Starting phenix.real_space_refine on Wed Sep 17 14:38:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hbu_0190/09_2025/6hbu_0190.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hbu_0190/09_2025/6hbu_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 { model { file = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2025/6hbu_0190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2025/6hbu_0190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2025/6hbu_0190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hbu_0190/09_2025/6hbu_0190.map" } 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-2.0-5805/lib/python3.9/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: 3.59, per 1000 atoms: 0.39 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: 0.84 Conformation dependent library (CDL) restraints added in 346.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.22 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: 1.39 Time building geometry restraints manager: 1.11 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: 5200 15.33 - 30.67: 270 30.67 - 46.00: 78 46.00 - 61.33: 21 61.33 - 76.67: 10 Dihedral angle restraints: 5579 sinusoidal: 2211 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 5576 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.760 Find NCS groups from input model: 0.060 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 11.560 76.667 3406 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 aren 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 covalent geometry : bond 0.00889 ( 9336) covalent geometry : angle 1.17676 (12648) SS BOND : bond 0.01126 ( 3) SS BOND : angle 2.37902 ( 6) hydrogen bonds : bond 0.29836 ( 462) hydrogen bonds : angle 10.32380 ( 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 : 0.385 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: 0.1102 time to fit residues: 27.3242 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 : 0.223 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3477 r_free = 0.3477 target = 0.139009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.121704 restraints weight = 9840.778| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 0.86 r_work: 0.2990 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9339 Z= 0.128 Angle : 0.683 7.964 12654 Z= 0.357 Chirality : 0.043 0.159 1466 Planarity : 0.006 0.087 1566 Dihedral : 9.806 85.785 1314 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.34 % Favored : 95.49 % Rotamer: Outliers : 1.71 % Allowed : 6.63 % Favored : 91.67 % 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 aren not related in a simple way. whole: -2.61 (0.22), residues: 1152 helix: -1.39 (0.18), residues: 640 sheet: -1.53 (0.46), residues: 76 loop : -2.08 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.015 0.001 TYR B 605 PHE 0.012 0.001 PHE B 385 TRP 0.010 0.001 TRP B 379 HIS 0.005 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9336) covalent geometry : angle 0.68267 (12648) SS BOND : bond 0.00180 ( 3) SS BOND : angle 1.04174 ( 6) hydrogen bonds : bond 0.04103 ( 462) hydrogen bonds : angle 4.24294 ( 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 148 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.363 Fit side-chains REVERT: A 71 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7623 (mtt) REVERT: A 105 ASP cc_start: 0.8179 (p0) cc_final: 0.7936 (p0) REVERT: A 206 ILE cc_start: 0.9013 (mt) cc_final: 0.8660 (mt) REVERT: A 451 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7584 (tt0) REVERT: A 590 ASN cc_start: 0.7910 (t0) cc_final: 0.7683 (t0) REVERT: A 620 ASP cc_start: 0.7954 (t0) cc_final: 0.7629 (t0) REVERT: B 451 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7448 (tt0) REVERT: B 590 ASN cc_start: 0.7868 (t0) cc_final: 0.7655 (t0) outliers start: 17 outliers final: 12 residues processed: 142 average time/residue: 0.0803 time to fit residues: 16.9837 Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.130440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.105048 restraints weight = 9685.342| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.24 r_work: 0.2894 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.087 9339 Z= 0.386 Angle : 0.876 10.739 12654 Z= 0.437 Chirality : 0.054 0.218 1466 Planarity : 0.006 0.091 1566 Dihedral : 9.775 81.332 1314 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 3.01 % Allowed : 8.03 % Favored : 88.96 % 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 aren not related in a simple way. whole: -1.29 (0.24), residues: 1152 helix: -0.22 (0.20), residues: 642 sheet: -0.82 (0.52), residues: 78 loop : -1.72 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 575 TYR 0.024 0.003 TYR B 123 PHE 0.021 0.003 PHE B 489 TRP 0.011 0.002 TRP B 627 HIS 0.005 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00951 ( 9336) covalent geometry : angle 0.87625 (12648) SS BOND : bond 0.00184 ( 3) SS BOND : angle 1.04204 ( 6) hydrogen bonds : bond 0.04990 ( 462) hydrogen bonds : angle 4.21696 ( 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 139 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.375 Fit side-chains REVERT: A 451 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7565 (tt0) REVERT: A 590 ASN cc_start: 0.8283 (t0) cc_final: 0.8031 (t0) REVERT: B 451 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7399 (tt0) REVERT: B 590 ASN cc_start: 0.8235 (t0) cc_final: 0.7914 (t0) outliers start: 30 outliers final: 21 residues processed: 130 average time/residue: 0.0863 time to fit residues: 16.3437 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN 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 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 412 ILE 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 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 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.139524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.114010 restraints weight = 9471.565| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.29 r_work: 0.2970 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9339 Z= 0.122 Angle : 0.633 8.064 12654 Z= 0.324 Chirality : 0.043 0.157 1466 Planarity : 0.004 0.081 1566 Dihedral : 9.135 77.275 1314 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.21 % Allowed : 9.64 % Favored : 88.15 % 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 aren not related in a simple way. whole: -0.26 (0.25), residues: 1152 helix: 0.78 (0.21), residues: 644 sheet: -0.74 (0.52), residues: 78 loop : -1.49 (0.31), residues: 430 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 0.011 0.001 TRP A 379 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9336) covalent geometry : angle 0.63255 (12648) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.93759 ( 6) hydrogen bonds : bond 0.03260 ( 462) hydrogen bonds : angle 3.72897 ( 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 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.253 Fit side-chains REVERT: A 150 THR cc_start: 0.8669 (p) cc_final: 0.8427 (p) REVERT: A 299 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8456 (t0) REVERT: A 451 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7492 (tt0) REVERT: A 590 ASN cc_start: 0.8014 (t0) cc_final: 0.7628 (t0) REVERT: B 451 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7403 (tt0) REVERT: B 590 ASN cc_start: 0.7970 (t0) cc_final: 0.7560 (t0) outliers start: 22 outliers final: 18 residues processed: 116 average time/residue: 0.0842 time to fit residues: 14.3822 Evaluate side-chains 107 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 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 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 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: 3.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.138545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.113445 restraints weight = 9430.389| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.27 r_work: 0.2932 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9339 Z= 0.188 Angle : 0.666 8.740 12654 Z= 0.337 Chirality : 0.045 0.149 1466 Planarity : 0.005 0.084 1566 Dihedral : 9.116 78.393 1314 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.97 % Rotamer: Outliers : 2.71 % Allowed : 9.94 % Favored : 87.35 % 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 aren not related in a simple way. whole: -0.04 (0.25), residues: 1152 helix: 0.96 (0.21), residues: 642 sheet: -0.65 (0.52), residues: 78 loop : -1.38 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.012 0.002 TYR B 605 PHE 0.013 0.001 PHE B 39 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9336) covalent geometry : angle 0.66622 (12648) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.81662 ( 6) hydrogen bonds : bond 0.03530 ( 462) hydrogen bonds : angle 3.71073 ( 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 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.438 Fit side-chains REVERT: A 150 THR cc_start: 0.8660 (p) cc_final: 0.8429 (p) REVERT: A 299 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8594 (t0) REVERT: A 451 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7507 (tt0) REVERT: A 590 ASN cc_start: 0.8038 (t0) cc_final: 0.7595 (t0) REVERT: B 64 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8246 (mp) REVERT: B 451 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7396 (tt0) REVERT: B 590 ASN cc_start: 0.8024 (t0) cc_final: 0.7627 (t0) outliers start: 27 outliers final: 22 residues processed: 120 average time/residue: 0.0921 time to fit residues: 15.9863 Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN B 589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.134536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107153 restraints weight = 9556.370| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.38 r_work: 0.2917 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9339 Z= 0.168 Angle : 0.650 8.578 12654 Z= 0.329 Chirality : 0.044 0.147 1466 Planarity : 0.005 0.079 1566 Dihedral : 9.043 79.348 1314 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 3.01 % Allowed : 10.34 % Favored : 86.65 % 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 aren not related in a simple way. whole: 0.14 (0.25), residues: 1152 helix: 1.13 (0.21), residues: 642 sheet: -0.64 (0.53), residues: 78 loop : -1.33 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.011 0.001 TYR B 605 PHE 0.011 0.001 PHE A 489 TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9336) covalent geometry : angle 0.64982 (12648) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.79297 ( 6) hydrogen bonds : bond 0.03381 ( 462) hydrogen bonds : angle 3.65359 ( 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 127 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.366 Fit side-chains REVERT: A 64 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 150 THR cc_start: 0.8616 (p) cc_final: 0.8392 (p) REVERT: A 299 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8531 (t0) REVERT: A 451 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7435 (tt0) REVERT: A 590 ASN cc_start: 0.7996 (t0) cc_final: 0.7544 (t0) REVERT: B 64 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8215 (mp) REVERT: B 451 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7325 (tt0) REVERT: B 590 ASN cc_start: 0.7993 (t0) cc_final: 0.7585 (t0) outliers start: 30 outliers final: 26 residues processed: 122 average time/residue: 0.0898 time to fit residues: 15.9909 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 214 THR 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 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.108575 restraints weight = 9647.338| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.39 r_work: 0.2968 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 0.026 9339 Z= 0.118 Angle : 0.606 7.853 12654 Z= 0.308 Chirality : 0.042 0.145 1466 Planarity : 0.004 0.080 1566 Dihedral : 8.750 75.675 1314 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.31 % Allowed : 11.55 % 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 aren not related in a simple way. whole: 0.37 (0.26), residues: 1152 helix: 1.34 (0.21), residues: 650 sheet: -0.70 (0.53), residues: 78 loop : -1.29 (0.31), 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 0.009 0.001 PHE A 489 TRP 0.010 0.001 TRP B 379 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9336) covalent geometry : angle 0.60601 (12648) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.75710 ( 6) hydrogen bonds : bond 0.03012 ( 462) hydrogen bonds : angle 3.56351 ( 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 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.383 Fit side-chains REVERT: A 150 THR cc_start: 0.8565 (p) cc_final: 0.8364 (p) REVERT: A 299 ASN cc_start: 0.8843 (t0) cc_final: 0.8550 (t0) REVERT: A 451 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7470 (tt0) REVERT: A 590 ASN cc_start: 0.7910 (t0) cc_final: 0.7443 (t0) REVERT: B 451 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7304 (tt0) REVERT: B 590 ASN cc_start: 0.7840 (t0) cc_final: 0.7419 (t0) outliers start: 23 outliers final: 21 residues processed: 115 average time/residue: 0.0912 time to fit residues: 15.2163 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 214 THR Chi-restraints excluded: chain A residue 248 SER 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 595 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 589 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.137599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.110826 restraints weight = 9552.465| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.37 r_work: 0.2986 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9339 Z= 0.124 Angle : 0.599 7.856 12654 Z= 0.304 Chirality : 0.042 0.139 1466 Planarity : 0.004 0.077 1566 Dihedral : 8.466 70.298 1314 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 2.51 % Allowed : 11.75 % 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 aren not related in a simple way. whole: 0.68 (0.26), residues: 1152 helix: 1.57 (0.21), residues: 652 sheet: -0.64 (0.53), residues: 78 loop : -1.11 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 465 TYR 0.010 0.001 TYR B 605 PHE 0.011 0.001 PHE B 39 TRP 0.009 0.001 TRP B 379 HIS 0.002 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9336) covalent geometry : angle 0.59851 (12648) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.78172 ( 6) hydrogen bonds : bond 0.02946 ( 462) hydrogen bonds : angle 3.49342 ( 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 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.421 Fit side-chains REVERT: A 299 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8371 (t0) REVERT: A 451 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7508 (tt0) REVERT: A 590 ASN cc_start: 0.7807 (t0) cc_final: 0.7366 (t0) REVERT: B 64 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8232 (mp) REVERT: B 451 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7324 (tt0) REVERT: B 590 ASN cc_start: 0.7773 (t0) cc_final: 0.7346 (t0) outliers start: 25 outliers final: 20 residues processed: 118 average time/residue: 0.0899 time to fit residues: 15.4175 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 214 THR 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 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 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 412 ILE Chi-restraints excluded: chain B residue 554 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: 3.9990 chunk 29 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3447 r_free = 0.3447 target = 0.136621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.109754 restraints weight = 9555.193| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.37 r_work: 0.2986 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9339 Z= 0.155 Angle : 0.620 8.117 12654 Z= 0.313 Chirality : 0.043 0.144 1466 Planarity : 0.005 0.078 1566 Dihedral : 8.540 71.459 1314 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.51 % Allowed : 11.85 % 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 aren not related in a simple way. whole: 0.70 (0.26), residues: 1152 helix: 1.56 (0.21), residues: 652 sheet: -0.49 (0.53), residues: 78 loop : -1.08 (0.32), residues: 422 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 0.012 0.001 PHE B 39 TRP 0.009 0.001 TRP A 379 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9336) covalent geometry : angle 0.62025 (12648) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.84022 ( 6) hydrogen bonds : bond 0.03125 ( 462) hydrogen bonds : angle 3.52795 ( 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: 25 poor density : 97 time to evaluate : 0.361 Fit side-chains REVERT: A 288 ASN cc_start: 0.7625 (m-40) cc_final: 0.6848 (t0) REVERT: A 451 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7567 (tt0) REVERT: A 590 ASN cc_start: 0.7837 (t0) cc_final: 0.7414 (t0) REVERT: B 64 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 150 THR cc_start: 0.8584 (p) cc_final: 0.8346 (p) REVERT: B 288 ASN cc_start: 0.7629 (m110) cc_final: 0.6814 (t0) REVERT: B 451 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7349 (tt0) REVERT: B 590 ASN cc_start: 0.7814 (t0) cc_final: 0.7398 (t0) outliers start: 25 outliers final: 21 residues processed: 119 average time/residue: 0.0919 time to fit residues: 15.9743 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 : 0.363 ------------------------------------------------------------------------------- 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 214 THR 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 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 412 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 0.0670 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.136275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.118866 restraints weight = 9846.160| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.81 r_work: 0.2927 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9339 Z= 0.124 Angle : 0.601 7.823 12654 Z= 0.308 Chirality : 0.042 0.142 1466 Planarity : 0.004 0.076 1566 Dihedral : 8.349 68.587 1314 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 2.21 % Allowed : 12.25 % Favored : 85.54 % 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 aren not related in a simple way. whole: 0.91 (0.26), residues: 1152 helix: 1.78 (0.21), residues: 650 sheet: -0.40 (0.55), residues: 78 loop : -1.07 (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 0.009 0.001 PHE B 39 TRP 0.008 0.001 TRP B 379 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9336) covalent geometry : angle 0.60123 (12648) SS BOND : bond 0.00122 ( 3) SS BOND : angle 0.87272 ( 6) hydrogen bonds : bond 0.02914 ( 462) hydrogen bonds : angle 3.46023 ( 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 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.368 Fit side-chains REVERT: A 288 ASN cc_start: 0.7520 (m-40) cc_final: 0.6861 (t0) REVERT: A 451 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7657 (tt0) REVERT: A 590 ASN cc_start: 0.7620 (t0) cc_final: 0.7355 (t0) REVERT: B 64 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8274 (mp) REVERT: B 288 ASN cc_start: 0.7545 (m110) cc_final: 0.6897 (t0) REVERT: B 451 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7424 (tt0) REVERT: B 590 ASN cc_start: 0.7659 (t0) cc_final: 0.7388 (t0) outliers start: 22 outliers final: 19 residues processed: 119 average time/residue: 0.0890 time to fit residues: 15.4503 Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 214 THR 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 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 609 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.137362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.117687 restraints weight = 9434.201| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.95 r_work: 0.3011 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9339 Z= 0.118 Angle : 0.597 7.800 12654 Z= 0.303 Chirality : 0.042 0.142 1466 Planarity : 0.004 0.077 1566 Dihedral : 8.246 65.556 1314 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 2.31 % Allowed : 12.45 % Favored : 85.24 % 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 aren not related in a simple way. whole: 1.10 (0.26), residues: 1152 helix: 1.95 (0.21), residues: 644 sheet: -0.27 (0.56), residues: 78 loop : -0.99 (0.32), residues: 430 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 0.009 0.001 PHE B 39 TRP 0.008 0.001 TRP A 379 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9336) covalent geometry : angle 0.59656 (12648) SS BOND : bond 0.00118 ( 3) SS BOND : angle 0.88834 ( 6) hydrogen bonds : bond 0.02872 ( 462) hydrogen bonds : angle 3.42887 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.12 seconds wall clock time: 40 minutes 18.60 seconds (2418.60 seconds total)