Starting phenix.real_space_refine on Fri Jun 6 03:55:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6o_37330/06_2025/8w6o_37330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6o_37330/06_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_37330/06_2025/8w6o_37330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6o_37330/06_2025/8w6o_37330.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6o_37330/06_2025/8w6o_37330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6o_37330/06_2025/8w6o_37330.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.65, per 1000 atoms: 0.65 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: 1.66 Conformation dependent library (CDL) restraints added in 899.9 milliseconds 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: 0.76 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: 2.11 Time building geometry restraints manager: 1.86 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 587 or resid 701 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: 0.930 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.180 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP A 122 HIS 0.013 0.003 HIS B 105 PHE 0.022 0.002 PHE A 287 TYR 0.016 0.002 TYR B 39 ARG 0.002 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.16657 ( 373) hydrogen bonds : angle 6.59459 ( 1113) covalent geometry : bond 0.00530 ( 7349) covalent geometry : angle 1.03699 (10060) *********************** 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 : 0.758 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: 0.7987 (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: 1.1705 time to fit residues: 164.4616 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 : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3588 r_free = 0.3588 target = 0.146008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132906 restraints weight = 8401.958| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 0.87 r_work: 0.3392 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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= 0.142 Angle : 0.720 10.117 10060 Z= 0.360 Chirality : 0.044 0.227 1234 Planarity : 0.008 0.111 1176 Dihedral : 5.617 37.072 1063 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 1.91 % Allowed : 12.36 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.27), residues: 883 helix: -0.67 (0.19), residues: 635 sheet: None (None), residues: 0 loop : -3.51 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 572 HIS 0.008 0.002 HIS B 105 PHE 0.011 0.001 PHE B 15 TYR 0.014 0.001 TYR A 418 ARG 0.003 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 373) hydrogen bonds : angle 4.24920 ( 1113) covalent geometry : bond 0.00329 ( 7349) covalent geometry : angle 0.72023 (10060) *********************** 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 120 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.673 Fit side-chains REVERT: A 72 MET cc_start: 0.6405 (mmm) cc_final: 0.5860 (mpt) REVERT: A 232 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7935 (tttp) REVERT: B 378 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: B 390 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 552 LYS cc_start: 0.7717 (tptt) cc_final: 0.7324 (mtpt) outliers start: 15 outliers final: 4 residues processed: 113 average time/residue: 1.1886 time to fit residues: 142.2513 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 : 0.753 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.145742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131165 restraints weight = 8629.328| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.07 r_work: 0.3367 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: 0.8148 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7349 Z= 0.125 Angle : 0.688 12.378 10060 Z= 0.339 Chirality : 0.042 0.238 1234 Planarity : 0.007 0.106 1176 Dihedral : 5.259 35.559 1063 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.46 % Favored : 93.43 % Rotamer: Outliers : 2.04 % Allowed : 13.63 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.29), residues: 883 helix: 0.26 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -3.24 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 572 HIS 0.007 0.001 HIS B 31 PHE 0.010 0.001 PHE B 15 TYR 0.017 0.001 TYR A 418 ARG 0.007 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 373) hydrogen bonds : angle 4.02397 ( 1113) covalent geometry : bond 0.00286 ( 7349) covalent geometry : angle 0.68792 (10060) *********************** 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 123 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.771 Fit side-chains REVERT: A 72 MET cc_start: 0.6516 (mmm) cc_final: 0.5971 (mpt) REVERT: A 232 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7825 (tttp) REVERT: A 338 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.5974 (mp-120) REVERT: B 128 MET cc_start: 0.9163 (mtp) cc_final: 0.8736 (mtp) REVERT: B 378 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6522 (pm20) REVERT: B 552 LYS cc_start: 0.7598 (tptt) cc_final: 0.7253 (mtpt) outliers start: 16 outliers final: 5 residues processed: 114 average time/residue: 1.3216 time to fit residues: 159.0662 Evaluate side-chains 102 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 82 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 346 GLN B 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.145729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131138 restraints weight = 8612.359| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.06 r_work: 0.3376 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7349 Z= 0.126 Angle : 0.673 12.304 10060 Z= 0.333 Chirality : 0.043 0.241 1234 Planarity : 0.007 0.103 1176 Dihedral : 5.120 35.061 1063 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 2.29 % Allowed : 14.78 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.30), residues: 883 helix: 0.57 (0.22), residues: 632 sheet: None (None), residues: 0 loop : -3.10 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.007 0.001 HIS B 31 PHE 0.011 0.001 PHE B 15 TYR 0.017 0.001 TYR A 418 ARG 0.002 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 373) hydrogen bonds : angle 3.96816 ( 1113) covalent geometry : bond 0.00294 ( 7349) covalent geometry : angle 0.67292 (10060) *********************** 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 119 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.778 Fit side-chains REVERT: A 72 MET cc_start: 0.6431 (mmm) cc_final: 0.5897 (mpt) REVERT: A 232 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7788 (tttp) REVERT: B 378 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: B 390 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8352 (mt) REVERT: B 447 ASP cc_start: 0.7860 (m-30) cc_final: 0.7544 (m-30) REVERT: B 552 LYS cc_start: 0.7658 (tptt) cc_final: 0.7170 (ttpt) outliers start: 18 outliers final: 8 residues processed: 111 average time/residue: 1.3063 time to fit residues: 153.6707 Evaluate side-chains 105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 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 71 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.143751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129187 restraints weight = 8609.829| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.07 r_work: 0.3359 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7349 Z= 0.147 Angle : 0.689 9.802 10060 Z= 0.342 Chirality : 0.045 0.243 1234 Planarity : 0.007 0.104 1176 Dihedral : 5.228 35.070 1063 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.47 % Favored : 92.41 % Rotamer: Outliers : 2.42 % Allowed : 15.16 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 883 helix: 0.71 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -3.05 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.008 0.002 HIS B 31 PHE 0.013 0.001 PHE B 15 TYR 0.016 0.002 TYR A 418 ARG 0.004 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 373) hydrogen bonds : angle 3.97173 ( 1113) covalent geometry : bond 0.00356 ( 7349) covalent geometry : angle 0.68945 (10060) *********************** 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 116 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.473 Fit side-chains REVERT: A 72 MET cc_start: 0.6420 (mmm) cc_final: 0.5884 (mpt) REVERT: A 338 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6443 (mp-120) REVERT: B 378 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: B 552 LYS cc_start: 0.7720 (tptt) cc_final: 0.7247 (ttpt) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 1.6501 time to fit residues: 192.3895 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 : 2.275 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS B 105 HIS B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.144786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130261 restraints weight = 8565.375| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.06 r_work: 0.3359 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1967 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= 0.130 Angle : 0.669 11.591 10060 Z= 0.331 Chirality : 0.043 0.235 1234 Planarity : 0.007 0.103 1176 Dihedral : 5.101 34.125 1063 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 2.42 % Allowed : 16.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.31), residues: 883 helix: 0.87 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -2.97 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 572 HIS 0.008 0.001 HIS B 31 PHE 0.012 0.001 PHE B 15 TYR 0.016 0.002 TYR A 418 ARG 0.003 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 373) hydrogen bonds : angle 3.91350 ( 1113) covalent geometry : bond 0.00309 ( 7349) covalent geometry : angle 0.66908 (10060) *********************** 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 115 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.762 Fit side-chains REVERT: A 72 MET cc_start: 0.6329 (mmm) cc_final: 0.5854 (mpt) REVERT: A 232 LYS cc_start: 0.7934 (ttmm) cc_final: 0.7418 (tptp) REVERT: A 338 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6387 (mp-120) REVERT: B 378 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: B 552 LYS cc_start: 0.7681 (tptt) cc_final: 0.7179 (ttpt) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 1.0735 time to fit residues: 124.5385 Evaluate side-chains 105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 119 ASN B 105 HIS B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.143203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128720 restraints weight = 8560.726| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.05 r_work: 0.3339 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7349 Z= 0.147 Angle : 0.690 10.120 10060 Z= 0.343 Chirality : 0.045 0.240 1234 Planarity : 0.007 0.104 1176 Dihedral : 5.179 33.913 1063 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.25 % Favored : 92.64 % Rotamer: Outliers : 2.42 % Allowed : 16.56 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.31), residues: 883 helix: 0.88 (0.22), residues: 633 sheet: None (None), residues: 0 loop : -2.95 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 585 HIS 0.006 0.001 HIS B 31 PHE 0.013 0.001 PHE B 15 TYR 0.020 0.002 TYR B 418 ARG 0.003 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 373) hydrogen bonds : angle 3.94217 ( 1113) covalent geometry : bond 0.00357 ( 7349) covalent geometry : angle 0.68989 (10060) *********************** 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 113 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.741 Fit side-chains REVERT: A 72 MET cc_start: 0.6299 (mmm) cc_final: 0.5850 (mpt) REVERT: A 232 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7499 (tptp) REVERT: A 338 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6379 (mp-120) REVERT: B 378 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6435 (pm20) REVERT: B 552 LYS cc_start: 0.7714 (tptt) cc_final: 0.7195 (ttpt) outliers start: 19 outliers final: 12 residues processed: 107 average time/residue: 1.0372 time to fit residues: 118.1594 Evaluate side-chains 105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 387 THR 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 243 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 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 = 0.146677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132120 restraints weight = 8602.395| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.02 r_work: 0.3386 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2118 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= 0.120 Angle : 0.647 9.255 10060 Z= 0.321 Chirality : 0.042 0.237 1234 Planarity : 0.007 0.101 1176 Dihedral : 4.936 33.090 1063 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.32 % Rotamer: Outliers : 2.17 % Allowed : 16.69 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.31), residues: 883 helix: 1.02 (0.22), residues: 627 sheet: None (None), residues: 0 loop : -2.86 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 572 HIS 0.003 0.001 HIS B 31 PHE 0.011 0.001 PHE B 15 TYR 0.021 0.001 TYR B 418 ARG 0.002 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 373) hydrogen bonds : angle 3.87280 ( 1113) covalent geometry : bond 0.00274 ( 7349) covalent geometry : angle 0.64693 (10060) *********************** 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 115 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.768 Fit side-chains REVERT: A 72 MET cc_start: 0.6196 (mmm) cc_final: 0.5809 (mpt) REVERT: A 115 MET cc_start: 0.6507 (mtp) cc_final: 0.6087 (mtp) REVERT: A 128 MET cc_start: 0.9120 (mtp) cc_final: 0.8784 (mtp) REVERT: A 338 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6380 (mp-120) REVERT: B 447 ASP cc_start: 0.7400 (m-30) cc_final: 0.7017 (m-30) REVERT: B 552 LYS cc_start: 0.7640 (tptt) cc_final: 0.7171 (ttpt) outliers start: 17 outliers final: 10 residues processed: 111 average time/residue: 1.0466 time to fit residues: 123.6457 Evaluate side-chains 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 148 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 156 GLN B 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.145534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130715 restraints weight = 8595.366| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.02 r_work: 0.3377 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2163 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= 0.131 Angle : 0.668 8.100 10060 Z= 0.334 Chirality : 0.044 0.237 1234 Planarity : 0.007 0.101 1176 Dihedral : 4.964 33.048 1063 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.47 % Favored : 92.41 % Rotamer: Outliers : 1.78 % Allowed : 17.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.31), residues: 883 helix: 1.02 (0.22), residues: 628 sheet: None (None), residues: 0 loop : -2.81 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 585 HIS 0.004 0.001 HIS A 105 PHE 0.019 0.001 PHE A 354 TYR 0.021 0.002 TYR B 418 ARG 0.003 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 373) hydrogen bonds : angle 3.90347 ( 1113) covalent geometry : bond 0.00313 ( 7349) covalent geometry : angle 0.66833 (10060) *********************** 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 110 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.812 Fit side-chains REVERT: A 72 MET cc_start: 0.6181 (mmm) cc_final: 0.5800 (mpt) REVERT: A 115 MET cc_start: 0.6481 (mtp) cc_final: 0.6050 (mtp) REVERT: A 338 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6326 (mp-120) REVERT: B 128 MET cc_start: 0.9073 (mtp) cc_final: 0.8715 (mtp) REVERT: B 347 GLU cc_start: 0.8270 (pt0) cc_final: 0.8069 (mt-10) REVERT: B 552 LYS cc_start: 0.7670 (tptt) cc_final: 0.7166 (ttpt) outliers start: 14 outliers final: 9 residues processed: 106 average time/residue: 1.1530 time to fit residues: 129.9298 Evaluate side-chains 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 243 CYS Chi-restraints excluded: chain B residue 256 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 B 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.147892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135038 restraints weight = 8680.676| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 0.86 r_work: 0.3373 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7349 Z= 0.125 Angle : 0.656 8.053 10060 Z= 0.327 Chirality : 0.043 0.237 1234 Planarity : 0.007 0.101 1176 Dihedral : 4.899 32.824 1063 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 1.66 % Allowed : 17.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.31), residues: 883 helix: 1.03 (0.22), residues: 634 sheet: None (None), residues: 0 loop : -2.83 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 585 HIS 0.003 0.001 HIS A 105 PHE 0.016 0.001 PHE A 354 TYR 0.020 0.001 TYR B 418 ARG 0.002 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 373) hydrogen bonds : angle 3.87941 ( 1113) covalent geometry : bond 0.00292 ( 7349) covalent geometry : angle 0.65592 (10060) ********************** 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 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.721 Fit side-chains REVERT: A 17 VAL cc_start: 0.8496 (m) cc_final: 0.8255 (t) REVERT: A 72 MET cc_start: 0.6082 (mmm) cc_final: 0.5735 (mpt) REVERT: A 115 MET cc_start: 0.6335 (mtp) cc_final: 0.5897 (mtp) REVERT: A 338 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6347 (mp-120) REVERT: B 552 LYS cc_start: 0.7619 (tptt) cc_final: 0.7119 (ttpt) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 1.0573 time to fit residues: 116.0552 Evaluate side-chains 105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 87 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 256 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 17 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.145663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130584 restraints weight = 8568.521| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.05 r_work: 0.3387 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2273 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= 0.123 Angle : 0.657 7.903 10060 Z= 0.328 Chirality : 0.043 0.234 1234 Planarity : 0.007 0.101 1176 Dihedral : 4.876 32.617 1063 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 1.66 % Allowed : 17.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.31), residues: 883 helix: 1.08 (0.22), residues: 632 sheet: None (None), residues: 0 loop : -2.83 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.004 0.001 HIS B 105 PHE 0.016 0.001 PHE A 354 TYR 0.019 0.001 TYR B 418 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 373) hydrogen bonds : angle 3.89064 ( 1113) covalent geometry : bond 0.00285 ( 7349) covalent geometry : angle 0.65683 (10060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5003.39 seconds wall clock time: 88 minutes 22.02 seconds (5302.02 seconds total)