Starting phenix.real_space_refine on Wed Apr 30 03:35:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hbu_0190/04_2025/6hbu_0190.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hbu_0190/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6hbu_0190/04_2025/6hbu_0190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hbu_0190/04_2025/6hbu_0190.map" model { file = "/net/cci-nas-00/data/ceres_data/6hbu_0190/04_2025/6hbu_0190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hbu_0190/04_2025/6hbu_0190.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 8.68, per 1000 atoms: 0.95 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: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.96 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: 2.56 Time building geometry restraints manager: 2.79 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: 0.04 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.870 Find NCS groups from input model: 0.150 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP B 624 HIS 0.013 0.003 HIS A 583 PHE 0.032 0.003 PHE A 578 TYR 0.039 0.003 TYR A 463 ARG 0.010 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.29836 ( 462) hydrogen bonds : angle 10.32380 ( 1332) SS BOND : bond 0.01126 ( 3) SS BOND : angle 2.37902 ( 6) covalent geometry : bond 0.00889 ( 9336) covalent geometry : angle 1.17676 (12648) *********************** 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 : 1.043 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: 0.2766 time to fit residues: 69.6951 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 : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.137739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.120686 restraints weight = 9774.518| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 0.86 r_work: 0.2975 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9339 Z= 0.149 Angle : 0.698 8.093 12654 Z= 0.363 Chirality : 0.044 0.190 1466 Planarity : 0.006 0.087 1566 Dihedral : 9.780 84.244 1314 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.57 % Rotamer: Outliers : 1.71 % Allowed : 6.83 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.22), residues: 1152 helix: -1.47 (0.18), residues: 640 sheet: -1.35 (0.48), residues: 76 loop : -2.05 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 627 HIS 0.005 0.001 HIS B 243 PHE 0.014 0.002 PHE A 578 TYR 0.015 0.002 TYR B 605 ARG 0.003 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 462) hydrogen bonds : angle 4.32482 ( 1332) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.86983 ( 6) covalent geometry : bond 0.00349 ( 9336) covalent geometry : angle 0.69830 (12648) *********************** 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 147 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.591 Fit side-chains REVERT: A 71 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7628 (mtt) REVERT: A 105 ASP cc_start: 0.8186 (p0) cc_final: 0.7936 (p0) REVERT: A 206 ILE cc_start: 0.9047 (mt) cc_final: 0.8668 (mt) REVERT: A 251 LYS cc_start: 0.8432 (ttpm) cc_final: 0.8222 (mtpt) REVERT: A 451 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7571 (tt0) REVERT: A 590 ASN cc_start: 0.7932 (t0) cc_final: 0.7723 (t0) REVERT: A 620 ASP cc_start: 0.7984 (t0) cc_final: 0.7675 (t0) REVERT: B 237 THR cc_start: 0.8915 (t) cc_final: 0.8708 (m) REVERT: B 451 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7460 (tt0) outliers start: 17 outliers final: 11 residues processed: 141 average time/residue: 0.2069 time to fit residues: 43.1668 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 49 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 375 HIS B 436 ASN B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.133504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114694 restraints weight = 9898.130| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 0.90 r_work: 0.2886 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2340 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= 0.219 Angle : 0.727 8.669 12654 Z= 0.368 Chirality : 0.047 0.170 1466 Planarity : 0.006 0.089 1566 Dihedral : 9.355 77.087 1314 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.61 % Allowed : 8.73 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.24), residues: 1152 helix: 0.04 (0.20), residues: 642 sheet: -1.02 (0.48), residues: 78 loop : -1.61 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 627 HIS 0.004 0.001 HIS B 243 PHE 0.018 0.002 PHE B 489 TYR 0.013 0.002 TYR B 463 ARG 0.003 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 462) hydrogen bonds : angle 3.98062 ( 1332) SS BOND : bond 0.00234 ( 3) SS BOND : angle 1.04206 ( 6) covalent geometry : bond 0.00543 ( 9336) covalent geometry : angle 0.72728 (12648) *********************** 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 132 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.620 Fit side-chains REVERT: A 71 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8042 (mtp) REVERT: A 105 ASP cc_start: 0.8311 (p0) cc_final: 0.8094 (p0) REVERT: A 251 LYS cc_start: 0.8526 (ttpm) cc_final: 0.8310 (mtpt) REVERT: A 299 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.8877 (t0) REVERT: A 451 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7634 (tt0) REVERT: A 620 ASP cc_start: 0.8114 (t0) cc_final: 0.7883 (t0) REVERT: B 237 THR cc_start: 0.8997 (t) cc_final: 0.8697 (m) REVERT: B 451 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7485 (tt0) outliers start: 26 outliers final: 18 residues processed: 127 average time/residue: 0.1910 time to fit residues: 35.1694 Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 108 ILE Chi-restraints excluded: chain A residue 171 ASP 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 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 609 THR 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 412 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN B 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.136380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118720 restraints weight = 9729.753| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.86 r_work: 0.2917 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9339 Z= 0.123 Angle : 0.629 7.992 12654 Z= 0.321 Chirality : 0.043 0.145 1466 Planarity : 0.005 0.080 1566 Dihedral : 9.019 75.021 1314 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 2.81 % Allowed : 9.54 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1152 helix: 0.83 (0.21), residues: 640 sheet: -0.92 (0.49), residues: 78 loop : -1.40 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS A 243 PHE 0.012 0.001 PHE A 489 TYR 0.012 0.001 TYR B 605 ARG 0.003 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 462) hydrogen bonds : angle 3.71428 ( 1332) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.79601 ( 6) covalent geometry : bond 0.00291 ( 9336) covalent geometry : angle 0.62912 (12648) *********************** 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 130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.949 Fit side-chains REVERT: A 105 ASP cc_start: 0.8246 (p0) cc_final: 0.7925 (p0) REVERT: A 150 THR cc_start: 0.8705 (p) cc_final: 0.8436 (p) REVERT: A 251 LYS cc_start: 0.8585 (ttpm) cc_final: 0.8375 (mtpt) REVERT: A 451 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7628 (tt0) REVERT: B 451 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7506 (tt0) outliers start: 28 outliers final: 22 residues processed: 122 average time/residue: 0.1816 time to fit residues: 32.5275 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 171 ASP 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 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 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 Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 77 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 overall best weight: 1.5400 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.134014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.115918 restraints weight = 9841.817| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 0.88 r_work: 0.2873 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9339 Z= 0.175 Angle : 0.664 8.193 12654 Z= 0.335 Chirality : 0.045 0.177 1466 Planarity : 0.005 0.082 1566 Dihedral : 9.016 76.657 1314 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 2.71 % Allowed : 10.14 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1152 helix: 1.19 (0.21), residues: 630 sheet: -0.75 (0.52), residues: 78 loop : -1.30 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS B 243 PHE 0.013 0.001 PHE A 489 TYR 0.012 0.002 TYR B 123 ARG 0.003 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 462) hydrogen bonds : angle 3.71745 ( 1332) SS BOND : bond 0.00123 ( 3) SS BOND : angle 0.84480 ( 6) covalent geometry : bond 0.00428 ( 9336) covalent geometry : angle 0.66428 (12648) *********************** 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 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.040 Fit side-chains REVERT: A 150 THR cc_start: 0.8677 (p) cc_final: 0.8420 (p) REVERT: A 251 LYS cc_start: 0.8600 (ttpm) cc_final: 0.8400 (mtpt) REVERT: A 451 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7638 (tt0) REVERT: B 451 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7505 (tt0) outliers start: 27 outliers final: 24 residues processed: 120 average time/residue: 0.1886 time to fit residues: 33.2952 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 : 1.032 ------------------------------------------------------------------------------- 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 108 ILE Chi-restraints excluded: chain A residue 171 ASP 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 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 Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3406 r_free = 0.3406 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105079 restraints weight = 9599.443| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.41 r_work: 0.2899 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9339 Z= 0.242 Angle : 0.726 9.146 12654 Z= 0.364 Chirality : 0.047 0.194 1466 Planarity : 0.005 0.078 1566 Dihedral : 9.257 80.474 1314 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 3.41 % Allowed : 10.14 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1152 helix: 0.97 (0.21), residues: 652 sheet: -0.62 (0.53), residues: 78 loop : -1.24 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS B 243 PHE 0.015 0.002 PHE A 39 TYR 0.021 0.002 TYR B 123 ARG 0.003 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 462) hydrogen bonds : angle 3.81128 ( 1332) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.90330 ( 6) covalent geometry : bond 0.00604 ( 9336) covalent geometry : angle 0.72581 (12648) *********************** 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 132 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 1.098 Fit side-chains REVERT: A 64 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 150 THR cc_start: 0.8654 (p) cc_final: 0.8403 (p) REVERT: A 251 LYS cc_start: 0.8568 (ttpm) cc_final: 0.8276 (mtpt) REVERT: A 378 ARG cc_start: 0.8302 (mtm180) cc_final: 0.7544 (mmt-90) REVERT: A 451 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7529 (tt0) REVERT: B 64 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8303 (mp) REVERT: B 451 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7379 (tt0) outliers start: 34 outliers final: 23 residues processed: 124 average time/residue: 0.2134 time to fit residues: 38.0789 Evaluate side-chains 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 171 ASP 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 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 374 CYS Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.0070 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 111 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.143223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.118361 restraints weight = 9514.959| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.27 r_work: 0.2997 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.002 0.027 9339 Z= 0.105 Angle : 0.608 8.999 12654 Z= 0.307 Chirality : 0.042 0.158 1466 Planarity : 0.004 0.077 1566 Dihedral : 8.613 74.255 1314 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 2.11 % Allowed : 11.85 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1152 helix: 1.51 (0.21), residues: 650 sheet: -0.63 (0.55), residues: 78 loop : -1.18 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.002 0.000 HIS B 375 PHE 0.009 0.001 PHE B 470 TYR 0.011 0.001 TYR B 605 ARG 0.002 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 462) hydrogen bonds : angle 3.57863 ( 1332) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.79449 ( 6) covalent geometry : bond 0.00237 ( 9336) covalent geometry : angle 0.60810 (12648) *********************** 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 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.108 Fit side-chains REVERT: A 150 THR cc_start: 0.8511 (p) cc_final: 0.8305 (p) REVERT: A 251 LYS cc_start: 0.8526 (ttpm) cc_final: 0.8273 (mtpt) REVERT: A 451 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7435 (tt0) REVERT: A 541 MET cc_start: 0.9005 (mmm) cc_final: 0.8779 (mmm) REVERT: B 64 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 451 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7313 (tt0) outliers start: 21 outliers final: 19 residues processed: 117 average time/residue: 0.2172 time to fit residues: 36.3192 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 ASP 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 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 590 ASN 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 31 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.136795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.119537 restraints weight = 9960.141| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 0.81 r_work: 0.2945 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9339 Z= 0.115 Angle : 0.607 8.406 12654 Z= 0.306 Chirality : 0.042 0.153 1466 Planarity : 0.004 0.075 1566 Dihedral : 8.332 66.529 1314 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 2.41 % Allowed : 11.75 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1152 helix: 1.67 (0.21), residues: 658 sheet: -0.55 (0.55), residues: 78 loop : -0.99 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 379 HIS 0.002 0.001 HIS B 375 PHE 0.011 0.001 PHE B 39 TYR 0.010 0.001 TYR A 336 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.02913 ( 462) hydrogen bonds : angle 3.49750 ( 1332) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.80135 ( 6) covalent geometry : bond 0.00272 ( 9336) covalent geometry : angle 0.60716 (12648) *********************** 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: 24 poor density : 99 time to evaluate : 0.946 Fit side-chains REVERT: A 288 ASN cc_start: 0.7550 (m-40) cc_final: 0.6919 (t0) REVERT: A 451 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7581 (tt0) REVERT: B 64 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8237 (mp) REVERT: B 150 THR cc_start: 0.8551 (p) cc_final: 0.8331 (p) REVERT: B 288 ASN cc_start: 0.7526 (m110) cc_final: 0.6897 (t0) REVERT: B 451 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7404 (tt0) outliers start: 24 outliers final: 20 residues processed: 119 average time/residue: 0.1974 time to fit residues: 33.6028 Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 ASP 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 590 ASN Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 112 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.135910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.118651 restraints weight = 9811.079| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.81 r_work: 0.2929 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9339 Z= 0.136 Angle : 0.631 9.798 12654 Z= 0.315 Chirality : 0.043 0.156 1466 Planarity : 0.004 0.076 1566 Dihedral : 8.365 67.371 1314 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1152 helix: 1.70 (0.21), residues: 658 sheet: -0.38 (0.55), residues: 78 loop : -0.92 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS B 375 PHE 0.011 0.001 PHE B 39 TYR 0.010 0.001 TYR A 336 ARG 0.002 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 462) hydrogen bonds : angle 3.50964 ( 1332) SS BOND : bond 0.00091 ( 3) SS BOND : angle 0.91599 ( 6) covalent geometry : bond 0.00328 ( 9336) covalent geometry : angle 0.63056 (12648) *********************** 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: 23 poor density : 99 time to evaluate : 1.058 Fit side-chains REVERT: A 288 ASN cc_start: 0.7555 (m-40) cc_final: 0.6965 (t0) REVERT: A 451 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7625 (tt0) REVERT: B 64 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8265 (mp) REVERT: B 150 THR cc_start: 0.8559 (p) cc_final: 0.8319 (p) REVERT: B 288 ASN cc_start: 0.7561 (m110) cc_final: 0.6963 (t0) REVERT: B 451 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7422 (tt0) outliers start: 23 outliers final: 20 residues processed: 117 average time/residue: 0.2034 time to fit residues: 34.6255 Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 ASP 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 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 590 ASN 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 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 overall best weight: 0.5670 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.138785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.120859 restraints weight = 9593.750| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.83 r_work: 0.3056 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9339 Z= 0.109 Angle : 0.597 8.334 12654 Z= 0.301 Chirality : 0.042 0.155 1466 Planarity : 0.004 0.075 1566 Dihedral : 8.063 61.807 1314 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.56 % Favored : 94.27 % Rotamer: Outliers : 2.11 % Allowed : 12.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1152 helix: 1.90 (0.21), residues: 658 sheet: -0.24 (0.58), residues: 78 loop : -0.87 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 379 HIS 0.002 0.001 HIS A 243 PHE 0.010 0.001 PHE B 39 TYR 0.010 0.001 TYR A 336 ARG 0.002 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 462) hydrogen bonds : angle 3.42263 ( 1332) SS BOND : bond 0.00129 ( 3) SS BOND : angle 0.90714 ( 6) covalent geometry : bond 0.00256 ( 9336) covalent geometry : angle 0.59670 (12648) ********************** 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: 21 poor density : 98 time to evaluate : 0.962 Fit side-chains REVERT: A 288 ASN cc_start: 0.7503 (m-40) cc_final: 0.6915 (t0) REVERT: A 451 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7469 (tt0) REVERT: B 64 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 288 ASN cc_start: 0.7465 (m110) cc_final: 0.6810 (t0) REVERT: B 451 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7266 (tt0) outliers start: 21 outliers final: 19 residues processed: 115 average time/residue: 0.1983 time to fit residues: 32.6389 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 ASP 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 554 LEU Chi-restraints excluded: chain B residue 590 ASN 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 82 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.134223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116141 restraints weight = 9562.833| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 0.86 r_work: 0.2977 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9339 Z= 0.206 Angle : 0.680 9.982 12654 Z= 0.340 Chirality : 0.046 0.165 1466 Planarity : 0.005 0.076 1566 Dihedral : 8.597 71.251 1314 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 2.51 % Allowed : 12.05 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1152 helix: 1.57 (0.21), residues: 658 sheet: -0.08 (0.57), residues: 78 loop : -0.84 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.003 0.001 HIS B 375 PHE 0.014 0.001 PHE B 39 TYR 0.015 0.002 TYR B 123 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 462) hydrogen bonds : angle 3.60861 ( 1332) SS BOND : bond 0.00059 ( 3) SS BOND : angle 1.07858 ( 6) covalent geometry : bond 0.00510 ( 9336) covalent geometry : angle 0.67983 (12648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4590.15 seconds wall clock time: 81 minutes 53.67 seconds (4913.67 seconds total)