Starting phenix.real_space_refine on Tue Jul 29 12:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ylu_39391/07_2025/8ylu_39391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ylu_39391/07_2025/8ylu_39391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ylu_39391/07_2025/8ylu_39391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ylu_39391/07_2025/8ylu_39391.map" model { file = "/net/cci-nas-00/data/ceres_data/8ylu_39391/07_2025/8ylu_39391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ylu_39391/07_2025/8ylu_39391.cif" } resolution = 2.8 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= 0.001 sd= 0.186 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: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 7175 2.51 5 N 1947 2.21 5 O 2236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11441 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3554 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain: "B" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3554 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1715 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1715 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.23, per 1000 atoms: 0.63 Number of scatterers: 11441 At special positions: 0 Unit cell: (94.64, 118.56, 126.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 44 15.00 Mg 1 11.99 O 2236 8.00 N 1947 7.00 C 7175 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: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 46.6% alpha, 12.3% beta 22 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.852A pdb=" N ALA A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.738A pdb=" N GLY A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.549A pdb=" N GLY A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.842A pdb=" N ALA A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.760A pdb=" N ASN A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 161' Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.655A pdb=" N LEU A 251 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.660A pdb=" N ARG A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 365 removed outlier: 4.156A pdb=" N LEU A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.569A pdb=" N LEU A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.704A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.743A pdb=" N ILE A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.646A pdb=" N ALA B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.848A pdb=" N GLY B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 76 through 88 removed outlier: 4.006A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 removed outlier: 3.576A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 319 through 362 removed outlier: 3.873A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.004A pdb=" N SER B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 404 through 426 removed outlier: 3.565A pdb=" N LYS B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 494 through 504 Processing helix chain 'C' and resid 536 through 545 removed outlier: 4.613A pdb=" N ASP C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 561 removed outlier: 3.574A pdb=" N LEU C 561 " --> pdb=" O LEU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 572 Processing helix chain 'C' and resid 583 through 592 removed outlier: 3.510A pdb=" N LEU C 587 " --> pdb=" O ASN C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 604 removed outlier: 3.572A pdb=" N TRP C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.707A pdb=" N ILE D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 504 removed outlier: 5.182A pdb=" N TYR D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Proline residue: D 497 - end of helix Processing helix chain 'D' and resid 506 through 512 removed outlier: 3.950A pdb=" N PHE D 510 " --> pdb=" O TRP D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 removed outlier: 3.583A pdb=" N ALA D 543 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP D 545 " --> pdb=" O GLU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 561 removed outlier: 3.526A pdb=" N LEU D 561 " --> pdb=" O LEU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 595 through 604 removed outlier: 4.125A pdb=" N ARG D 599 " --> pdb=" O ASN D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 5.559A pdb=" N ILE D 515 " --> pdb=" O VAL D 578 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU D 411 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET D 484 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU D 413 " --> pdb=" O MET D 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 223 removed outlier: 5.971A pdb=" N THR A 220 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 308 removed outlier: 4.431A pdb=" N ILE A 305 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 7 removed outlier: 5.579A pdb=" N ILE C 515 " --> pdb=" O VAL C 578 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 481 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL C 518 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE C 483 " --> pdb=" O VAL C 518 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU C 411 " --> pdb=" O ALA C 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'B' and resid 207 through 211 Processing sheet with id=AB2, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.160A pdb=" N THR B 220 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 305 through 308 removed outlier: 4.136A pdb=" N ILE B 305 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 530 through 534 Processing sheet with id=AB5, first strand: chain 'D' and resid 530 through 534 removed outlier: 3.662A pdb=" N SER D 551 " --> pdb=" O HIS D 526 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2990 1.33 - 1.45: 2315 1.45 - 1.57: 6313 1.57 - 1.69: 86 1.69 - 1.81: 70 Bond restraints: 11774 Sorted by residual: bond pdb=" CB ASN B 253 " pdb=" CG ASN B 253 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.43e+00 bond pdb=" CB ASP C 408 " pdb=" CG ASP C 408 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB GLU A 285 " pdb=" CG GLU A 285 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CA ASP C 408 " pdb=" CB ASP C 408 " ideal model delta sigma weight residual 1.528 1.541 -0.013 1.35e-02 5.49e+03 9.54e-01 bond pdb=" CA ASN B 253 " pdb=" CB ASN B 253 " ideal model delta sigma weight residual 1.527 1.537 -0.010 1.15e-02 7.56e+03 7.94e-01 ... (remaining 11769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 15795 1.72 - 3.44: 243 3.44 - 5.16: 20 5.16 - 6.88: 5 6.88 - 8.60: 1 Bond angle restraints: 16064 Sorted by residual: angle pdb=" CA ASN B 253 " pdb=" CB ASN B 253 " pdb=" CG ASN B 253 " ideal model delta sigma weight residual 112.60 115.45 -2.85 1.00e+00 1.00e+00 8.15e+00 angle pdb=" C GLY D 421 " pdb=" N TYR D 422 " pdb=" CA TYR D 422 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.80e+00 angle pdb=" CA LEU D 492 " pdb=" CB LEU D 492 " pdb=" CG LEU D 492 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.04e+00 angle pdb=" CB GLU A 285 " pdb=" CG GLU A 285 " pdb=" CD GLU A 285 " ideal model delta sigma weight residual 112.60 116.70 -4.10 1.70e+00 3.46e-01 5.81e+00 angle pdb=" CA ASP C 408 " pdb=" CB ASP C 408 " pdb=" CG ASP C 408 " ideal model delta sigma weight residual 112.60 115.01 -2.41 1.00e+00 1.00e+00 5.80e+00 ... (remaining 16059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 6244 28.11 - 56.22: 676 56.22 - 84.33: 58 84.33 - 112.44: 3 112.44 - 140.55: 1 Dihedral angle restraints: 6982 sinusoidal: 3170 harmonic: 3812 Sorted by residual: dihedral pdb=" CA PHE A 36 " pdb=" C PHE A 36 " pdb=" N LYS A 37 " pdb=" CA LYS A 37 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TYR B 238 " pdb=" C TYR B 238 " pdb=" N ASP B 239 " pdb=" CA ASP B 239 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE B 36 " pdb=" C PHE B 36 " pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 6979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1080 0.030 - 0.060: 476 0.060 - 0.091: 106 0.091 - 0.121: 63 0.121 - 0.151: 15 Chirality restraints: 1740 Sorted by residual: chirality pdb=" CA ASP C 408 " pdb=" N ASP C 408 " pdb=" C ASP C 408 " pdb=" CB ASP C 408 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ASN B 253 " pdb=" N ASN B 253 " pdb=" C ASN B 253 " pdb=" CB ASN B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 217 " pdb=" N ILE A 217 " pdb=" C ILE A 217 " pdb=" CB ILE A 217 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1737 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 253 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C ASN B 253 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN B 253 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS B 254 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 14 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C ASN B 14 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN B 14 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU B 15 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 88 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C ALA B 88 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA B 88 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 89 " 0.011 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 345 2.70 - 3.25: 10397 3.25 - 3.80: 18907 3.80 - 4.35: 25437 4.35 - 4.90: 41735 Nonbonded interactions: 96821 Sorted by model distance: nonbonded pdb=" OD1 ASP A 7 " pdb=" OG SER A 10 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR A 117 " pdb=" OP1 DA E 10 " model vdw 2.190 3.040 nonbonded pdb=" N GLU B 284 " pdb=" OE1 GLU B 284 " model vdw 2.212 3.120 nonbonded pdb=" O VAL B 369 " pdb=" NZ LYS B 373 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR B 73 " pdb=" OP2 DA E 8 " model vdw 2.223 3.040 ... (remaining 96816 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' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 393 through 605) } 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: 0.860 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.410 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 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:20.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.003 0.039 11774 Z= 0.140 Angle : 0.511 8.602 16064 Z= 0.285 Chirality : 0.040 0.151 1740 Planarity : 0.003 0.039 1904 Dihedral : 20.360 140.552 4538 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.89 % Allowed : 29.70 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.23), residues: 1300 helix: 0.97 (0.23), residues: 548 sheet: -0.44 (0.42), residues: 154 loop : -0.79 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.002 0.001 HIS A 144 PHE 0.013 0.001 PHE A 401 TYR 0.013 0.001 TYR D 575 ARG 0.004 0.000 ARG B 351 Details of bonding type rmsd hydrogen bonds : bond 0.12905 ( 517) hydrogen bonds : angle 5.76202 ( 1424) covalent geometry : bond 0.00316 (11774) covalent geometry : angle 0.51124 (16064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.299 Fit side-chains REVERT: B 387 MET cc_start: 0.6910 (ttt) cc_final: 0.6666 (tmm) REVERT: D 569 MET cc_start: 0.8847 (ptt) cc_final: 0.8542 (ptt) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 1.4604 time to fit residues: 203.6938 Evaluate side-chains 123 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 486 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.2980 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 81 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.137898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114036 restraints weight = 13280.562| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.51 r_work: 0.3272 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11774 Z= 0.191 Angle : 0.541 7.757 16064 Z= 0.300 Chirality : 0.042 0.151 1740 Planarity : 0.004 0.040 1904 Dihedral : 16.595 142.121 1937 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.46 % Allowed : 26.42 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.23 (0.22), residues: 1300 helix: 0.83 (0.22), residues: 558 sheet: -0.69 (0.40), residues: 164 loop : -0.91 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 602 HIS 0.002 0.001 HIS B 230 PHE 0.018 0.001 PHE B 401 TYR 0.012 0.001 TYR B 172 ARG 0.003 0.000 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 517) hydrogen bonds : angle 4.74769 ( 1424) covalent geometry : bond 0.00445 (11774) covalent geometry : angle 0.54127 (16064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 1.133 Fit side-chains REVERT: A 92 ASN cc_start: 0.8127 (t0) cc_final: 0.7889 (t0) REVERT: A 241 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: A 338 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6325 (ttm170) REVERT: B 124 LYS cc_start: 0.8226 (pttt) cc_final: 0.8008 (pttp) REVERT: B 361 LYS cc_start: 0.6037 (OUTLIER) cc_final: 0.5458 (tptp) REVERT: B 416 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.5973 (tptp) REVERT: C 601 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7830 (mp0) REVERT: D 512 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8264 (mp10) outliers start: 39 outliers final: 18 residues processed: 158 average time/residue: 1.3875 time to fit residues: 235.6712 Evaluate side-chains 145 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 530 LYS Chi-restraints excluded: chain D residue 551 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 0.0010 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 89 ASN C 505 ASN C 605 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116291 restraints weight = 13443.886| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.52 r_work: 0.3314 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11774 Z= 0.133 Angle : 0.496 7.693 16064 Z= 0.276 Chirality : 0.040 0.147 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.437 143.356 1928 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.84 % Allowed : 26.86 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.23), residues: 1300 helix: 1.01 (0.23), residues: 558 sheet: -0.66 (0.41), residues: 164 loop : -0.90 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.002 0.000 HIS B 75 PHE 0.016 0.001 PHE B 401 TYR 0.014 0.001 TYR D 575 ARG 0.002 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 517) hydrogen bonds : angle 4.56168 ( 1424) covalent geometry : bond 0.00303 (11774) covalent geometry : angle 0.49628 (16064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.104 Fit side-chains REVERT: A 241 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: A 338 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6205 (ttm170) REVERT: B 124 LYS cc_start: 0.8054 (pttt) cc_final: 0.7770 (pttp) REVERT: B 261 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8063 (t0) REVERT: B 361 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5362 (tptp) REVERT: B 416 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.5878 (tptp) REVERT: C 417 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: C 553 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8244 (ttp80) REVERT: D 512 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8154 (mt0) outliers start: 32 outliers final: 12 residues processed: 151 average time/residue: 1.4219 time to fit residues: 230.0300 Evaluate side-chains 141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 553 ARG Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116709 restraints weight = 13371.443| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.52 r_work: 0.3317 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11774 Z= 0.129 Angle : 0.488 7.051 16064 Z= 0.272 Chirality : 0.040 0.145 1740 Planarity : 0.003 0.042 1904 Dihedral : 16.377 143.274 1927 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.66 % Allowed : 26.60 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.23), residues: 1300 helix: 1.10 (0.23), residues: 558 sheet: -0.38 (0.43), residues: 154 loop : -0.98 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.002 0.000 HIS A 288 PHE 0.014 0.001 PHE A 401 TYR 0.014 0.001 TYR D 575 ARG 0.002 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 517) hydrogen bonds : angle 4.47276 ( 1424) covalent geometry : bond 0.00294 (11774) covalent geometry : angle 0.48770 (16064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.589 Fit side-chains REVERT: A 226 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6135 (mpp-170) REVERT: A 228 GLN cc_start: 0.7847 (mt0) cc_final: 0.7477 (mt0) REVERT: A 241 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: A 338 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6285 (ttm170) REVERT: A 384 LYS cc_start: 0.6898 (tptt) cc_final: 0.6695 (ttmt) REVERT: B 124 LYS cc_start: 0.8094 (pttt) cc_final: 0.7823 (pttp) REVERT: B 261 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8092 (t0) REVERT: B 361 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.5267 (tptp) REVERT: B 416 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.5891 (tptp) REVERT: C 417 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: D 512 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8174 (mp10) outliers start: 30 outliers final: 11 residues processed: 147 average time/residue: 1.5561 time to fit residues: 246.9766 Evaluate side-chains 139 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 402 HIS C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116975 restraints weight = 13207.870| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.50 r_work: 0.3321 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11774 Z= 0.129 Angle : 0.486 6.702 16064 Z= 0.271 Chirality : 0.040 0.144 1740 Planarity : 0.003 0.042 1904 Dihedral : 16.344 143.224 1926 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.57 % Allowed : 27.66 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.02 (0.23), residues: 1300 helix: 1.15 (0.23), residues: 558 sheet: -0.35 (0.43), residues: 154 loop : -0.97 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.006 0.001 HIS B 402 PHE 0.011 0.001 PHE A 149 TYR 0.015 0.001 TYR D 575 ARG 0.003 0.000 ARG B 351 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 517) hydrogen bonds : angle 4.41664 ( 1424) covalent geometry : bond 0.00292 (11774) covalent geometry : angle 0.48598 (16064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.992 Fit side-chains REVERT: A 226 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6135 (mpp-170) REVERT: A 228 GLN cc_start: 0.7833 (mt0) cc_final: 0.7477 (mt0) REVERT: A 241 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: A 338 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6384 (ttm170) REVERT: A 384 LYS cc_start: 0.6945 (tptt) cc_final: 0.6741 (ttmt) REVERT: B 124 LYS cc_start: 0.8092 (pttt) cc_final: 0.7805 (pttp) REVERT: B 261 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 361 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.5553 (tmtt) REVERT: B 416 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5844 (tptp) REVERT: C 417 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: D 512 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8173 (mp10) outliers start: 29 outliers final: 11 residues processed: 146 average time/residue: 2.2410 time to fit residues: 351.5359 Evaluate side-chains 139 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 128 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114121 restraints weight = 13490.756| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.53 r_work: 0.3273 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11774 Z= 0.187 Angle : 0.535 6.551 16064 Z= 0.295 Chirality : 0.042 0.154 1740 Planarity : 0.004 0.043 1904 Dihedral : 16.426 141.189 1926 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.93 % Allowed : 27.75 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.12 (0.23), residues: 1300 helix: 0.99 (0.22), residues: 558 sheet: -0.38 (0.43), residues: 154 loop : -1.01 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 602 HIS 0.003 0.001 HIS B 402 PHE 0.015 0.001 PHE A 149 TYR 0.019 0.001 TYR D 575 ARG 0.004 0.000 ARG B 351 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 517) hydrogen bonds : angle 4.52877 ( 1424) covalent geometry : bond 0.00442 (11774) covalent geometry : angle 0.53474 (16064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 2.314 Fit side-chains REVERT: A 92 ASN cc_start: 0.8179 (t0) cc_final: 0.7820 (t0) REVERT: A 226 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6105 (mpp-170) REVERT: A 228 GLN cc_start: 0.7835 (mt0) cc_final: 0.7533 (mt0) REVERT: A 241 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: A 338 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6306 (ttm170) REVERT: A 384 LYS cc_start: 0.6910 (tptt) cc_final: 0.6684 (ttmt) REVERT: A 440 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7206 (mp0) REVERT: B 124 LYS cc_start: 0.8162 (pttt) cc_final: 0.7896 (pttp) REVERT: B 261 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 361 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5496 (tptp) REVERT: C 417 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: D 512 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: D 544 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7489 (ttmt) outliers start: 33 outliers final: 15 residues processed: 144 average time/residue: 1.6248 time to fit residues: 250.9748 Evaluate side-chains 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 544 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115425 restraints weight = 13451.048| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.52 r_work: 0.3301 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11774 Z= 0.146 Angle : 0.512 6.816 16064 Z= 0.283 Chirality : 0.040 0.148 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.376 142.798 1926 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.93 % Allowed : 27.75 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.04 (0.23), residues: 1300 helix: 1.13 (0.23), residues: 556 sheet: -0.38 (0.43), residues: 154 loop : -1.03 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 602 HIS 0.002 0.001 HIS A 288 PHE 0.014 0.001 PHE B 401 TYR 0.017 0.001 TYR D 575 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 517) hydrogen bonds : angle 4.46448 ( 1424) covalent geometry : bond 0.00337 (11774) covalent geometry : angle 0.51154 (16064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.015 Fit side-chains REVERT: A 92 ASN cc_start: 0.8131 (t0) cc_final: 0.7788 (t0) REVERT: A 226 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6053 (mpp-170) REVERT: A 228 GLN cc_start: 0.7829 (mt0) cc_final: 0.7529 (mt0) REVERT: A 241 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: A 338 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6316 (ttm170) REVERT: A 384 LYS cc_start: 0.6949 (tptt) cc_final: 0.6717 (ttmt) REVERT: B 124 LYS cc_start: 0.8159 (pttt) cc_final: 0.7890 (pttp) REVERT: B 261 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8066 (t0) REVERT: B 361 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5579 (tmtt) REVERT: B 416 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.5909 (tptp) REVERT: C 417 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: D 512 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: D 590 MET cc_start: 0.8581 (tmm) cc_final: 0.8251 (tmm) outliers start: 33 outliers final: 14 residues processed: 147 average time/residue: 2.2489 time to fit residues: 359.2096 Evaluate side-chains 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 55 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117446 restraints weight = 13400.274| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.53 r_work: 0.3329 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11774 Z= 0.123 Angle : 0.496 6.959 16064 Z= 0.275 Chirality : 0.040 0.143 1740 Planarity : 0.003 0.040 1904 Dihedral : 16.291 143.674 1926 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.86 % Allowed : 28.37 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.23), residues: 1300 helix: 1.24 (0.23), residues: 556 sheet: -0.37 (0.43), residues: 154 loop : -0.99 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 602 HIS 0.002 0.000 HIS A 288 PHE 0.010 0.001 PHE A 149 TYR 0.015 0.001 TYR D 575 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 517) hydrogen bonds : angle 4.35634 ( 1424) covalent geometry : bond 0.00280 (11774) covalent geometry : angle 0.49583 (16064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 3.150 Fit side-chains REVERT: A 227 THR cc_start: 0.7918 (p) cc_final: 0.7717 (p) REVERT: A 228 GLN cc_start: 0.7835 (mt0) cc_final: 0.7458 (mt0) REVERT: A 338 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6361 (ttm170) REVERT: B 124 LYS cc_start: 0.8137 (pttt) cc_final: 0.7874 (pttp) REVERT: B 261 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8152 (t0) REVERT: B 361 LYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5703 (tmtt) REVERT: B 416 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5820 (tptp) REVERT: C 417 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: C 601 GLU cc_start: 0.7757 (mp0) cc_final: 0.7527 (mm-30) REVERT: D 512 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8142 (mp10) outliers start: 21 outliers final: 11 residues processed: 140 average time/residue: 1.4598 time to fit residues: 220.2525 Evaluate side-chains 133 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 0.0370 chunk 23 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 0.0470 chunk 24 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118004 restraints weight = 13401.607| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.53 r_work: 0.3345 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11774 Z= 0.116 Angle : 0.497 6.645 16064 Z= 0.275 Chirality : 0.039 0.148 1740 Planarity : 0.003 0.040 1904 Dihedral : 16.262 143.701 1926 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.04 % Allowed : 28.46 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.11 (0.23), residues: 1300 helix: 1.31 (0.23), residues: 556 sheet: -0.66 (0.42), residues: 164 loop : -0.90 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 602 HIS 0.008 0.001 HIS B 402 PHE 0.018 0.001 PHE A 401 TYR 0.014 0.001 TYR D 575 ARG 0.004 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 517) hydrogen bonds : angle 4.31988 ( 1424) covalent geometry : bond 0.00260 (11774) covalent geometry : angle 0.49734 (16064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.179 Fit side-chains REVERT: A 226 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6000 (mpp-170) REVERT: A 228 GLN cc_start: 0.7800 (mt0) cc_final: 0.7422 (mt0) REVERT: A 241 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: A 338 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6378 (ttm170) REVERT: B 124 LYS cc_start: 0.8106 (pttt) cc_final: 0.7832 (pttp) REVERT: B 261 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8199 (t0) REVERT: B 361 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5692 (tmtt) REVERT: B 416 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5788 (tptp) REVERT: C 417 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: C 601 GLU cc_start: 0.7723 (mp0) cc_final: 0.7487 (mm-30) outliers start: 23 outliers final: 14 residues processed: 134 average time/residue: 1.4456 time to fit residues: 207.8218 Evaluate side-chains 136 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 125 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN C 605 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114893 restraints weight = 13374.365| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.51 r_work: 0.3294 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11774 Z= 0.184 Angle : 0.546 7.346 16064 Z= 0.299 Chirality : 0.042 0.161 1740 Planarity : 0.004 0.042 1904 Dihedral : 16.362 141.570 1926 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.22 % Allowed : 28.46 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.23), residues: 1300 helix: 1.11 (0.23), residues: 556 sheet: -0.79 (0.42), residues: 164 loop : -0.95 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.010 0.001 HIS B 402 PHE 0.016 0.001 PHE A 401 TYR 0.019 0.001 TYR D 575 ARG 0.004 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 517) hydrogen bonds : angle 4.44072 ( 1424) covalent geometry : bond 0.00432 (11774) covalent geometry : angle 0.54624 (16064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.295 Fit side-chains REVERT: A 92 ASN cc_start: 0.8157 (t0) cc_final: 0.7810 (t0) REVERT: A 226 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6039 (mpp-170) REVERT: A 241 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: A 338 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6340 (ttm170) REVERT: B 124 LYS cc_start: 0.8197 (pttt) cc_final: 0.7928 (pttp) REVERT: B 361 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5784 (tmtt) REVERT: C 408 ASP cc_start: 0.7649 (p0) cc_final: 0.7423 (t0) REVERT: C 417 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: C 601 GLU cc_start: 0.7779 (mp0) cc_final: 0.7531 (mm-30) REVERT: D 512 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: D 544 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7564 (ttmt) REVERT: D 590 MET cc_start: 0.8633 (tmm) cc_final: 0.8363 (tmm) outliers start: 25 outliers final: 13 residues processed: 143 average time/residue: 1.5254 time to fit residues: 233.5960 Evaluate side-chains 140 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 544 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 119 optimal weight: 1.9990 chunk 123 optimal weight: 0.0270 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN B 89 ASN C 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118406 restraints weight = 13274.212| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.52 r_work: 0.3344 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11774 Z= 0.118 Angle : 0.500 7.643 16064 Z= 0.276 Chirality : 0.039 0.146 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.252 144.208 1926 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.68 % Allowed : 29.26 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.08 (0.23), residues: 1300 helix: 1.30 (0.23), residues: 556 sheet: -0.77 (0.42), residues: 164 loop : -0.89 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 602 HIS 0.007 0.000 HIS B 402 PHE 0.017 0.001 PHE A 401 TYR 0.014 0.001 TYR D 575 ARG 0.004 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 517) hydrogen bonds : angle 4.30169 ( 1424) covalent geometry : bond 0.00267 (11774) covalent geometry : angle 0.49958 (16064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9258.15 seconds wall clock time: 167 minutes 34.72 seconds (10054.72 seconds total)