Starting phenix.real_space_refine on Fri Jul 3 19:53:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpa_47100/07_2026/9dpa_47100.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpa_47100/07_2026/9dpa_47100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dpa_47100/07_2026/9dpa_47100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpa_47100/07_2026/9dpa_47100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dpa_47100/07_2026/9dpa_47100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpa_47100/07_2026/9dpa_47100.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7580 atoms to isotropic. 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 78 5.49 5 S 56 5.16 5 Na 1 4.78 5 C 5996 2.51 5 N 1691 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9878 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4100 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 29, 'TRANS': 476} Chain: "B" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4092 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 29, 'TRANS': 475} Chain: "C" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 17, 'rna3p': 58} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1, 'peptide': 1} Modifications used: {'COO': 1, 'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 2.40, per 1000 atoms: 0.24 Number of scatterers: 9878 At special positions: 0 Unit cell: (84.53, 101.65, 128.4, 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 56 16.00 P 78 15.00 Na 1 11.00 O 2056 8.00 N 1691 7.00 C 5996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 232.2 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 9 sheets defined 38.4% alpha, 22.4% beta 26 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.549A pdb=" N ILE A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 238 through 261 removed outlier: 3.858A pdb=" N GLN A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 346 through 366 removed outlier: 4.346A pdb=" N GLU A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.631A pdb=" N ARG A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.626A pdb=" N LEU A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 530 through 539 removed outlier: 3.545A pdb=" N TYR A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.856A pdb=" N PHE A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 4.158A pdb=" N VAL A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 238 through 261 Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 349 through 367 removed outlier: 3.735A pdb=" N ILE B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 404 Processing helix chain 'B' and resid 416 through 430 Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.552A pdb=" N LYS B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 530 through 539 Processing helix chain 'B' and resid 551 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 137 removed outlier: 5.980A pdb=" N ILE A 132 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG A 148 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 134 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU A 196 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 155 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 157 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN A 159 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N GLU A 202 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN A 185 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE A 203 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A 183 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU A 205 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE A 181 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265 removed outlier: 5.856A pdb=" N LEU A 264 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 495 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 488 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 497 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE A 486 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG A 392 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 removed outlier: 3.720A pdb=" N TYR A 295 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 466 Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 137 removed outlier: 6.262A pdb=" N ILE B 132 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG B 148 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 134 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU B 196 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 155 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 198 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 157 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASN B 159 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLU B 202 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN B 185 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE B 203 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY B 183 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU B 205 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 181 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 265 removed outlier: 5.869A pdb=" N LEU B 264 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE B 318 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 342 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 495 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 490 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS B 496 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS B 465 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG B 485 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N CYS B 463 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU B 487 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 461 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG B 392 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N CYS B 463 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE B 394 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N HIS B 465 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 271 through 272 removed outlier: 3.651A pdb=" N MET B 292 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 370 through 373 363 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 0.97 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: 2635 1.33 - 1.46: 2404 1.46 - 1.58: 4974 1.58 - 1.70: 153 1.70 - 1.82: 96 Bond restraints: 10262 Sorted by residual: bond pdb=" C LYS A 370 " pdb=" N VAL A 371 " ideal model delta sigma weight residual 1.331 1.243 0.088 1.32e-02 5.74e+03 4.47e+01 bond pdb=" C MET B 527 " pdb=" N PHE B 528 " ideal model delta sigma weight residual 1.329 1.438 -0.109 1.76e-02 3.23e+03 3.85e+01 bond pdb=" C PHE B 335 " pdb=" N THR B 336 " ideal model delta sigma weight residual 1.329 1.413 -0.084 1.43e-02 4.89e+03 3.45e+01 bond pdb=" C4 AMP B 602 " pdb=" C5 AMP B 602 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 AMP A 601 " pdb=" C5 AMP A 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 ... (remaining 10257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 13749 2.29 - 4.58: 429 4.58 - 6.88: 43 6.88 - 9.17: 11 9.17 - 11.46: 7 Bond angle restraints: 14239 Sorted by residual: angle pdb=" C GLY B 186 " pdb=" N ASN B 187 " pdb=" CA ASN B 187 " ideal model delta sigma weight residual 120.94 131.32 -10.38 1.90e+00 2.77e-01 2.98e+01 angle pdb=" O MET B 527 " pdb=" C MET B 527 " pdb=" N PHE B 528 " ideal model delta sigma weight residual 122.68 128.75 -6.07 1.17e+00 7.31e-01 2.69e+01 angle pdb=" O ARG A 420 " pdb=" C ARG A 420 " pdb=" N LYS A 421 " ideal model delta sigma weight residual 122.12 127.28 -5.16 1.06e+00 8.90e-01 2.37e+01 angle pdb=" N PRO B 436 " pdb=" CA PRO B 436 " pdb=" C PRO B 436 " ideal model delta sigma weight residual 110.70 116.45 -5.75 1.22e+00 6.72e-01 2.22e+01 angle pdb=" O2 U C 66 " pdb=" C2 U C 66 " pdb=" N3 U C 66 " ideal model delta sigma weight residual 122.20 119.01 3.19 7.00e-01 2.04e+00 2.07e+01 ... (remaining 14234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 5893 34.04 - 68.08: 397 68.08 - 102.12: 39 102.12 - 136.17: 2 136.17 - 170.21: 3 Dihedral angle restraints: 6334 sinusoidal: 3383 harmonic: 2951 Sorted by residual: dihedral pdb=" O4' U C 66 " pdb=" C1' U C 66 " pdb=" N1 U C 66 " pdb=" C2 U C 66 " ideal model delta sinusoidal sigma weight residual -160.00 -4.39 -155.61 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" C5' AMP B 602 " pdb=" O5' AMP B 602 " pdb=" P AMP B 602 " pdb=" O3P AMP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 -171.93 111.93 1 2.00e+01 2.50e-03 3.30e+01 dihedral pdb=" CA TYR A 499 " pdb=" C TYR A 499 " pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 6331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1516 0.106 - 0.211: 87 0.211 - 0.317: 8 0.317 - 0.422: 0 0.422 - 0.528: 2 Chirality restraints: 1613 Sorted by residual: chirality pdb=" P C C 48 " pdb=" OP1 C C 48 " pdb=" OP2 C C 48 " pdb=" O5' C C 48 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.97e+00 chirality pdb=" P U C 47 " pdb=" OP1 U C 47 " pdb=" OP2 U C 47 " pdb=" O5' U C 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C3' U C 47 " pdb=" C4' U C 47 " pdb=" O3' U C 47 " pdb=" C2' U C 47 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1610 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 528 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C PHE B 528 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE B 528 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE B 529 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 241 " 0.214 9.50e-02 1.11e+02 9.57e-02 5.63e+00 pdb=" NE ARG B 241 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 241 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 241 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 241 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 260 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" CD GLU A 260 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU A 260 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 260 " 0.014 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 827 2.74 - 3.28: 9754 3.28 - 3.82: 17661 3.82 - 4.36: 21245 4.36 - 4.90: 34765 Nonbonded interactions: 84252 Sorted by model distance: nonbonded pdb=" O ILE A 109 " pdb=" OG SER A 113 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR B 286 " pdb=" OD1 ASP B 291 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 286 " pdb=" OD1 ASP A 291 " model vdw 2.233 3.040 nonbonded pdb=" O LEU A 413 " pdb=" OG1 THR A 416 " model vdw 2.246 3.040 nonbonded pdb=" O2' G C 65 " pdb=" OP1 U C 66 " model vdw 2.261 3.040 ... (remaining 84247 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' and (resid 72 through 576 or resid 601)) selection = (chain 'B' and (resid 72 through 576 or resid 602)) } 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.330 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.007 0.111 10262 Z= 0.441 Angle : 0.853 11.462 14239 Z= 0.572 Chirality : 0.053 0.528 1613 Planarity : 0.006 0.096 1552 Dihedral : 20.533 170.207 4436 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.56 % Allowed : 26.53 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.26), residues: 1007 helix: 1.01 (0.28), residues: 356 sheet: -0.84 (0.35), residues: 225 loop : -1.35 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 442 TYR 0.021 0.001 TYR B 499 PHE 0.022 0.001 PHE B 340 TRP 0.013 0.002 TRP B 547 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.44 (10262) covalent geometry : angle 0.85307 / 0.57 (14239) hydrogen bonds : bond 0.17148 / 11.75 ( 430) hydrogen bonds : angle 7.21757 / 5.05 ( 1163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.352 Fit side-chains REVERT: A 434 CYS cc_start: 0.8269 (t) cc_final: 0.7325 (t) REVERT: A 442 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7314 (ttp-170) REVERT: A 451 PHE cc_start: 0.8402 (m-80) cc_final: 0.7973 (m-80) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.5745 time to fit residues: 66.6297 Evaluate side-chains 82 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 217 HIS B 237 ASN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.115861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.080029 restraints weight = 17159.555| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.43 r_work: 0.2970 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10262 Z= 0.201 Angle : 0.622 7.544 14239 Z= 0.325 Chirality : 0.040 0.240 1613 Planarity : 0.005 0.056 1552 Dihedral : 19.732 165.340 2339 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.34 % Allowed : 26.64 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.26), residues: 1007 helix: 1.36 (0.27), residues: 371 sheet: -0.56 (0.35), residues: 221 loop : -1.37 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 247 TYR 0.028 0.001 TYR B 499 PHE 0.030 0.002 PHE A 340 TRP 0.014 0.003 TRP A 547 HIS 0.004 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (10262) covalent geometry : angle 0.62234 / 0.32 (14239) hydrogen bonds : bond 0.05432 / 3.94 ( 430) hydrogen bonds : angle 5.30208 / 3.73 ( 1163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.392 Fit side-chains REVERT: A 406 MET cc_start: 0.8182 (ptp) cc_final: 0.7910 (ptm) REVERT: A 434 CYS cc_start: 0.8154 (t) cc_final: 0.7142 (t) REVERT: A 442 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7604 (ttp-170) REVERT: B 221 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8572 (mmmm) outliers start: 30 outliers final: 11 residues processed: 99 average time/residue: 0.5307 time to fit residues: 56.9247 Evaluate side-chains 81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 0.0670 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.116422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081267 restraints weight = 17358.929| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.45 r_work: 0.3016 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10262 Z= 0.148 Angle : 0.583 7.820 14239 Z= 0.302 Chirality : 0.039 0.234 1613 Planarity : 0.005 0.055 1552 Dihedral : 19.643 163.758 2329 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.68 % Allowed : 25.42 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.26), residues: 1007 helix: 1.45 (0.27), residues: 372 sheet: -0.46 (0.36), residues: 220 loop : -1.33 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 420 TYR 0.025 0.001 TYR B 499 PHE 0.028 0.002 PHE A 340 TRP 0.013 0.002 TRP A 547 HIS 0.003 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (10262) covalent geometry : angle 0.58279 / 0.30 (14239) hydrogen bonds : bond 0.04919 / 3.60 ( 430) hydrogen bonds : angle 4.96987 / 3.51 ( 1163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.217 Fit side-chains REVERT: A 406 MET cc_start: 0.8201 (ptp) cc_final: 0.7995 (ptm) REVERT: A 434 CYS cc_start: 0.8123 (t) cc_final: 0.7097 (t) REVERT: A 442 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7682 (ttp-170) REVERT: B 141 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8823 (tppp) outliers start: 33 outliers final: 11 residues processed: 105 average time/residue: 0.5134 time to fit residues: 58.0774 Evaluate side-chains 82 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 499 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 105 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.115711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079152 restraints weight = 17446.875| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.55 r_work: 0.2984 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10262 Z= 0.176 Angle : 0.594 8.758 14239 Z= 0.307 Chirality : 0.040 0.235 1613 Planarity : 0.005 0.083 1552 Dihedral : 19.590 163.986 2327 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.68 % Allowed : 25.20 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.26), residues: 1007 helix: 1.48 (0.27), residues: 373 sheet: -0.42 (0.36), residues: 220 loop : -1.35 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 420 TYR 0.026 0.001 TYR B 499 PHE 0.029 0.002 PHE A 340 TRP 0.015 0.003 TRP A 547 HIS 0.002 0.001 HIS B 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10262) covalent geometry : angle 0.59395 / 0.31 (14239) hydrogen bonds : bond 0.04855 / 3.55 ( 430) hydrogen bonds : angle 4.82689 / 3.42 ( 1163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.287 Fit side-chains REVERT: A 396 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8060 (ttp) REVERT: A 406 MET cc_start: 0.8285 (ptp) cc_final: 0.8083 (ptm) REVERT: A 434 CYS cc_start: 0.8173 (t) cc_final: 0.7135 (t) REVERT: A 442 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7722 (ttp-170) REVERT: A 450 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: A 451 PHE cc_start: 0.9021 (m-80) cc_final: 0.8359 (m-80) REVERT: B 74 ASN cc_start: 0.8762 (p0) cc_final: 0.8515 (p0) REVERT: B 396 MET cc_start: 0.7819 (tmt) cc_final: 0.7555 (tmm) REVERT: B 406 MET cc_start: 0.5662 (pmm) cc_final: 0.5365 (pp-130) outliers start: 33 outliers final: 12 residues processed: 98 average time/residue: 0.4861 time to fit residues: 51.7992 Evaluate side-chains 81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.116225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080488 restraints weight = 17296.357| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.47 r_work: 0.3004 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10262 Z= 0.134 Angle : 0.583 8.476 14239 Z= 0.299 Chirality : 0.039 0.230 1613 Planarity : 0.005 0.054 1552 Dihedral : 19.559 163.461 2327 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.01 % Allowed : 25.42 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1007 helix: 1.51 (0.27), residues: 373 sheet: -0.36 (0.36), residues: 220 loop : -1.36 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 420 TYR 0.023 0.001 TYR B 499 PHE 0.027 0.002 PHE A 340 TRP 0.013 0.002 TRP A 547 HIS 0.002 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10262) covalent geometry : angle 0.58316 / 0.30 (14239) hydrogen bonds : bond 0.04597 / 3.38 ( 430) hydrogen bonds : angle 4.66663 / 3.31 ( 1163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.356 Fit side-chains REVERT: A 395 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7809 (t0) REVERT: A 434 CYS cc_start: 0.8176 (t) cc_final: 0.7158 (t) REVERT: A 442 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.7666 (ttp-170) REVERT: B 141 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8795 (tppp) outliers start: 27 outliers final: 14 residues processed: 98 average time/residue: 0.4800 time to fit residues: 51.0941 Evaluate side-chains 85 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.116345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081195 restraints weight = 17458.563| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.44 r_work: 0.3008 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10262 Z= 0.135 Angle : 0.582 8.913 14239 Z= 0.299 Chirality : 0.039 0.230 1613 Planarity : 0.005 0.055 1552 Dihedral : 19.517 163.521 2327 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.12 % Allowed : 26.09 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1007 helix: 1.52 (0.27), residues: 373 sheet: -0.35 (0.36), residues: 219 loop : -1.36 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 420 TYR 0.023 0.001 TYR B 499 PHE 0.027 0.001 PHE A 340 TRP 0.014 0.002 TRP A 547 HIS 0.002 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10262) covalent geometry : angle 0.58157 / 0.30 (14239) hydrogen bonds : bond 0.04499 / 3.31 ( 430) hydrogen bonds : angle 4.58379 / 3.25 ( 1163) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.358 Fit side-chains REVERT: A 395 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7809 (t0) REVERT: A 434 CYS cc_start: 0.8181 (t) cc_final: 0.7168 (t) REVERT: A 442 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7660 (ttm110) REVERT: B 74 ASN cc_start: 0.8717 (p0) cc_final: 0.8487 (p0) REVERT: B 141 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8839 (tppp) REVERT: B 406 MET cc_start: 0.5536 (pmm) cc_final: 0.5092 (pp-130) outliers start: 28 outliers final: 16 residues processed: 97 average time/residue: 0.5007 time to fit residues: 52.7607 Evaluate side-chains 89 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 0.0470 chunk 86 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.116264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081156 restraints weight = 17431.101| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.44 r_work: 0.3008 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10262 Z= 0.134 Angle : 0.601 9.957 14239 Z= 0.305 Chirality : 0.039 0.229 1613 Planarity : 0.005 0.055 1552 Dihedral : 19.491 163.564 2327 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.12 % Allowed : 26.64 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.26), residues: 1007 helix: 1.55 (0.27), residues: 373 sheet: -0.35 (0.36), residues: 219 loop : -1.37 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 177 TYR 0.023 0.001 TYR B 499 PHE 0.026 0.001 PHE A 340 TRP 0.014 0.002 TRP A 547 HIS 0.002 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10262) covalent geometry : angle 0.60053 / 0.30 (14239) hydrogen bonds : bond 0.04427 / 3.26 ( 430) hydrogen bonds : angle 4.55407 / 3.23 ( 1163) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.351 Fit side-chains REVERT: A 395 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7846 (t0) REVERT: A 421 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9094 (mmmm) REVERT: A 434 CYS cc_start: 0.8182 (t) cc_final: 0.7156 (t) REVERT: A 442 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7730 (ttm110) REVERT: B 141 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8786 (tppp) REVERT: B 406 MET cc_start: 0.5450 (pmm) cc_final: 0.5083 (pp-130) REVERT: B 451 PHE cc_start: 0.8260 (m-80) cc_final: 0.7907 (m-10) outliers start: 28 outliers final: 15 residues processed: 95 average time/residue: 0.4853 time to fit residues: 50.2571 Evaluate side-chains 88 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.116469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080541 restraints weight = 17329.595| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.49 r_work: 0.3007 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10262 Z= 0.138 Angle : 0.596 9.161 14239 Z= 0.304 Chirality : 0.039 0.229 1613 Planarity : 0.005 0.056 1552 Dihedral : 19.464 163.756 2327 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.56 % Allowed : 27.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1007 helix: 1.53 (0.27), residues: 373 sheet: -0.32 (0.36), residues: 219 loop : -1.38 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 420 TYR 0.023 0.001 TYR B 499 PHE 0.026 0.001 PHE A 340 TRP 0.015 0.002 TRP A 547 HIS 0.005 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10262) covalent geometry : angle 0.59581 / 0.30 (14239) hydrogen bonds : bond 0.04424 / 3.25 ( 430) hydrogen bonds : angle 4.53873 / 3.22 ( 1163) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.280 Fit side-chains REVERT: A 217 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6666 (t-170) REVERT: A 395 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7781 (t0) REVERT: A 421 LYS cc_start: 0.9450 (mmmm) cc_final: 0.9073 (mmmm) REVERT: A 434 CYS cc_start: 0.8194 (t) cc_final: 0.7179 (t) REVERT: A 442 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7489 (ttp-170) REVERT: A 453 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: B 74 ASN cc_start: 0.8780 (p0) cc_final: 0.8564 (p0) REVERT: B 396 MET cc_start: 0.7716 (tmt) cc_final: 0.7486 (tmm) REVERT: B 406 MET cc_start: 0.5490 (pmm) cc_final: 0.5121 (pp-130) REVERT: B 451 PHE cc_start: 0.8282 (m-80) cc_final: 0.7922 (m-10) outliers start: 23 outliers final: 13 residues processed: 94 average time/residue: 0.5142 time to fit residues: 52.3742 Evaluate side-chains 87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080693 restraints weight = 17451.759| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.55 r_work: 0.3016 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10262 Z= 0.129 Angle : 0.611 11.256 14239 Z= 0.307 Chirality : 0.040 0.343 1613 Planarity : 0.005 0.056 1552 Dihedral : 19.448 163.660 2327 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.45 % Allowed : 27.31 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1007 helix: 1.54 (0.27), residues: 373 sheet: -0.29 (0.37), residues: 219 loop : -1.36 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 420 TYR 0.022 0.001 TYR B 499 PHE 0.025 0.001 PHE A 340 TRP 0.014 0.002 TRP A 547 HIS 0.006 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10262) covalent geometry : angle 0.61059 / 0.31 (14239) hydrogen bonds : bond 0.04341 / 3.20 ( 430) hydrogen bonds : angle 4.50554 / 3.20 ( 1163) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.285 Fit side-chains REVERT: A 395 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7732 (t0) REVERT: A 421 LYS cc_start: 0.9440 (mmmm) cc_final: 0.9126 (mmmm) REVERT: A 434 CYS cc_start: 0.8141 (t) cc_final: 0.7607 (t) REVERT: A 442 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7478 (ttp-170) REVERT: B 74 ASN cc_start: 0.8765 (p0) cc_final: 0.8553 (p0) REVERT: B 88 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8875 (ttmt) REVERT: B 161 ARG cc_start: 0.8394 (mtm180) cc_final: 0.8075 (mtm180) REVERT: B 396 MET cc_start: 0.7763 (tmt) cc_final: 0.7504 (tmm) REVERT: B 406 MET cc_start: 0.5478 (pmm) cc_final: 0.5231 (pp-130) REVERT: B 451 PHE cc_start: 0.8291 (m-80) cc_final: 0.7933 (m-10) outliers start: 22 outliers final: 13 residues processed: 98 average time/residue: 0.5174 time to fit residues: 54.7196 Evaluate side-chains 85 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.0270 chunk 102 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.115915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.080224 restraints weight = 17243.045| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.45 r_work: 0.2997 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10262 Z= 0.166 Angle : 0.625 12.716 14239 Z= 0.316 Chirality : 0.041 0.376 1613 Planarity : 0.005 0.057 1552 Dihedral : 19.438 164.211 2327 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.01 % Allowed : 27.98 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1007 helix: 1.51 (0.26), residues: 373 sheet: -0.25 (0.37), residues: 220 loop : -1.36 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.023 0.001 TYR B 499 PHE 0.032 0.002 PHE A 340 TRP 0.021 0.003 TRP B 547 HIS 0.004 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (10262) covalent geometry : angle 0.62538 / 0.32 (14239) hydrogen bonds : bond 0.04492 / 3.29 ( 430) hydrogen bonds : angle 4.57192 / 3.25 ( 1163) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.311 Fit side-chains REVERT: A 395 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7763 (t0) REVERT: A 434 CYS cc_start: 0.8093 (t) cc_final: 0.7277 (t) REVERT: A 442 ARG cc_start: 0.7943 (ttp-110) cc_final: 0.7432 (ttp-170) REVERT: A 499 TYR cc_start: 0.8195 (m-80) cc_final: 0.7990 (m-80) REVERT: B 74 ASN cc_start: 0.8777 (p0) cc_final: 0.8565 (p0) REVERT: B 88 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8882 (ttmt) REVERT: B 161 ARG cc_start: 0.8446 (mtm180) cc_final: 0.8126 (mtm180) REVERT: B 406 MET cc_start: 0.5485 (pmm) cc_final: 0.5091 (pp-130) REVERT: B 420 ARG cc_start: 0.8726 (tmm160) cc_final: 0.8268 (tmt-80) REVERT: B 451 PHE cc_start: 0.8313 (m-80) cc_final: 0.7956 (m-10) outliers start: 18 outliers final: 13 residues processed: 83 average time/residue: 0.5042 time to fit residues: 45.2840 Evaluate side-chains 84 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 434 CYS Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 554 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 0.0470 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.081238 restraints weight = 17464.344| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.49 r_work: 0.3019 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10262 Z= 0.127 Angle : 0.633 14.157 14239 Z= 0.314 Chirality : 0.040 0.363 1613 Planarity : 0.005 0.056 1552 Dihedral : 19.434 163.704 2327 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.67 % Allowed : 28.32 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.26), residues: 1007 helix: 1.53 (0.26), residues: 373 sheet: -0.28 (0.37), residues: 220 loop : -1.35 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 420 TYR 0.022 0.001 TYR B 499 PHE 0.028 0.001 PHE A 340 TRP 0.012 0.002 TRP A 547 HIS 0.004 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10262) covalent geometry : angle 0.63269 / 0.31 (14239) hydrogen bonds : bond 0.04307 / 3.18 ( 430) hydrogen bonds : angle 4.50826 / 3.20 ( 1163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.33 seconds wall clock time: 42 minutes 35.34 seconds (2555.34 seconds total)