb=" CA ALA A 121 " pdb=" C ALA A 121 " pdb=" N TRP A 122 " pdb=" CA TRP A 122 " ideal model delta harmonic sigma weight residual -180.00 -145.39 -34.61 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA PRO B 27 " pdb=" C PRO B 27 " pdb=" N ILE B 28 " pdb=" CA ILE B 28 " ideal model delta harmonic sigma weight residual 180.00 147.24 32.76 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 4349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 995 0.068 - 0.136: 211 0.136 - 0.205: 27 0.205 - 0.273: 0 0.273 - 0.341: 1 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA SER A 502 " pdb=" N SER A 502 " pdb=" C SER A 502 " pdb=" CB SER A 502 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CB ILE B 343 " pdb=" CA ILE B 343 " pdb=" CG1 ILE B 343 " pdb=" CG2 ILE B 343 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 1231 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.081 5.00e-02 4.00e+02 1.23e-01 2.40e+01 pdb=" N PRO A 27 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 26 " -0.079 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO B 27 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " -0.062 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO B 535 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " -0.051 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1494 2.78 - 3.31: 6490 3.31 - 3.84: 11635 3.84 - 4.37: 14042 4.37 - 4.90: 24547 Nonbonded interactions: 58208 Sorted by model distance: nonbonded pdb=" O CYS B 243 " pdb=" OG SER B 247 " model vdw 2.246 3.040 nonbonded pdb=" O CYS A 243 " pdb=" OG SER A 247 " model vdw 2.259 3.040 nonbonded pdb=" O LEU B 567 " pdb=" OG1 THR B 571 " model vdw 2.280 3.040 nonbonded pdb=" O LEU A 567 " pdb=" OG1 THR A 571 " model vdw 2.284 3.040 nonbonded pdb=" O SER A 519 " pdb=" OG1 THR A 523 " model vdw 2.304 3.040 ... (remaining 58203 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 73 or resid 83 through 159 or resid 232 through \ 363 or resid 382 through 405 or resid 416 through 703)) } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.005 0.061 7349 Z= 0.240 Angle : 1.037 10.693 10060 Z= 0.551 Chirality : 0.055 0.341 1234 Planarity : 0.011 0.123 1176 Dihedral : 13.102 89.139 2636 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.57 % Favored : 92.98 % Rotamer: Outliers : 0.13 % Allowed : 7.13 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.36 % 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 aren not related in a simple way. whole: -4.81 (0.21), residues: 883 helix: -2.70 (0.14), residues: 624 sheet: None (None), residues: 0 loop : -4.00 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.016 0.002 TYR B 39 PHE 0.022 0.002 PHE A 287 TRP 0.016 0.002 TRP A 122 HIS 0.013 0.003 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 7349) covalent geometry : angle 1.03699 (10060) hydrogen bonds : bond 0.16657 ( 373) hydrogen bonds : angle 6.59459 ( 1113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.315 Fit side-chains REVERT: A 72 MET cc_start: 0.6259 (mmm) cc_final: 0.5676 (mpt) REVERT: A 232 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7986 (tttp) REVERT: B 72 MET cc_start: 0.6438 (mmt) cc_final: 0.6171 (mpt) REVERT: B 552 LYS cc_start: 0.7643 (tptt) cc_final: 0.7116 (ttpt) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.4421 time to fit residues: 62.0548 Evaluate side-chains 102 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS A 338 GLN A 558 ASN B 119 ASN B 156 GLN B 234 HIS B 338 GLN B 558 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.145721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132555 restraints weight = 8464.463| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.88 r_work: 0.3379 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7349 Z= 0.144 Angle : 0.724 10.324 10060 Z= 0.362 Chirality : 0.044 0.227 1234 Planarity : 0.008 0.111 1176 Dihedral : 5.639 37.224 1063 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 1.91 % Allowed : 12.23 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.24 % 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 aren not related in a simple way. whole: -2.23 (0.27), residues: 883 helix: -0.66 (0.19), residues: 635 sheet: None (None), residues: 0 loop : -3.51 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.014 0.001 TYR A 418 PHE 0.012 0.001 PHE A 15 TRP 0.014 0.001 TRP B 572 HIS 0.008 0.002 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7349) covalent geometry : angle 0.72393 (10060) hydrogen bonds : bond 0.04713 ( 373) hydrogen bonds : angle 4.26268 ( 1113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.268 Fit side-chains REVERT: A 72 MET cc_start: 0.6412 (mmm) cc_final: 0.5860 (mpt) REVERT: A 232 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7935 (tttp) REVERT: B 378 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: B 390 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8358 (mt) REVERT: B 552 LYS cc_start: 0.7719 (tptt) cc_final: 0.7308 (mtpt) outliers start: 15 outliers final: 4 residues processed: 111 average time/residue: 0.4514 time to fit residues: 53.0186 Evaluate side-chains 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 79 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS A 338 GLN A 558 ASN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131076 restraints weight = 8533.186| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.05 r_work: 0.3383 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7349 Z= 0.126 Angle : 0.687 11.747 10060 Z= 0.339 Chirality : 0.043 0.242 1234 Planarity : 0.007 0.106 1176 Dihedral : 5.267 35.523 1063 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.46 % Favored : 93.43 % Rotamer: Outliers : 2.04 % Allowed : 13.76 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -1.10 (0.29), residues: 883 helix: 0.26 (0.21), residues: 631 sheet: None (None), residues: 0 loop : -3.26 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 11 TYR 0.017 0.001 TYR A 418 PHE 0.010 0.001 PHE B 15 TRP 0.013 0.001 TRP B 572 HIS 0.007 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7349) covalent geometry : angle 0.68723 (10060) hydrogen bonds : bond 0.03913 ( 373) hydrogen bonds : angle 4.00902 ( 1113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.205 Fit side-chains REVERT: A 72 MET cc_start: 0.6446 (mmm) cc_final: 0.5896 (mpt) REVERT: A 338 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6040 (mp-120) REVERT: B 82 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5608 (p90) REVERT: B 378 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: B 552 LYS cc_start: 0.7605 (tptt) cc_final: 0.7253 (mtpt) outliers start: 16 outliers final: 6 residues processed: 115 average time/residue: 0.4504 time to fit residues: 54.7927 Evaluate side-chains 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN B 31 HIS B 346 GLN B 428 GLN B 558 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133293 restraints weight = 8528.228| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 0.89 r_work: 0.3381 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7349 Z= 0.128 Angle : 0.679 12.397 10060 Z= 0.336 Chirality : 0.043 0.242 1234 Planarity : 0.007 0.104 1176 Dihedral : 5.160 35.239 1063 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.55 % Allowed : 14.65 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -0.67 (0.30), residues: 883 helix: 0.57 (0.22), residues: 634 sheet: None (None), residues: 0 loop : -3.12 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 11 TYR 0.017 0.001 TYR A 418 PHE 0.011 0.001 PHE B 15 TRP 0.011 0.001 TRP B 572 HIS 0.007 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7349) covalent geometry : angle 0.67887 (10060) hydrogen bonds : bond 0.03839 ( 373) hydrogen bonds : angle 3.98402 ( 1113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.166 Fit side-chains REVERT: A 72 MET cc_start: 0.6336 (mmm) cc_final: 0.5810 (mpt) REVERT: A 128 MET cc_start: 0.9159 (mtp) cc_final: 0.8818 (mtp) REVERT: A 148 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8450 (tpt) REVERT: A 338 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: B 378 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6497 (pm20) REVERT: B 390 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 447 ASP cc_start: 0.7808 (m-30) cc_final: 0.7419 (m-30) REVERT: B 552 LYS cc_start: 0.7582 (tptt) cc_final: 0.7119 (ttpt) outliers start: 20 outliers final: 8 residues processed: 108 average time/residue: 0.4280 time to fit residues: 49.0011 Evaluate side-chains 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN A 558 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.144250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129524 restraints weight = 8713.688| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.07 r_work: 0.3383 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7349 Z= 0.128 Angle : 0.668 10.274 10060 Z= 0.331 Chirality : 0.043 0.242 1234 Planarity : 0.007 0.103 1176 Dihedral : 5.102 34.956 1063 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 2.55 % Allowed : 15.54 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -0.41 (0.31), residues: 883 helix: 0.77 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -3.04 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.016 0.002 TYR A 418 PHE 0.011 0.001 PHE B 15 TRP 0.010 0.001 TRP B 572 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7349) covalent geometry : angle 0.66830 (10060) hydrogen bonds : bond 0.03776 ( 373) hydrogen bonds : angle 3.93251 ( 1113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.253 Fit side-chains REVERT: A 72 MET cc_start: 0.6340 (mmm) cc_final: 0.5807 (mpt) REVERT: A 148 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8452 (tpt) REVERT: B 378 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: B 552 LYS cc_start: 0.7641 (tptt) cc_final: 0.7163 (ttpt) outliers start: 20 outliers final: 10 residues processed: 115 average time/residue: 0.3917 time to fit residues: 47.8619 Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 9.9990 chunk 79 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 156 GLN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.144973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130511 restraints weight = 8628.144| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.07 r_work: 0.3374 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7349 Z= 0.123 Angle : 0.659 11.960 10060 Z= 0.326 Chirality : 0.043 0.239 1234 Planarity : 0.007 0.102 1176 Dihedral : 5.002 34.672 1063 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.36 % Favored : 92.53 % Rotamer: Outliers : 3.18 % Allowed : 15.41 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -0.26 (0.31), residues: 883 helix: 0.88 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -2.98 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.017 0.001 TYR B 418 PHE 0.011 0.001 PHE B 15 TRP 0.010 0.001 TRP B 572 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7349) covalent geometry : angle 0.65876 (10060) hydrogen bonds : bond 0.03643 ( 373) hydrogen bonds : angle 3.89384 ( 1113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.251 Fit side-chains REVERT: A 72 MET cc_start: 0.6281 (mmm) cc_final: 0.5804 (mpt) REVERT: A 338 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6315 (mp-120) REVERT: B 378 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6424 (pm20) REVERT: B 390 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 447 ASP cc_start: 0.7432 (m-30) cc_final: 0.7123 (m-30) REVERT: B 552 LYS cc_start: 0.7669 (tptt) cc_final: 0.7173 (ttpt) outliers start: 25 outliers final: 12 residues processed: 115 average time/residue: 0.4041 time to fit residues: 49.4295 Evaluate side-chains 109 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 452 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 79 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129192 restraints weight = 8706.789| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.07 r_work: 0.3376 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7349 Z= 0.129 Angle : 0.665 10.280 10060 Z= 0.331 Chirality : 0.043 0.238 1234 Planarity : 0.007 0.102 1176 Dihedral : 4.991 34.171 1063 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 2.17 % Allowed : 17.07 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -0.16 (0.31), residues: 883 helix: 0.97 (0.22), residues: 626 sheet: None (None), residues: 0 loop : -2.88 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.020 0.001 TYR B 418 PHE 0.011 0.001 PHE B 15 TRP 0.010 0.001 TRP A 585 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7349) covalent geometry : angle 0.66484 (10060) hydrogen bonds : bond 0.03802 ( 373) hydrogen bonds : angle 3.90942 ( 1113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.273 Fit side-chains REVERT: A 72 MET cc_start: 0.6258 (mmm) cc_final: 0.5836 (mpt) REVERT: A 115 MET cc_start: 0.6612 (mtp) cc_final: 0.6201 (mtp) REVERT: A 148 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8436 (tpt) REVERT: A 338 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6317 (mp-120) REVERT: B 378 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: B 390 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 447 ASP cc_start: 0.7484 (m-30) cc_final: 0.7260 (m-30) REVERT: B 552 LYS cc_start: 0.7686 (tptt) cc_final: 0.7228 (ttpt) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 0.4420 time to fit residues: 51.1346 Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 54 optimal weight: 0.0050 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN B 105 HIS B 156 GLN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130523 restraints weight = 8716.888| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.08 r_work: 0.3366 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7349 Z= 0.125 Angle : 0.656 9.567 10060 Z= 0.326 Chirality : 0.043 0.233 1234 Planarity : 0.007 0.101 1176 Dihedral : 4.925 33.598 1063 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 2.29 % Allowed : 16.05 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -0.08 (0.31), residues: 883 helix: 1.01 (0.22), residues: 627 sheet: None (None), residues: 0 loop : -2.84 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.022 0.001 TYR B 418 PHE 0.011 0.001 PHE B 15 TRP 0.010 0.001 TRP B 572 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7349) covalent geometry : angle 0.65556 (10060) hydrogen bonds : bond 0.03632 ( 373) hydrogen bonds : angle 3.88397 ( 1113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.160 Fit side-chains REVERT: A 72 MET cc_start: 0.6154 (mmm) cc_final: 0.5788 (mpt) REVERT: A 115 MET cc_start: 0.6653 (mtp) cc_final: 0.6227 (mtp) REVERT: A 232 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7594 (tptt) REVERT: A 338 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6250 (mp-120) REVERT: B 390 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 552 LYS cc_start: 0.7652 (tptt) cc_final: 0.7179 (ttpt) outliers start: 18 outliers final: 10 residues processed: 111 average time/residue: 0.3983 time to fit residues: 46.8894 Evaluate side-chains 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 53 optimal weight: 0.0270 chunk 47 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN B 105 HIS B 156 GLN B 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.133689 restraints weight = 8567.140| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 0.85 r_work: 0.3376 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7349 Z= 0.130 Angle : 0.665 8.186 10060 Z= 0.332 Chirality : 0.044 0.234 1234 Planarity : 0.007 0.101 1176 Dihedral : 4.935 33.349 1063 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.25 % Favored : 92.64 % Rotamer: Outliers : 2.55 % Allowed : 16.82 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -0.06 (0.31), residues: 883 helix: 1.03 (0.22), residues: 627 sheet: None (None), residues: 0 loop : -2.82 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.021 0.002 TYR B 418 PHE 0.011 0.001 PHE B 15 TRP 0.010 0.001 TRP A 585 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7349) covalent geometry : angle 0.66522 (10060) hydrogen bonds : bond 0.03736 ( 373) hydrogen bonds : angle 3.88887 ( 1113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.254 Fit side-chains REVERT: A 72 MET cc_start: 0.6098 (mmm) cc_final: 0.5743 (mpt) REVERT: A 115 MET cc_start: 0.6472 (mtp) cc_final: 0.6040 (mtp) REVERT: A 232 LYS cc_start: 0.8020 (ttmm) cc_final: 0.7600 (tptt) REVERT: A 338 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6306 (mp-120) REVERT: B 390 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 552 LYS cc_start: 0.7643 (tptt) cc_final: 0.7173 (ttpt) outliers start: 20 outliers final: 11 residues processed: 110 average time/residue: 0.4163 time to fit residues: 48.5878 Evaluate side-chains 106 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.0060 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN B 105 HIS B 156 GLN B 346 GLN B 428 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.146578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133487 restraints weight = 8617.427| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 0.87 r_work: 0.3388 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7349 Z= 0.125 Angle : 0.657 7.998 10060 Z= 0.328 Chirality : 0.043 0.234 1234 Planarity : 0.007 0.101 1176 Dihedral : 4.897 33.078 1063 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.17 % Allowed : 17.45 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -0.02 (0.31), residues: 883 helix: 1.04 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -2.85 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.020 0.001 TYR B 418 PHE 0.010 0.001 PHE B 15 TRP 0.010 0.001 TRP A 585 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7349) covalent geometry : angle 0.65679 (10060) hydrogen bonds : bond 0.03640 ( 373) hydrogen bonds : angle 3.89182 ( 1113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.169 Fit side-chains REVERT: A 17 VAL cc_start: 0.8511 (m) cc_final: 0.8264 (t) REVERT: A 72 MET cc_start: 0.6069 (mmm) cc_final: 0.5721 (mpt) REVERT: A 232 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7782 (tppt) REVERT: A 338 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6291 (mp-120) REVERT: B 390 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8364 (mt) REVERT: B 552 LYS cc_start: 0.7619 (tptt) cc_final: 0.7142 (ttpt) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 0.4336 time to fit residues: 49.2348 Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 544 HIS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 0.0020 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 58 optimal weight: 0.0570 chunk 32 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.4708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN B 105 HIS B 156 GLN B 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.146787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131581 restraints weight = 8639.588| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.07 r_work: 0.3398 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7349 Z= 0.119 Angle : 0.646 7.881 10060 Z= 0.322 Chirality : 0.043 0.231 1234 Planarity : 0.007 0.101 1176 Dihedral : 4.796 32.663 1063 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 2.04 % Allowed : 17.07 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: 0.02 (0.31), residues: 883 helix: 1.09 (0.22), residues: 636 sheet: None (None), residues: 0 loop : -2.96 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.019 0.001 TYR B 418 PHE 0.010 0.001 PHE B 15 TRP 0.011 0.001 TRP B 572 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7349) covalent geometry : angle 0.64603 (10060) hydrogen bonds : bond 0.03412 ( 373) hydrogen bonds : angle 3.85600 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.71 seconds wall clock time: 31 minutes 21.01 seconds (1881.01 seconds total)