Starting phenix.real_space_refine on Fri Jan 17 21:39:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ylu_39391/01_2025/8ylu_39391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ylu_39391/01_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_39391/01_2025/8ylu_39391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ylu_39391/01_2025/8ylu_39391.map" model { file = "/net/cci-nas-00/data/ceres_data/8ylu_39391/01_2025/8ylu_39391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ylu_39391/01_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-5571/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: 7.29, per 1000 atoms: 0.64 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: 3.03 Conformation dependent library (CDL) restraints added in 1.4 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: 4.26 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: 3.91 Time building geometry restraints manager: 3.23 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: 1.140 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.320 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- 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= 0.200 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 *********************** 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 : 1.194 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: 1.5694 time to fit residues: 219.0247 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 : 1.500 ------------------------------------------------------------------------------- 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 = 13280.551| |-----------------------------------------------------------------------------| 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: 0.3171 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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= 0.281 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 *********************** 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 : 1.339 Fit side-chains REVERT: A 92 ASN cc_start: 0.8121 (t0) cc_final: 0.7883 (t0) REVERT: A 241 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: A 338 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6325 (ttm170) REVERT: B 124 LYS cc_start: 0.8227 (pttt) cc_final: 0.8010 (pttp) REVERT: B 361 LYS cc_start: 0.6032 (OUTLIER) cc_final: 0.5454 (tptp) REVERT: B 416 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.5975 (tptp) REVERT: C 601 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7834 (mp0) REVERT: D 512 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8266 (mp10) outliers start: 39 outliers final: 18 residues processed: 158 average time/residue: 1.4945 time to fit residues: 252.9969 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 : 1.189 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 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: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.139617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115846 restraints weight = 13446.478| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.52 r_work: 0.3305 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0698 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= 0.200 Angle : 0.502 7.791 16064 Z= 0.280 Chirality : 0.040 0.148 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.454 143.041 1928 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.93 % Allowed : 26.95 % 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: -0.12 (0.23), residues: 1300 helix: 0.98 (0.23), residues: 558 sheet: -0.68 (0.41), residues: 164 loop : -0.91 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.002 0.001 HIS B 75 PHE 0.017 0.001 PHE B 401 TYR 0.014 0.001 TYR D 575 ARG 0.003 0.000 ARG B 205 *********************** 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 159 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.330 Fit side-chains REVERT: A 92 ASN cc_start: 0.8085 (t0) cc_final: 0.7849 (t0) REVERT: A 241 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: A 338 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6288 (ttm170) REVERT: B 124 LYS cc_start: 0.8101 (pttt) cc_final: 0.7831 (pttp) REVERT: B 261 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 361 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5404 (tptp) REVERT: B 416 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5903 (tptp) REVERT: C 417 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: D 512 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8166 (mt0) outliers start: 33 outliers final: 12 residues processed: 152 average time/residue: 1.6010 time to fit residues: 261.1152 Evaluate side-chains 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3682 r_free = 0.3682 target = 0.141195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117556 restraints weight = 13364.790| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.51 r_work: 0.3331 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11774 Z= 0.163 Angle : 0.479 7.158 16064 Z= 0.268 Chirality : 0.039 0.145 1740 Planarity : 0.003 0.043 1904 Dihedral : 16.361 143.755 1927 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.48 % Allowed : 27.04 % Favored : 70.48 % 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: 1.15 (0.23), residues: 558 sheet: -0.37 (0.43), residues: 154 loop : -0.95 (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 0.015 0.001 PHE A 401 TYR 0.014 0.001 TYR D 575 ARG 0.002 0.000 ARG B 205 *********************** 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 153 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 1.277 Fit side-chains REVERT: A 228 GLN cc_start: 0.7823 (mt0) cc_final: 0.7447 (mt0) REVERT: A 241 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 338 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6330 (ttm170) REVERT: B 124 LYS cc_start: 0.8069 (pttt) cc_final: 0.7787 (pttp) REVERT: B 261 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8096 (t0) REVERT: B 361 LYS cc_start: 0.5681 (OUTLIER) cc_final: 0.5441 (tmtt) REVERT: B 416 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.5817 (tptp) REVERT: C 417 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: D 512 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8148 (mp10) outliers start: 28 outliers final: 9 residues processed: 148 average time/residue: 1.4854 time to fit residues: 235.7731 Evaluate side-chains 132 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 193 LYS 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 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS 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: 0.1980 chunk 110 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.139814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116193 restraints weight = 13226.351| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.51 r_work: 0.3310 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0883 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= 0.203 Angle : 0.495 6.557 16064 Z= 0.275 Chirality : 0.040 0.145 1740 Planarity : 0.003 0.043 1904 Dihedral : 16.359 142.644 1926 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.75 % Allowed : 27.48 % 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: -0.01 (0.23), residues: 1300 helix: 1.11 (0.23), residues: 558 sheet: -0.37 (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 0.002 0.001 HIS B 288 PHE 0.012 0.001 PHE A 149 TYR 0.016 0.001 TYR D 575 ARG 0.003 0.000 ARG B 351 *********************** 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 155 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.228 Fit side-chains REVERT: A 226 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6087 (mpp-170) REVERT: A 228 GLN cc_start: 0.7869 (mt0) cc_final: 0.7517 (mt0) REVERT: A 241 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: A 338 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6337 (ttm170) REVERT: B 124 LYS cc_start: 0.8062 (pttt) cc_final: 0.7824 (pttp) REVERT: B 261 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8084 (t0) REVERT: B 361 LYS cc_start: 0.5791 (OUTLIER) cc_final: 0.5320 (tptp) REVERT: B 416 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5858 (tptp) REVERT: C 417 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: D 512 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: D 590 MET cc_start: 0.8608 (tmm) cc_final: 0.8389 (tmm) outliers start: 31 outliers final: 11 residues processed: 148 average time/residue: 1.5294 time to fit residues: 242.6222 Evaluate side-chains 137 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 128 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.140456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116810 restraints weight = 13433.502| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.53 r_work: 0.3322 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11774 Z= 0.188 Angle : 0.492 6.400 16064 Z= 0.274 Chirality : 0.040 0.144 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.323 143.218 1926 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.48 % Allowed : 28.10 % 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: 0.04 (0.23), residues: 1300 helix: 1.17 (0.23), residues: 558 sheet: -0.33 (0.43), residues: 154 loop : -0.96 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.005 0.001 HIS B 402 PHE 0.012 0.001 PHE A 149 TYR 0.016 0.001 TYR D 575 ARG 0.004 0.000 ARG B 351 *********************** 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 152 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.347 Fit side-chains REVERT: A 226 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6080 (mpp-170) REVERT: A 228 GLN cc_start: 0.7819 (mt0) cc_final: 0.7484 (mt0) REVERT: A 241 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 338 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6399 (ttm170) REVERT: A 440 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7160 (mp0) REVERT: B 124 LYS cc_start: 0.8103 (pttt) cc_final: 0.7851 (pttp) REVERT: B 261 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8128 (t0) REVERT: B 361 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5548 (tmtt) REVERT: B 416 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.5842 (tptp) REVERT: C 417 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: D 512 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8149 (mp10) outliers start: 28 outliers final: 11 residues processed: 143 average time/residue: 1.5184 time to fit residues: 232.9695 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 : 1.356 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.140655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117017 restraints weight = 13427.566| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.52 r_work: 0.3322 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11774 Z= 0.189 Angle : 0.498 6.323 16064 Z= 0.276 Chirality : 0.040 0.144 1740 Planarity : 0.003 0.041 1904 Dihedral : 16.306 143.106 1926 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.66 % Allowed : 28.01 % 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: 0.07 (0.23), residues: 1300 helix: 1.19 (0.23), residues: 558 sheet: -0.30 (0.44), residues: 154 loop : -0.95 (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 B 402 PHE 0.012 0.001 PHE A 149 TYR 0.016 0.001 TYR D 575 ARG 0.003 0.000 ARG B 205 *********************** 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 154 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.198 Fit side-chains REVERT: A 226 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6088 (mpp-170) REVERT: A 228 GLN cc_start: 0.7826 (mt0) cc_final: 0.7564 (mt0) REVERT: A 241 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: A 338 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6398 (ttm170) REVERT: A 440 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7220 (mp0) REVERT: B 124 LYS cc_start: 0.8125 (pttt) cc_final: 0.7872 (pttp) REVERT: B 261 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8165 (t0) REVERT: B 361 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5593 (tmtt) REVERT: B 416 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5846 (tptp) REVERT: C 417 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: D 512 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8151 (mp10) outliers start: 30 outliers final: 14 residues processed: 147 average time/residue: 1.5431 time to fit residues: 243.6455 Evaluate side-chains 146 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 123 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117267 restraints weight = 13421.240| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.52 r_work: 0.3330 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11774 Z= 0.187 Angle : 0.503 6.304 16064 Z= 0.278 Chirality : 0.040 0.148 1740 Planarity : 0.003 0.039 1904 Dihedral : 16.293 143.204 1926 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.22 % Allowed : 28.72 % 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: 0.09 (0.23), residues: 1300 helix: 1.24 (0.23), residues: 556 sheet: -0.34 (0.43), residues: 154 loop : -0.97 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 602 HIS 0.003 0.000 HIS B 402 PHE 0.014 0.001 PHE B 401 TYR 0.015 0.001 TYR D 575 ARG 0.003 0.000 ARG B 205 *********************** 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 149 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.203 Fit side-chains REVERT: A 226 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6071 (mpp-170) REVERT: A 228 GLN cc_start: 0.7778 (mt0) cc_final: 0.7518 (mt0) REVERT: A 241 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: A 338 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6338 (ttm170) REVERT: B 124 LYS cc_start: 0.8099 (pttt) cc_final: 0.7834 (pttp) REVERT: B 261 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8186 (t0) REVERT: B 361 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5580 (tmtt) REVERT: B 416 LYS cc_start: 0.6402 (OUTLIER) cc_final: 0.5808 (tptp) REVERT: C 417 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: C 601 GLU cc_start: 0.7807 (mp0) cc_final: 0.7570 (mp0) REVERT: D 512 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8125 (mp10) outliers start: 25 outliers final: 12 residues processed: 143 average time/residue: 1.5287 time to fit residues: 234.8499 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 : 1.216 ------------------------------------------------------------------------------- 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 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 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: 0.0970 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.0020 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 95 optimal weight: 0.0070 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.3204 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.143975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120572 restraints weight = 13409.275| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.53 r_work: 0.3378 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11774 Z= 0.142 Angle : 0.482 6.375 16064 Z= 0.267 Chirality : 0.039 0.141 1740 Planarity : 0.003 0.040 1904 Dihedral : 16.208 144.742 1926 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.51 % Allowed : 29.43 % 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: 0.23 (0.23), residues: 1300 helix: 1.41 (0.23), residues: 556 sheet: -0.36 (0.43), residues: 154 loop : -0.92 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.004 0.000 HIS B 402 PHE 0.018 0.001 PHE A 401 TYR 0.013 0.001 TYR D 575 ARG 0.003 0.000 ARG B 205 *********************** 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 149 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.372 Fit side-chains REVERT: A 226 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6069 (mpp-170) REVERT: A 228 GLN cc_start: 0.7662 (mt0) cc_final: 0.7441 (mt0) REVERT: A 338 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6480 (ttm170) REVERT: B 124 LYS cc_start: 0.8113 (pttt) cc_final: 0.7865 (pttp) REVERT: B 261 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8191 (t0) REVERT: B 361 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5507 (tmtt) REVERT: B 416 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5803 (tptp) REVERT: C 417 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: C 601 GLU cc_start: 0.7728 (mp0) cc_final: 0.7527 (mp0) outliers start: 17 outliers final: 8 residues processed: 144 average time/residue: 1.5387 time to fit residues: 238.1860 Evaluate side-chains 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 226 ARG 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 360 ILE Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 416 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 125 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.139924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116335 restraints weight = 13376.150| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.51 r_work: 0.3318 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11774 Z= 0.226 Angle : 0.525 7.492 16064 Z= 0.289 Chirality : 0.041 0.155 1740 Planarity : 0.003 0.040 1904 Dihedral : 16.271 142.052 1926 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 29.43 % Favored : 68.97 % 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: 1.26 (0.23), residues: 556 sheet: -0.70 (0.41), residues: 164 loop : -0.88 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 602 HIS 0.004 0.001 HIS B 402 PHE 0.017 0.001 PHE A 401 TYR 0.017 0.001 TYR D 575 ARG 0.004 0.000 ARG B 205 ********************** 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 139 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.310 Fit side-chains REVERT: A 92 ASN cc_start: 0.8113 (t0) cc_final: 0.7781 (t0) REVERT: A 210 GLU cc_start: 0.7257 (tp30) cc_final: 0.7021 (tp30) REVERT: A 226 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6061 (mpp-170) REVERT: A 228 GLN cc_start: 0.7789 (mt0) cc_final: 0.7544 (mt0) REVERT: A 338 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6392 (ttm170) REVERT: B 124 LYS cc_start: 0.8173 (pttt) cc_final: 0.7916 (pttp) REVERT: B 261 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 361 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5660 (tmtt) REVERT: C 417 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: C 601 GLU cc_start: 0.7770 (mp0) cc_final: 0.7528 (mm-30) outliers start: 18 outliers final: 11 residues processed: 133 average time/residue: 1.5465 time to fit residues: 220.4880 Evaluate side-chains 133 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 266 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 129 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 119 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117011 restraints weight = 13289.783| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.52 r_work: 0.3326 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1115 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= 0.198 Angle : 0.513 7.829 16064 Z= 0.282 Chirality : 0.040 0.144 1740 Planarity : 0.003 0.039 1904 Dihedral : 16.256 143.197 1926 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.95 % Allowed : 29.17 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.23), residues: 556 sheet: -0.73 (0.41), residues: 164 loop : -0.89 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 602 HIS 0.003 0.000 HIS B 402 PHE 0.017 0.001 PHE A 401 TYR 0.016 0.001 TYR D 575 ARG 0.004 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7633.52 seconds wall clock time: 139 minutes 11.40 seconds (8351.40 seconds total)