Starting phenix.real_space_refine on Fri Sep 11 11:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hbu_0190/09_2026/6hbu_0190.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hbu_0190/09_2026/6hbu_0190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2026/6hbu_0190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2026/6hbu_0190.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2026/6hbu_0190.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2026/6hbu_0190.cif" model { file = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2026/6hbu_0190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2026/6hbu_0190.cif" } resolution = 3.09 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= 0.001 sd= 0.011 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 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5910 2.51 5 N 1512 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9146 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4541 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 20, 'TRANS': 563} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 3.77, per 1000 atoms: 0.41 Number of scatterers: 9146 At special positions: 0 Unit cell: (81.81, 89.91, 132.84, 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 58 16.00 P 6 15.00 Mg 2 11.99 O 1658 8.00 N 1512 7.00 C 5910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.01 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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: 0.75 Conformation dependent library (CDL) restraints added in 333.4 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 57.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.542A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.761A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.694A pdb=" N ASN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.718A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.819A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.506A pdb=" N ARG A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 413 Processing helix chain 'A' and resid 422 through 440 removed outlier: 4.106A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 removed outlier: 3.782A pdb=" N GLU A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 448 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.651A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.767A pdb=" N PHE A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 529 removed outlier: 3.791A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.690A pdb=" N LEU A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.503A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.722A pdb=" N TYR A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.678A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.542A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.762A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.695A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 289 through 298 removed outlier: 3.717A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 308 Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.819A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.506A pdb=" N ARG B 378 " --> pdb=" O CYS B 374 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 413 Processing helix chain 'B' and resid 422 through 440 removed outlier: 4.105A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.782A pdb=" N GLU B 446 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 448 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.652A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.768A pdb=" N PHE B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 529 removed outlier: 3.791A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.690A pdb=" N LEU B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.503A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.723A pdb=" N TYR B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.677A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 640 " --> pdb=" O MET B 636 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.560A pdb=" N ILE A 67 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 41 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.013A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.560A pdb=" N ILE B 67 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN B 41 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.014A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1332 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: 1.54 Time building geometry restraints manager: 0.99 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: 2434 1.33 - 1.45: 1814 1.45 - 1.57: 4984 1.57 - 1.70: 10 1.70 - 1.82: 94 Bond restraints: 9336 Sorted by residual: bond pdb=" C4 ATP B1501 " pdb=" C5 ATP B1501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C5 ATP B1501 " pdb=" C6 ATP B1501 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.06e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.05e+01 bond pdb=" C4 ATP B1501 " pdb=" N9 ATP B1501 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.50e+01 ... (remaining 9331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 12413 3.63 - 7.25: 191 7.25 - 10.88: 38 10.88 - 14.51: 4 14.51 - 18.13: 2 Bond angle restraints: 12648 Sorted by residual: angle pdb=" PB ATP B1501 " pdb=" O3B ATP B1501 " pdb=" PG ATP B1501 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PA ATP B1501 " pdb=" O3A ATP B1501 " pdb=" PB ATP B1501 " ideal model delta sigma weight residual 136.83 123.39 13.44 1.00e+00 1.00e+00 1.81e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 123.43 13.40 1.00e+00 1.00e+00 1.80e+02 angle pdb=" C5 ATP B1501 " pdb=" C4 ATP B1501 " pdb=" N3 ATP B1501 " ideal model delta sigma weight residual 126.80 119.17 7.63 1.00e+00 1.00e+00 5.82e+01 ... (remaining 12643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 5168 15.33 - 30.67: 252 30.67 - 46.00: 74 46.00 - 61.33: 15 61.33 - 76.67: 8 Dihedral angle restraints: 5517 sinusoidal: 2149 harmonic: 3368 Sorted by residual: dihedral pdb=" CA ASN B 604 " pdb=" C ASN B 604 " pdb=" N TYR B 605 " pdb=" CA TYR B 605 " ideal model delta harmonic sigma weight residual 180.00 108.75 71.25 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ASN A 604 " pdb=" C ASN A 604 " pdb=" N TYR A 605 " pdb=" CA TYR A 605 " ideal model delta harmonic sigma weight residual 180.00 108.79 71.21 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ALA B 115 " pdb=" C ALA B 115 " pdb=" N ASN B 116 " pdb=" CA ASN B 116 " ideal model delta harmonic sigma weight residual 180.00 123.00 57.00 0 5.00e+00 4.00e-02 1.30e+02 ... (remaining 5514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1213 0.075 - 0.150: 230 0.150 - 0.226: 14 0.226 - 0.301: 7 0.301 - 0.376: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA GLN B 589 " pdb=" N GLN B 589 " pdb=" C GLN B 589 " pdb=" CB GLN B 589 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA GLN A 589 " pdb=" N GLN A 589 " pdb=" C GLN A 589 " pdb=" CB GLN A 589 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU A 225 " pdb=" CB LEU A 225 " pdb=" CD1 LEU A 225 " pdb=" CD2 LEU A 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1463 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 601 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 602 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 601 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 602 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 602 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 602 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 588 " -0.013 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C GLY A 588 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY A 588 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN A 589 " -0.016 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 50 2.55 - 3.14: 6596 3.14 - 3.73: 13922 3.73 - 4.31: 21187 4.31 - 4.90: 34775 Nonbonded interactions: 76530 Sorted by model distance: nonbonded pdb=" CE LYS B 500 " pdb=" OE1 GLN B 589 " model vdw 1.965 3.440 nonbonded pdb=" CE LYS A 500 " pdb=" OE1 GLN A 589 " model vdw 1.977 3.440 nonbonded pdb=" NH2 ARG B 184 " pdb=" O1A ATP A1501 " model vdw 2.315 3.120 nonbonded pdb=" OG1 THR A 133 " pdb=" ND2 ASN A 387 " model vdw 2.373 3.120 nonbonded pdb=" OG1 THR B 133 " pdb=" ND2 ASN B 387 " model vdw 2.374 3.120 ... (remaining 76525 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: 0.02 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 0.074 9339 Z= 0.409 Angle : 1.178 18.132 12654 Z= 0.683 Chirality : 0.060 0.376 1466 Planarity : 0.008 0.102 1566 Dihedral : 11.063 76.667 3344 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.86 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.71 % 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: -5.40 (0.17), residues: 1152 helix: -4.20 (0.10), residues: 648 sheet: -1.86 (0.42), residues: 76 loop : -2.49 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 96 TYR 0.039 0.003 TYR A 463 PHE 0.032 0.003 PHE A 578 TRP 0.019 0.003 TRP B 624 HIS 0.013 0.003 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00889 / 0.41 ( 9336) covalent geometry : angle 1.17676 / 0.68 (12648) SS BOND : bond 0.01126 / 0.63 ( 3) SS BOND : angle 2.37902 / 1.30 ( 6) hydrogen bonds : bond 0.29836 / 20.23 ( 462) hydrogen bonds : angle 10.32380 / 7.12 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.384 Fit side-chains REVERT: A 251 LYS cc_start: 0.8156 (ttpm) cc_final: 0.7946 (mtpt) REVERT: A 451 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7597 (tt0) REVERT: B 451 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7475 (tt0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1168 time to fit residues: 29.3200 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 211 GLN A 387 ASN A 437 GLN A 557 ASN A 583 HIS B 154 ASN B 211 GLN B 387 ASN B 437 GLN B 531 GLN B 557 ASN B 583 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.138694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.121473 restraints weight = 9842.497| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 0.86 r_work: 0.2985 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9339 Z= 0.131 Angle : 0.685 7.981 12654 Z= 0.358 Chirality : 0.043 0.168 1466 Planarity : 0.006 0.088 1566 Dihedral : 7.897 86.015 1252 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.08 % Favored : 95.75 % Rotamer: Outliers : 1.71 % Allowed : 6.53 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.80 % 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: -2.62 (0.22), residues: 1152 helix: -1.41 (0.18), residues: 640 sheet: -1.51 (0.47), residues: 76 loop : -2.08 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 113 TYR 0.015 0.001 TYR B 605 PHE 0.013 0.001 PHE A 578 TRP 0.010 0.002 TRP B 627 HIS 0.005 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9336) covalent geometry : angle 0.68505 / 0.36 (12648) SS BOND : bond 0.00132 / 0.07 ( 3) SS BOND : angle 1.03124 / 0.56 ( 6) hydrogen bonds : bond 0.04284 / 2.83 ( 462) hydrogen bonds : angle 4.26196 / 3.01 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.365 Fit side-chains REVERT: A 71 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7611 (mtt) REVERT: A 105 ASP cc_start: 0.8173 (p0) cc_final: 0.7931 (p0) REVERT: A 206 ILE cc_start: 0.9012 (mt) cc_final: 0.8657 (mt) REVERT: A 451 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7583 (tt0) REVERT: A 590 ASN cc_start: 0.7948 (t0) cc_final: 0.7737 (t0) REVERT: B 451 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7480 (tt0) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.0847 time to fit residues: 17.4033 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.133021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115255 restraints weight = 9793.983| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 0.86 r_work: 0.2901 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9339 Z= 0.226 Angle : 0.741 8.443 12654 Z= 0.375 Chirality : 0.047 0.174 1466 Planarity : 0.006 0.089 1566 Dihedral : 7.654 84.414 1252 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 2.71 % Allowed : 7.73 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.71 % 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: -1.02 (0.24), residues: 1152 helix: 0.05 (0.20), residues: 642 sheet: -1.14 (0.48), residues: 78 loop : -1.59 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 383 TYR 0.014 0.002 TYR B 463 PHE 0.019 0.002 PHE B 489 TRP 0.011 0.002 TRP A 627 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 ( 9336) covalent geometry : angle 0.74052 / 0.37 (12648) SS BOND : bond 0.00198 / 0.11 ( 3) SS BOND : angle 1.01661 / 0.55 ( 6) hydrogen bonds : bond 0.04257 / 2.85 ( 462) hydrogen bonds : angle 3.98429 / 2.81 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.347 Fit side-chains REVERT: A 71 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8018 (mtp) REVERT: A 105 ASP cc_start: 0.8256 (p0) cc_final: 0.8032 (p0) REVERT: A 451 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7665 (tt0) REVERT: A 590 ASN cc_start: 0.8047 (t0) cc_final: 0.7840 (t0) REVERT: B 451 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7481 (tt0) outliers start: 27 outliers final: 19 residues processed: 126 average time/residue: 0.0965 time to fit residues: 17.4960 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN B 166 GLN B 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.137282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.119611 restraints weight = 9834.121| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 0.86 r_work: 0.2931 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9339 Z= 0.115 Angle : 0.616 7.983 12654 Z= 0.315 Chirality : 0.042 0.155 1466 Planarity : 0.004 0.080 1566 Dihedral : 7.307 83.603 1252 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.11 % Allowed : 10.04 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.71 % 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 (0.25), residues: 1152 helix: 0.93 (0.21), residues: 638 sheet: -0.85 (0.51), residues: 76 loop : -1.37 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.012 0.001 TYR B 605 PHE 0.012 0.001 PHE B 489 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9336) covalent geometry : angle 0.61620 / 0.31 (12648) SS BOND : bond 0.00148 / 0.09 ( 3) SS BOND : angle 0.89800 / 0.52 ( 6) hydrogen bonds : bond 0.03137 / 2.07 ( 462) hydrogen bonds : angle 3.67875 / 2.62 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.367 Fit side-chains REVERT: A 105 ASP cc_start: 0.8211 (p0) cc_final: 0.7901 (p0) REVERT: A 150 THR cc_start: 0.8666 (p) cc_final: 0.8395 (p) REVERT: A 299 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8512 (t0) REVERT: A 451 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7635 (tt0) REVERT: A 590 ASN cc_start: 0.7823 (t0) cc_final: 0.7493 (t0) REVERT: B 105 ASP cc_start: 0.7726 (p0) cc_final: 0.7521 (p0) REVERT: B 451 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7522 (tt0) outliers start: 21 outliers final: 16 residues processed: 117 average time/residue: 0.0897 time to fit residues: 15.4895 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.135280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.117488 restraints weight = 9842.468| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.86 r_work: 0.2930 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9339 Z= 0.158 Angle : 0.633 8.113 12654 Z= 0.321 Chirality : 0.043 0.146 1466 Planarity : 0.005 0.083 1566 Dihedral : 7.179 82.771 1252 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 2.51 % Allowed : 9.84 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.62 % 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: 0.12 (0.25), residues: 1152 helix: 1.13 (0.21), residues: 644 sheet: -0.78 (0.52), residues: 78 loop : -1.35 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.011 0.001 TYR B 605 PHE 0.012 0.001 PHE B 39 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 9336) covalent geometry : angle 0.63328 / 0.32 (12648) SS BOND : bond 0.00137 / 0.08 ( 3) SS BOND : angle 0.72683 / 0.40 ( 6) hydrogen bonds : bond 0.03295 / 2.17 ( 462) hydrogen bonds : angle 3.65977 / 2.61 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.404 Fit side-chains REVERT: A 105 ASP cc_start: 0.8177 (p0) cc_final: 0.7869 (p0) REVERT: A 150 THR cc_start: 0.8634 (p) cc_final: 0.8393 (p) REVERT: A 299 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8569 (t0) REVERT: A 451 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7605 (tt0) REVERT: A 590 ASN cc_start: 0.7792 (t0) cc_final: 0.7501 (t0) REVERT: B 105 ASP cc_start: 0.7714 (p0) cc_final: 0.7467 (p0) REVERT: B 451 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7475 (tt0) outliers start: 25 outliers final: 23 residues processed: 117 average time/residue: 0.0887 time to fit residues: 15.4383 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN B 375 HIS B 589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.134475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.107114 restraints weight = 9567.358| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.39 r_work: 0.2938 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9339 Z= 0.217 Angle : 0.683 8.875 12654 Z= 0.343 Chirality : 0.046 0.189 1466 Planarity : 0.005 0.078 1566 Dihedral : 7.207 82.493 1252 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 3.01 % Allowed : 10.04 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.62 % 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 (0.25), residues: 1152 helix: 1.10 (0.21), residues: 644 sheet: -0.61 (0.52), residues: 78 loop : -1.32 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.014 0.002 TYR B 123 PHE 0.013 0.002 PHE B 39 TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 ( 9336) covalent geometry : angle 0.68246 / 0.34 (12648) SS BOND : bond 0.00098 / 0.06 ( 3) SS BOND : angle 0.81569 / 0.48 ( 6) hydrogen bonds : bond 0.03633 / 2.40 ( 462) hydrogen bonds : angle 3.72402 / 2.64 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.340 Fit side-chains REVERT: A 64 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 105 ASP cc_start: 0.8206 (p0) cc_final: 0.7911 (p0) REVERT: A 150 THR cc_start: 0.8601 (p) cc_final: 0.8366 (p) REVERT: A 299 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8464 (t0) REVERT: A 451 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7555 (tt0) REVERT: A 590 ASN cc_start: 0.7918 (t0) cc_final: 0.7477 (t0) REVERT: B 64 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 451 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7402 (tt0) outliers start: 30 outliers final: 22 residues processed: 123 average time/residue: 0.0923 time to fit residues: 16.5248 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 61 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.136411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.119129 restraints weight = 9877.974| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.84 r_work: 0.2938 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9339 Z= 0.112 Angle : 0.601 7.829 12654 Z= 0.305 Chirality : 0.041 0.145 1466 Planarity : 0.004 0.079 1566 Dihedral : 6.991 82.332 1252 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 2.31 % Allowed : 10.64 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: 0.47 (0.26), residues: 1152 helix: 1.41 (0.21), residues: 650 sheet: -0.64 (0.53), residues: 78 loop : -1.23 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.011 0.001 TYR B 605 PHE 0.010 0.001 PHE A 489 TRP 0.009 0.001 TRP A 379 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9336) covalent geometry : angle 0.60126 / 0.31 (12648) SS BOND : bond 0.00139 / 0.08 ( 3) SS BOND : angle 0.76676 / 0.44 ( 6) hydrogen bonds : bond 0.02969 / 1.95 ( 462) hydrogen bonds : angle 3.57796 / 2.57 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.370 Fit side-chains REVERT: A 105 ASP cc_start: 0.8173 (p0) cc_final: 0.7882 (p0) REVERT: A 150 THR cc_start: 0.8580 (p) cc_final: 0.8365 (p) REVERT: A 451 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7608 (tt0) REVERT: A 590 ASN cc_start: 0.7677 (t0) cc_final: 0.7334 (t0) REVERT: B 64 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 451 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7440 (tt0) outliers start: 23 outliers final: 20 residues processed: 118 average time/residue: 0.0915 time to fit residues: 15.7375 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.133914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.116487 restraints weight = 9781.456| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 0.84 r_work: 0.2962 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9339 Z= 0.182 Angle : 0.656 8.425 12654 Z= 0.332 Chirality : 0.044 0.154 1466 Planarity : 0.004 0.076 1566 Dihedral : 6.978 82.036 1252 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 2.61 % Allowed : 11.24 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: 0.53 (0.26), residues: 1152 helix: 1.44 (0.21), residues: 644 sheet: -0.50 (0.53), residues: 78 loop : -1.17 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.013 0.001 TYR B 123 PHE 0.013 0.001 PHE B 39 TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 ( 9336) covalent geometry : angle 0.65626 / 0.33 (12648) SS BOND : bond 0.00098 / 0.06 ( 3) SS BOND : angle 0.85285 / 0.50 ( 6) hydrogen bonds : bond 0.03394 / 2.24 ( 462) hydrogen bonds : angle 3.64377 / 2.60 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.349 Fit side-chains REVERT: A 105 ASP cc_start: 0.8269 (p0) cc_final: 0.7968 (p0) REVERT: A 150 THR cc_start: 0.8608 (p) cc_final: 0.8384 (p) REVERT: A 451 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7632 (tt0) REVERT: A 590 ASN cc_start: 0.7845 (t0) cc_final: 0.7425 (t0) REVERT: B 64 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 451 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7452 (tt0) outliers start: 26 outliers final: 21 residues processed: 120 average time/residue: 0.0891 time to fit residues: 15.6069 Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.136088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.118804 restraints weight = 9777.842| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.85 r_work: 0.2952 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9339 Z= 0.127 Angle : 0.608 7.900 12654 Z= 0.308 Chirality : 0.042 0.152 1466 Planarity : 0.004 0.077 1566 Dihedral : 6.804 81.433 1252 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.41 % Allowed : 11.95 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: 0.77 (0.26), residues: 1152 helix: 1.64 (0.21), residues: 650 sheet: -0.46 (0.54), residues: 78 loop : -1.09 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.010 0.001 TYR B 605 PHE 0.010 0.001 PHE B 39 TRP 0.008 0.001 TRP A 379 HIS 0.003 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9336) covalent geometry : angle 0.60739 / 0.31 (12648) SS BOND : bond 0.00108 / 0.06 ( 3) SS BOND : angle 0.86551 / 0.50 ( 6) hydrogen bonds : bond 0.03002 / 1.98 ( 462) hydrogen bonds : angle 3.55135 / 2.55 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.510 Fit side-chains REVERT: A 105 ASP cc_start: 0.8165 (p0) cc_final: 0.7851 (p0) REVERT: A 150 THR cc_start: 0.8533 (p) cc_final: 0.8328 (p) REVERT: A 288 ASN cc_start: 0.7538 (m-40) cc_final: 0.6884 (t0) REVERT: A 451 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7578 (tt0) REVERT: A 590 ASN cc_start: 0.7611 (t0) cc_final: 0.7367 (t0) REVERT: B 64 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8228 (mp) REVERT: B 150 THR cc_start: 0.8640 (p) cc_final: 0.8387 (p) REVERT: B 288 ASN cc_start: 0.7526 (m110) cc_final: 0.6907 (t0) REVERT: B 451 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7420 (tt0) outliers start: 24 outliers final: 20 residues processed: 118 average time/residue: 0.0915 time to fit residues: 15.8895 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.138122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.120925 restraints weight = 9803.459| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 0.83 r_work: 0.2942 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9339 Z= 0.104 Angle : 0.589 7.690 12654 Z= 0.299 Chirality : 0.041 0.150 1466 Planarity : 0.004 0.075 1566 Dihedral : 6.554 78.691 1252 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 1.81 % Allowed : 12.05 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: 1.07 (0.26), residues: 1152 helix: 1.90 (0.21), residues: 650 sheet: -0.12 (0.57), residues: 76 loop : -1.03 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.010 0.001 TYR A 336 PHE 0.010 0.001 PHE B 39 TRP 0.007 0.001 TRP A 379 HIS 0.002 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 9336) covalent geometry : angle 0.58841 / 0.30 (12648) SS BOND : bond 0.00123 / 0.07 ( 3) SS BOND : angle 0.85446 / 0.49 ( 6) hydrogen bonds : bond 0.02767 / 1.82 ( 462) hydrogen bonds : angle 3.45179 / 2.50 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.341 Fit side-chains REVERT: A 105 ASP cc_start: 0.8112 (p0) cc_final: 0.7828 (p0) REVERT: A 288 ASN cc_start: 0.7524 (m-40) cc_final: 0.6874 (t0) REVERT: A 451 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7567 (tt0) REVERT: A 590 ASN cc_start: 0.7582 (t0) cc_final: 0.7329 (t0) REVERT: B 64 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8218 (mp) REVERT: B 102 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.7788 (mp) REVERT: B 150 THR cc_start: 0.8546 (p) cc_final: 0.8304 (p) REVERT: B 288 ASN cc_start: 0.7561 (m110) cc_final: 0.6929 (t0) REVERT: B 451 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7429 (tt0) outliers start: 18 outliers final: 16 residues processed: 117 average time/residue: 0.0898 time to fit residues: 15.2492 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 299 ASN ** 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 = 0.3402 r_free = 0.3402 target = 0.132778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.115380 restraints weight = 9710.413| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.83 r_work: 0.2912 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9339 Z= 0.228 Angle : 0.693 9.209 12654 Z= 0.347 Chirality : 0.046 0.159 1466 Planarity : 0.005 0.077 1566 Dihedral : 6.827 80.340 1252 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 2.31 % Allowed : 11.95 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: 0.76 (0.26), residues: 1152 helix: 1.59 (0.21), residues: 644 sheet: -0.13 (0.56), residues: 78 loop : -1.05 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.017 0.002 TYR B 123 PHE 0.015 0.002 PHE B 39 TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 ( 9336) covalent geometry : angle 0.69309 / 0.35 (12648) SS BOND : bond 0.00061 / 0.04 ( 3) SS BOND : angle 1.03731 / 0.61 ( 6) hydrogen bonds : bond 0.03666 / 2.43 ( 462) hydrogen bonds : angle 3.65993 / 2.60 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2070.81 seconds wall clock time: 36 minutes 52.58 seconds (2212.58 seconds total)