Starting phenix.real_space_refine on Sat Aug 3 14:16:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6d_37321/08_2024/8w6d_37321.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6d_37321/08_2024/8w6d_37321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6d_37321/08_2024/8w6d_37321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6d_37321/08_2024/8w6d_37321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6d_37321/08_2024/8w6d_37321.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6d_37321/08_2024/8w6d_37321.cif" } resolution = 2.5 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= -0.000 sd= 0.006 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 2 5.49 5 S 56 5.16 5 Na 2 4.78 5 C 5566 2.51 5 N 1286 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "B ASP 530": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8304 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4068 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 495} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4068 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 495} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' NA': 1, '3PH': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' NA': 1, '3PH': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.28, per 1000 atoms: 0.64 Number of scatterers: 8304 At special positions: 0 Unit cell: (88.047, 107.613, 89.134, 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 2 15.00 Na 2 11.00 O 1392 8.00 N 1286 7.00 C 5566 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 - 3.50 Amino acid : False - 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: 3.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 77.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.725A pdb=" N LEU A 8 " --> pdb=" O CYS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 33 through 52 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 70 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.667A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.567A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.781A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 Processing helix chain 'A' and resid 140 through 163 Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.661A pdb=" N SER A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.969A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 290 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 305 through 322 removed outlier: 3.695A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 346 removed outlier: 3.512A pdb=" N THR A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.933A pdb=" N PHE A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.641A pdb=" N VAL A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 453 Proline residue: A 450 - end of helix removed outlier: 4.309A pdb=" N SER A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 453' Processing helix chain 'A' and resid 455 through 474 removed outlier: 3.625A pdb=" N ALA A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.655A pdb=" N LEU A 484 " --> pdb=" O THR A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.523A pdb=" N ILE A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 509 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.519A pdb=" N VAL A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 556 removed outlier: 3.540A pdb=" N MET A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.621A pdb=" N GLN A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 3.726A pdb=" N LEU B 8 " --> pdb=" O CYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 24 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 33 through 52 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 62 through 70 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.667A pdb=" N VAL B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.567A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.781A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 136 Processing helix chain 'B' and resid 140 through 163 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 214 through 232 removed outlier: 3.660A pdb=" N SER B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 240 through 254 removed outlier: 3.968A pdb=" N LEU B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 290 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.695A pdb=" N GLN B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 346 removed outlier: 3.512A pdb=" N THR B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.934A pdb=" N PHE B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.641A pdb=" N VAL B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 453 Proline residue: B 450 - end of helix removed outlier: 4.309A pdb=" N SER B 453 " --> pdb=" O PRO B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 447 through 453' Processing helix chain 'B' and resid 455 through 474 removed outlier: 3.625A pdb=" N ALA B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 461 " --> pdb=" O PRO B 457 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 494 removed outlier: 3.656A pdb=" N LEU B 484 " --> pdb=" O THR B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 3.524A pdb=" N ILE B 494 " --> pdb=" O MET B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 509 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.519A pdb=" N VAL B 525 " --> pdb=" O PRO B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 556 removed outlier: 3.540A pdb=" N MET B 536 " --> pdb=" O LYS B 532 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.621A pdb=" N GLN B 573 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA2, first strand: chain 'B' and resid 392 through 393 501 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1305 1.32 - 1.44: 2218 1.44 - 1.56: 4915 1.56 - 1.69: 2 1.69 - 1.81: 92 Bond restraints: 8532 Sorted by residual: bond pdb=" O11 3PH A 802 " pdb=" P 3PH A 802 " ideal model delta sigma weight residual 1.703 1.611 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" O11 3PH B 802 " pdb=" P 3PH B 802 " ideal model delta sigma weight residual 1.703 1.612 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C1 3PH B 802 " pdb=" O11 3PH B 802 " ideal model delta sigma weight residual 1.385 1.451 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1 3PH A 802 " pdb=" O11 3PH A 802 " ideal model delta sigma weight residual 1.385 1.451 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C PRO B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.334 1.369 -0.035 1.51e-02 4.39e+03 5.35e+00 ... (remaining 8527 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.79: 255 105.79 - 112.89: 4564 112.89 - 119.98: 3267 119.98 - 127.08: 3405 127.08 - 134.17: 161 Bond angle restraints: 11652 Sorted by residual: angle pdb=" N PRO A 520 " pdb=" CA PRO A 520 " pdb=" C PRO A 520 " ideal model delta sigma weight residual 110.70 117.59 -6.89 1.22e+00 6.72e-01 3.19e+01 angle pdb=" N PRO B 520 " pdb=" CA PRO B 520 " pdb=" C PRO B 520 " ideal model delta sigma weight residual 110.70 117.57 -6.87 1.22e+00 6.72e-01 3.17e+01 angle pdb=" CA THR A 519 " pdb=" CB THR A 519 " pdb=" CG2 THR A 519 " ideal model delta sigma weight residual 110.50 118.13 -7.63 1.70e+00 3.46e-01 2.02e+01 angle pdb=" CA THR B 519 " pdb=" CB THR B 519 " pdb=" CG2 THR B 519 " ideal model delta sigma weight residual 110.50 118.10 -7.60 1.70e+00 3.46e-01 2.00e+01 angle pdb=" C SER A 557 " pdb=" N TRP A 558 " pdb=" CA TRP A 558 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 ... (remaining 11647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4634 17.13 - 34.25: 370 34.25 - 51.38: 80 51.38 - 68.51: 14 68.51 - 85.63: 8 Dihedral angle restraints: 5106 sinusoidal: 2050 harmonic: 3056 Sorted by residual: dihedral pdb=" CA GLU A 302 " pdb=" C GLU A 302 " pdb=" N LYS A 303 " pdb=" CA LYS A 303 " ideal model delta harmonic sigma weight residual 180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU B 302 " pdb=" C GLU B 302 " pdb=" N LYS B 303 " pdb=" CA LYS B 303 " ideal model delta harmonic sigma weight residual 180.00 -159.91 -20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ALA B 512 " pdb=" C ALA B 512 " pdb=" N PHE B 513 " pdb=" CA PHE B 513 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1049 0.062 - 0.124: 276 0.124 - 0.185: 52 0.185 - 0.247: 11 0.247 - 0.309: 4 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA THR A 519 " pdb=" N THR A 519 " pdb=" C THR A 519 " pdb=" CB THR A 519 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA THR B 519 " pdb=" N THR B 519 " pdb=" C THR B 519 " pdb=" CB THR B 519 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CBE Y01 A 803 " pdb=" CAP Y01 A 803 " pdb=" CBB Y01 A 803 " pdb=" CBI Y01 A 803 " both_signs ideal model delta sigma weight residual False 2.57 2.32 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1389 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 25 " -0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO B 26 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 25 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 26 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 67 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO A 68 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.038 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2962 2.89 - 3.39: 8074 3.39 - 3.90: 13776 3.90 - 4.40: 15511 4.40 - 4.90: 26347 Nonbonded interactions: 66670 Sorted by model distance: nonbonded pdb=" O VAL A 467 " pdb=" OG1 THR A 471 " model vdw 2.391 3.040 nonbonded pdb=" O VAL B 467 " pdb=" OG1 THR B 471 " model vdw 2.392 3.040 nonbonded pdb=" OG SER B 33 " pdb=" OE1 GLU B 35 " model vdw 2.414 3.040 nonbonded pdb=" OG SER A 33 " pdb=" OE1 GLU A 35 " model vdw 2.415 3.040 nonbonded pdb=" O TRP A 9 " pdb=" NH1 ARG A 12 " model vdw 2.422 3.120 ... (remaining 66665 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' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.009 0.092 8532 Z= 0.607 Angle : 1.076 12.515 11652 Z= 0.580 Chirality : 0.062 0.309 1392 Planarity : 0.009 0.067 1402 Dihedral : 13.667 85.633 3122 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.95 % Favored : 94.86 % Rotamer: Outliers : 0.23 % Allowed : 2.85 % Favored : 96.92 % 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: -2.77 (0.22), residues: 1050 helix: -1.06 (0.16), residues: 726 sheet: -4.33 (0.46), residues: 20 loop : -3.36 (0.30), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 410 HIS 0.008 0.002 HIS A 566 PHE 0.043 0.003 PHE B 344 TYR 0.011 0.002 TYR A 500 ARG 0.006 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.943 Fit side-chains REVERT: A 70 MET cc_start: 0.8160 (mtm) cc_final: 0.7951 (mtp) REVERT: A 137 MET cc_start: 0.8884 (mtp) cc_final: 0.8647 (mtp) REVERT: A 303 LYS cc_start: 0.7143 (tttm) cc_final: 0.6850 (tttp) REVERT: A 318 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 344 PHE cc_start: 0.7876 (m-80) cc_final: 0.7605 (t80) REVERT: A 417 MET cc_start: 0.9113 (tpp) cc_final: 0.8862 (tpp) REVERT: A 490 MET cc_start: 0.8214 (tmm) cc_final: 0.7771 (tmm) REVERT: B 70 MET cc_start: 0.8159 (mtm) cc_final: 0.7922 (mtp) REVERT: B 137 MET cc_start: 0.8883 (mtp) cc_final: 0.8651 (mtp) REVERT: B 303 LYS cc_start: 0.7133 (tttm) cc_final: 0.6840 (tttp) REVERT: B 318 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7406 (tp30) REVERT: B 344 PHE cc_start: 0.7877 (m-80) cc_final: 0.7606 (t80) REVERT: B 417 MET cc_start: 0.9113 (tpp) cc_final: 0.8870 (tpp) REVERT: B 490 MET cc_start: 0.8214 (tmm) cc_final: 0.7769 (tmm) outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 1.5188 time to fit residues: 201.1378 Evaluate side-chains 100 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 243 ASN A 257 ASN A 297 ASN A 305 GLN A 319 HIS A 356 ASN A 397 ASN A 414 ASN B 243 ASN B 257 ASN B 297 ASN B 305 GLN B 356 ASN B 397 ASN B 414 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8532 Z= 0.188 Angle : 0.622 7.611 11652 Z= 0.321 Chirality : 0.042 0.170 1392 Planarity : 0.006 0.057 1402 Dihedral : 9.602 58.436 1322 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.14 % Allowed : 8.79 % Favored : 90.07 % 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: -0.21 (0.26), residues: 1050 helix: 0.97 (0.19), residues: 748 sheet: -4.19 (0.48), residues: 20 loop : -2.87 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 558 HIS 0.002 0.001 HIS B 566 PHE 0.015 0.001 PHE A 344 TYR 0.005 0.001 TYR B 11 ARG 0.001 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.849 Fit side-chains REVERT: A 163 GLN cc_start: 0.7543 (mt0) cc_final: 0.7271 (mt0) REVERT: A 303 LYS cc_start: 0.7077 (tttm) cc_final: 0.6498 (ttpp) REVERT: A 318 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 325 MET cc_start: 0.8726 (mtp) cc_final: 0.8437 (mtp) REVERT: A 490 MET cc_start: 0.8137 (tmm) cc_final: 0.7678 (tmm) REVERT: B 163 GLN cc_start: 0.7543 (mt0) cc_final: 0.7274 (mt0) REVERT: B 303 LYS cc_start: 0.7067 (tttm) cc_final: 0.6492 (ttpp) REVERT: B 318 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7402 (tp30) REVERT: B 325 MET cc_start: 0.8728 (mtp) cc_final: 0.8440 (mtp) REVERT: B 490 MET cc_start: 0.8137 (tmm) cc_final: 0.7676 (tmm) outliers start: 10 outliers final: 4 residues processed: 113 average time/residue: 1.2734 time to fit residues: 152.5592 Evaluate side-chains 99 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8532 Z= 0.186 Angle : 0.600 7.579 11652 Z= 0.307 Chirality : 0.042 0.171 1392 Planarity : 0.006 0.058 1402 Dihedral : 9.481 58.000 1322 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.28 % Allowed : 7.99 % Favored : 89.73 % 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: 0.78 (0.27), residues: 1050 helix: 1.77 (0.19), residues: 748 sheet: -4.11 (0.52), residues: 20 loop : -2.70 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 410 HIS 0.002 0.001 HIS B 566 PHE 0.011 0.001 PHE A 568 TYR 0.006 0.001 TYR A 500 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.845 Fit side-chains REVERT: A 70 MET cc_start: 0.8283 (mtm) cc_final: 0.7985 (mtp) REVERT: A 163 GLN cc_start: 0.7441 (mt0) cc_final: 0.7147 (mt0) REVERT: A 303 LYS cc_start: 0.7053 (tttm) cc_final: 0.6632 (tttp) REVERT: A 304 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7371 (mmt) REVERT: A 318 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7405 (tp30) REVERT: A 490 MET cc_start: 0.8079 (tmm) cc_final: 0.7694 (tmm) REVERT: B 70 MET cc_start: 0.8283 (mtm) cc_final: 0.7989 (mtp) REVERT: B 163 GLN cc_start: 0.7453 (mt0) cc_final: 0.7162 (mt0) REVERT: B 303 LYS cc_start: 0.7045 (tttm) cc_final: 0.6625 (tttp) REVERT: B 304 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7372 (mmt) REVERT: B 490 MET cc_start: 0.8077 (tmm) cc_final: 0.7694 (tmm) outliers start: 20 outliers final: 8 residues processed: 110 average time/residue: 1.4048 time to fit residues: 163.3921 Evaluate side-chains 108 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.0070 chunk 83 optimal weight: 6.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8532 Z= 0.190 Angle : 0.611 9.792 11652 Z= 0.305 Chirality : 0.042 0.160 1392 Planarity : 0.005 0.059 1402 Dihedral : 9.513 59.619 1322 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.51 % Allowed : 8.68 % Favored : 88.81 % 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: 1.17 (0.28), residues: 1050 helix: 2.05 (0.20), residues: 748 sheet: -4.10 (0.53), residues: 20 loop : -2.54 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 410 HIS 0.002 0.001 HIS A 566 PHE 0.012 0.001 PHE B 568 TYR 0.006 0.001 TYR A 500 ARG 0.001 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.899 Fit side-chains REVERT: A 70 MET cc_start: 0.8292 (mtm) cc_final: 0.8017 (mtp) REVERT: A 163 GLN cc_start: 0.7374 (mt0) cc_final: 0.7038 (mt0) REVERT: A 295 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: A 303 LYS cc_start: 0.6838 (tttm) cc_final: 0.6479 (tttp) REVERT: A 304 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7386 (mmt) REVERT: A 318 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7407 (tp30) REVERT: A 490 MET cc_start: 0.8064 (tmm) cc_final: 0.7775 (tmm) REVERT: B 70 MET cc_start: 0.8293 (mtm) cc_final: 0.8023 (mtp) REVERT: B 101 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: B 163 GLN cc_start: 0.7372 (mt0) cc_final: 0.7043 (mt0) REVERT: B 295 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7186 (mtp180) REVERT: B 303 LYS cc_start: 0.6833 (tttm) cc_final: 0.6473 (tttp) REVERT: B 304 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7385 (mmt) REVERT: B 490 MET cc_start: 0.8061 (tmm) cc_final: 0.7772 (tmm) outliers start: 22 outliers final: 6 residues processed: 109 average time/residue: 1.2282 time to fit residues: 142.3411 Evaluate side-chains 108 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8532 Z= 0.189 Angle : 0.603 7.941 11652 Z= 0.304 Chirality : 0.043 0.241 1392 Planarity : 0.005 0.059 1402 Dihedral : 9.546 58.126 1322 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.28 % Allowed : 9.36 % Favored : 88.36 % 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: 1.43 (0.28), residues: 1050 helix: 2.24 (0.20), residues: 748 sheet: -4.00 (0.58), residues: 20 loop : -2.41 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 410 HIS 0.002 0.001 HIS B 566 PHE 0.013 0.001 PHE B 568 TYR 0.006 0.001 TYR A 500 ARG 0.002 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.909 Fit side-chains REVERT: A 70 MET cc_start: 0.8249 (mtm) cc_final: 0.7973 (mtp) REVERT: A 163 GLN cc_start: 0.7309 (mt0) cc_final: 0.6989 (mt0) REVERT: A 303 LYS cc_start: 0.6773 (tttm) cc_final: 0.6400 (tttp) REVERT: A 304 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7371 (mmt) REVERT: A 318 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7290 (tp30) REVERT: A 490 MET cc_start: 0.7994 (tmm) cc_final: 0.7711 (tmm) REVERT: B 70 MET cc_start: 0.8251 (mtm) cc_final: 0.7976 (mtp) REVERT: B 101 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: B 163 GLN cc_start: 0.7309 (mt0) cc_final: 0.6993 (mt0) REVERT: B 295 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7128 (mtp180) REVERT: B 303 LYS cc_start: 0.6766 (tttm) cc_final: 0.6393 (tttp) REVERT: B 304 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7368 (mmt) REVERT: B 490 MET cc_start: 0.7994 (tmm) cc_final: 0.7710 (tmm) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 1.3481 time to fit residues: 155.7866 Evaluate side-chains 110 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 0.0170 chunk 24 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.0030 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8532 Z= 0.188 Angle : 0.600 8.219 11652 Z= 0.302 Chirality : 0.043 0.231 1392 Planarity : 0.005 0.059 1402 Dihedral : 9.523 56.799 1322 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.05 % Allowed : 9.25 % Favored : 88.70 % 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: 1.56 (0.28), residues: 1050 helix: 2.32 (0.20), residues: 748 sheet: -3.87 (0.63), residues: 20 loop : -2.34 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 410 HIS 0.002 0.001 HIS A 497 PHE 0.011 0.001 PHE A 568 TYR 0.006 0.001 TYR B 500 ARG 0.002 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.955 Fit side-chains REVERT: A 18 PHE cc_start: 0.8026 (t80) cc_final: 0.7537 (m-80) REVERT: A 101 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: A 163 GLN cc_start: 0.7256 (mt0) cc_final: 0.7003 (mt0) REVERT: A 295 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7016 (mtp180) REVERT: A 303 LYS cc_start: 0.6747 (tttm) cc_final: 0.6375 (tttp) REVERT: A 304 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7336 (mmt) REVERT: A 318 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7296 (tp30) REVERT: A 490 MET cc_start: 0.8003 (tmm) cc_final: 0.7723 (tmm) REVERT: B 18 PHE cc_start: 0.8015 (t80) cc_final: 0.7531 (m-80) REVERT: B 101 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: B 163 GLN cc_start: 0.7256 (mt0) cc_final: 0.6966 (mt0) REVERT: B 295 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7089 (mtp180) REVERT: B 303 LYS cc_start: 0.6742 (tttm) cc_final: 0.6369 (tttp) REVERT: B 304 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7336 (mmt) REVERT: B 490 MET cc_start: 0.8000 (tmm) cc_final: 0.7721 (tmm) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 1.2367 time to fit residues: 135.5132 Evaluate side-chains 111 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 59 optimal weight: 0.0470 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8532 Z= 0.172 Angle : 0.577 7.571 11652 Z= 0.291 Chirality : 0.042 0.230 1392 Planarity : 0.005 0.060 1402 Dihedral : 9.338 56.112 1322 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.17 % Allowed : 9.13 % Favored : 88.70 % 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: 1.64 (0.28), residues: 1050 helix: 2.40 (0.19), residues: 756 sheet: -3.75 (0.66), residues: 20 loop : -2.51 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 410 HIS 0.002 0.001 HIS A 497 PHE 0.010 0.001 PHE B 351 TYR 0.006 0.001 TYR B 40 ARG 0.002 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.858 Fit side-chains REVERT: A 18 PHE cc_start: 0.7949 (t80) cc_final: 0.7547 (m-80) REVERT: A 163 GLN cc_start: 0.7187 (mt0) cc_final: 0.6931 (mt0) REVERT: A 303 LYS cc_start: 0.6576 (tttm) cc_final: 0.6251 (tttp) REVERT: A 304 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7359 (mmt) REVERT: A 318 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7299 (tp30) REVERT: A 490 MET cc_start: 0.7973 (tmm) cc_final: 0.7699 (tmm) REVERT: B 18 PHE cc_start: 0.7919 (t80) cc_final: 0.7505 (m-80) REVERT: B 70 MET cc_start: 0.8377 (mtm) cc_final: 0.8137 (mtp) REVERT: B 163 GLN cc_start: 0.7191 (mt0) cc_final: 0.6935 (mt0) REVERT: B 303 LYS cc_start: 0.6568 (tttm) cc_final: 0.6240 (tttp) REVERT: B 304 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7359 (mmt) REVERT: B 490 MET cc_start: 0.7973 (tmm) cc_final: 0.7698 (tmm) outliers start: 19 outliers final: 8 residues processed: 110 average time/residue: 1.2639 time to fit residues: 147.8700 Evaluate side-chains 108 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN B 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8532 Z= 0.395 Angle : 0.770 9.759 11652 Z= 0.385 Chirality : 0.050 0.223 1392 Planarity : 0.006 0.061 1402 Dihedral : 10.547 58.871 1322 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 1.94 % Allowed : 9.70 % Favored : 88.36 % 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: 1.01 (0.27), residues: 1050 helix: 1.64 (0.19), residues: 780 sheet: -3.51 (0.70), residues: 20 loop : -2.16 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 410 HIS 0.005 0.002 HIS A 566 PHE 0.021 0.003 PHE B 568 TYR 0.014 0.002 TYR A 500 ARG 0.004 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.936 Fit side-chains REVERT: A 18 PHE cc_start: 0.8041 (t80) cc_final: 0.7617 (m-80) REVERT: A 163 GLN cc_start: 0.7477 (mt0) cc_final: 0.7166 (mt0) REVERT: A 295 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7182 (mtp180) REVERT: A 303 LYS cc_start: 0.6698 (tttm) cc_final: 0.6306 (tttp) REVERT: A 318 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7293 (tp30) REVERT: A 490 MET cc_start: 0.8053 (tmm) cc_final: 0.7826 (tmm) REVERT: B 18 PHE cc_start: 0.8061 (t80) cc_final: 0.7599 (m-80) REVERT: B 70 MET cc_start: 0.8425 (mtm) cc_final: 0.8147 (mtp) REVERT: B 163 GLN cc_start: 0.7473 (mt0) cc_final: 0.7164 (mt0) REVERT: B 295 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7216 (mtp180) REVERT: B 303 LYS cc_start: 0.6693 (tttm) cc_final: 0.6302 (tttp) REVERT: B 490 MET cc_start: 0.8053 (tmm) cc_final: 0.7821 (tmm) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 1.2771 time to fit residues: 139.6793 Evaluate side-chains 107 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.0000 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8532 Z= 0.194 Angle : 0.613 7.928 11652 Z= 0.311 Chirality : 0.043 0.216 1392 Planarity : 0.005 0.059 1402 Dihedral : 10.086 57.535 1322 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.14 % Allowed : 10.96 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.28), residues: 1050 helix: 2.12 (0.19), residues: 772 sheet: -3.56 (0.71), residues: 20 loop : -2.25 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 410 HIS 0.003 0.001 HIS A 160 PHE 0.013 0.001 PHE B 568 TYR 0.007 0.001 TYR A 40 ARG 0.002 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.968 Fit side-chains REVERT: A 18 PHE cc_start: 0.7960 (t80) cc_final: 0.7527 (m-80) REVERT: A 163 GLN cc_start: 0.7271 (mt0) cc_final: 0.6958 (mt0) REVERT: A 303 LYS cc_start: 0.6654 (tttm) cc_final: 0.6269 (tttp) REVERT: A 318 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7279 (tp30) REVERT: A 490 MET cc_start: 0.8023 (tmm) cc_final: 0.7750 (tmm) REVERT: B 18 PHE cc_start: 0.7949 (t80) cc_final: 0.7517 (m-80) REVERT: B 163 GLN cc_start: 0.7294 (mt0) cc_final: 0.6985 (mt0) REVERT: B 295 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7119 (mtp180) REVERT: B 303 LYS cc_start: 0.6648 (tttm) cc_final: 0.6262 (tttp) REVERT: B 490 MET cc_start: 0.8001 (tmm) cc_final: 0.7720 (tmm) outliers start: 10 outliers final: 9 residues processed: 97 average time/residue: 1.2971 time to fit residues: 133.9449 Evaluate side-chains 102 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8532 Z= 0.180 Angle : 0.586 7.692 11652 Z= 0.296 Chirality : 0.042 0.227 1392 Planarity : 0.005 0.057 1402 Dihedral : 9.699 56.840 1322 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.26 % Allowed : 11.07 % Favored : 87.67 % 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: 1.78 (0.28), residues: 1050 helix: 2.41 (0.20), residues: 756 sheet: -3.52 (0.71), residues: 20 loop : -2.18 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 410 HIS 0.003 0.001 HIS A 160 PHE 0.010 0.001 PHE B 351 TYR 0.007 0.001 TYR A 40 ARG 0.004 0.000 ARG A 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.060 Fit side-chains REVERT: A 18 PHE cc_start: 0.7889 (t80) cc_final: 0.7487 (m-80) REVERT: A 163 GLN cc_start: 0.7298 (mt0) cc_final: 0.7045 (mt0) REVERT: A 295 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6965 (mtp180) REVERT: A 303 LYS cc_start: 0.6646 (tttm) cc_final: 0.6269 (tttp) REVERT: A 318 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7279 (tp30) REVERT: A 490 MET cc_start: 0.7970 (tmm) cc_final: 0.7701 (tmm) REVERT: B 18 PHE cc_start: 0.7889 (t80) cc_final: 0.7453 (m-80) REVERT: B 163 GLN cc_start: 0.7297 (mt0) cc_final: 0.7049 (mt0) REVERT: B 295 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7068 (mtp180) REVERT: B 303 LYS cc_start: 0.6637 (tttm) cc_final: 0.6261 (tttp) REVERT: B 490 MET cc_start: 0.7967 (tmm) cc_final: 0.7697 (tmm) outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 1.3526 time to fit residues: 148.2050 Evaluate side-chains 108 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.093242 restraints weight = 9579.817| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.37 r_work: 0.2875 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8532 Z= 0.223 Angle : 0.630 8.195 11652 Z= 0.318 Chirality : 0.044 0.216 1392 Planarity : 0.005 0.060 1402 Dihedral : 9.913 56.699 1322 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.60 % Allowed : 11.07 % Favored : 87.33 % 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: 1.66 (0.28), residues: 1050 helix: 2.22 (0.19), residues: 770 sheet: -3.47 (0.74), residues: 20 loop : -2.13 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 410 HIS 0.006 0.001 HIS B 160 PHE 0.015 0.002 PHE B 568 TYR 0.009 0.001 TYR A 500 ARG 0.003 0.000 ARG B 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.53 seconds wall clock time: 55 minutes 59.20 seconds (3359.20 seconds total)