Starting phenix.real_space_refine on Sun Mar 10 23:55:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzz_8943/03_2024/6dzz_8943_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzz_8943/03_2024/6dzz_8943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzz_8943/03_2024/6dzz_8943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzz_8943/03_2024/6dzz_8943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzz_8943/03_2024/6dzz_8943_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzz_8943/03_2024/6dzz_8943_updated.pdb" } resolution = 3.6 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= 0.036 sd= 1.351 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4046 2.51 5 N 965 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6141 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4314 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'HJM': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.83, per 1000 atoms: 0.62 Number of scatterers: 6141 At special positions: 0 Unit cell: (81.477, 79.008, 115.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1096 8.00 N 965 7.00 C 4046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 4 sheets defined 40.4% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.819A pdb=" N ASP A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.676A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.744A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.673A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.620A pdb=" N TYR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.975A pdb=" N TYR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.540A pdb=" N LEU A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 286 through 301 removed outlier: 4.765A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.924A pdb=" N SER A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 389 removed outlier: 3.864A pdb=" N LEU A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 removed outlier: 4.325A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 414 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 440 removed outlier: 3.630A pdb=" N ALA A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 removed outlier: 4.061A pdb=" N ILE A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 removed outlier: 3.758A pdb=" N ASP A 452 " --> pdb=" O ALA A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 452' Processing helix chain 'A' and resid 465 through 475 removed outlier: 3.719A pdb=" N VAL A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 491 through 494 No H-bonds generated for 'chain 'A' and resid 491 through 494' Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.713A pdb=" N VAL A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.549A pdb=" N ARG A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 526 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 545 through 558 removed outlier: 3.692A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET A 558 " --> pdb=" O CYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.530A pdb=" N THR A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.952A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing sheet with id= A, first strand: chain 'B' and resid 23 through 25 removed outlier: 3.615A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 102 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 97 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 112 through 117 removed outlier: 3.649A pdb=" N ILE B 70 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 68 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 76 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 109 through 114 removed outlier: 3.752A pdb=" N PHE C 60 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 113 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN C 61 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU C 70 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 87 through 90 165 hydrogen bonds defined for protein. 483 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: 1.74 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1783 1.34 - 1.46: 1438 1.46 - 1.58: 3054 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 6326 Sorted by residual: bond pdb=" C2 HJM A 701 " pdb=" C8 HJM A 701 " ideal model delta sigma weight residual 1.490 1.593 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C7 HJM A 701 " pdb=" N1 HJM A 701 " ideal model delta sigma weight residual 1.472 1.566 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C9 HJM A 701 " pdb=" N1 HJM A 701 " ideal model delta sigma weight residual 1.467 1.558 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C18 HJM A 701 " pdb=" C19 HJM A 701 " ideal model delta sigma weight residual 1.407 1.492 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O HJM A 701 " pdb=" C18 HJM A 701 " ideal model delta sigma weight residual 1.374 1.430 -0.056 2.00e-02 2.50e+03 7.83e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.11: 193 107.11 - 113.83: 3424 113.83 - 120.55: 2561 120.55 - 127.26: 2357 127.26 - 133.98: 79 Bond angle restraints: 8614 Sorted by residual: angle pdb=" C ASP A 216 " pdb=" N ASN A 217 " pdb=" CA ASN A 217 " ideal model delta sigma weight residual 122.46 129.63 -7.17 1.41e+00 5.03e-01 2.58e+01 angle pdb=" N GLY A 338 " pdb=" CA GLY A 338 " pdb=" C GLY A 338 " ideal model delta sigma weight residual 112.34 120.92 -8.58 2.04e+00 2.40e-01 1.77e+01 angle pdb=" C GLY B 121 " pdb=" N SER B 122 " pdb=" CA SER B 122 " ideal model delta sigma weight residual 120.63 127.40 -6.77 1.61e+00 3.86e-01 1.77e+01 angle pdb=" C ASN A 569 " pdb=" N TYR A 570 " pdb=" CA TYR A 570 " ideal model delta sigma weight residual 121.80 131.99 -10.19 2.44e+00 1.68e-01 1.74e+01 angle pdb=" N SER B 122 " pdb=" CA SER B 122 " pdb=" C SER B 122 " ideal model delta sigma weight residual 112.34 117.67 -5.33 1.30e+00 5.92e-01 1.68e+01 ... (remaining 8609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 3664 35.47 - 70.93: 25 70.93 - 106.40: 8 106.40 - 141.86: 0 141.86 - 177.33: 3 Dihedral angle restraints: 3700 sinusoidal: 1491 harmonic: 2209 Sorted by residual: dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 112 " pdb=" CB CYS C 112 " ideal model delta sinusoidal sigma weight residual 93.00 132.33 -39.33 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" C16 HJM A 701 " pdb=" O HJM A 701 " pdb=" C18 HJM A 701 " pdb=" C20 HJM A 701 " ideal model delta sinusoidal sigma weight residual -178.78 -1.45 -177.33 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 HJM A 701 " pdb=" O HJM A 701 " pdb=" C18 HJM A 701 " pdb=" C20 HJM A 701 " ideal model delta sinusoidal sigma weight residual 1.28 173.41 -172.13 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 3697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 843 0.073 - 0.146: 105 0.146 - 0.219: 7 0.219 - 0.292: 2 0.292 - 0.365: 2 Chirality restraints: 959 Sorted by residual: chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C2 HJM A 701 " pdb=" C1 HJM A 701 " pdb=" C5 HJM A 701 " pdb=" C8 HJM A 701 " both_signs ideal model delta sigma weight residual False -2.62 -2.28 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE C 99 " pdb=" CA ILE C 99 " pdb=" CG1 ILE C 99 " pdb=" CG2 ILE C 99 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 956 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O HJM A 701 " -0.042 2.00e-02 2.50e+03 7.19e-02 1.55e+02 pdb=" C11 HJM A 701 " 0.051 2.00e-02 2.50e+03 pdb=" C12 HJM A 701 " 0.086 2.00e-02 2.50e+03 pdb=" C13 HJM A 701 " -0.014 2.00e-02 2.50e+03 pdb=" C15 HJM A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C16 HJM A 701 " -0.129 2.00e-02 2.50e+03 pdb=" C17 HJM A 701 " 0.068 2.00e-02 2.50e+03 pdb=" C18 HJM A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C19 HJM A 701 " 0.105 2.00e-02 2.50e+03 pdb=" C2 HJM A 701 " -0.018 2.00e-02 2.50e+03 pdb=" C8 HJM A 701 " 0.013 2.00e-02 2.50e+03 pdb=" N2 HJM A 701 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 498 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 499 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 560 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO A 561 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.034 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 4 2.35 - 2.99: 2805 2.99 - 3.63: 8634 3.63 - 4.26: 13558 4.26 - 4.90: 21559 Nonbonded interactions: 46560 Sorted by model distance: nonbonded pdb=" OH TYR A 107 " pdb=" OE2 GLU A 493 " model vdw 1.715 2.440 nonbonded pdb=" OH TYR A 107 " pdb=" CD GLU A 493 " model vdw 1.910 3.270 nonbonded pdb=" OH TYR A 107 " pdb=" OE1 GLU A 493 " model vdw 2.001 2.440 nonbonded pdb=" CZ TYR A 107 " pdb=" OE2 GLU A 493 " model vdw 2.262 3.260 nonbonded pdb=" O5' LMT A 704 " pdb=" O6' LMT A 704 " model vdw 2.358 2.432 ... (remaining 46555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 3.460 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: 12.000 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.450 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 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 : 0.005 0.103 6326 Z= 0.312 Angle : 0.846 11.877 8614 Z= 0.427 Chirality : 0.052 0.365 959 Planarity : 0.008 0.072 1050 Dihedral : 11.997 177.328 2289 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.16 % Allowed : 1.40 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.22), residues: 762 helix: -4.59 (0.10), residues: 301 sheet: -2.47 (0.50), residues: 94 loop : -2.71 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 130 HIS 0.002 0.001 HIS A 143 PHE 0.035 0.001 PHE A 454 TYR 0.015 0.002 TYR C 73 ARG 0.012 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8563 (t80) cc_final: 0.8339 (t80) REVERT: A 145 ASN cc_start: 0.8176 (m110) cc_final: 0.7690 (m-40) REVERT: A 272 LYS cc_start: 0.6303 (mmtt) cc_final: 0.5992 (pttt) REVERT: A 326 TRP cc_start: 0.7372 (m-10) cc_final: 0.7098 (m-10) REVERT: A 385 TYR cc_start: 0.8146 (t80) cc_final: 0.7512 (t80) REVERT: A 558 MET cc_start: 0.4587 (tpt) cc_final: 0.3420 (mtt) REVERT: B 50 TYR cc_start: 0.4382 (t80) cc_final: 0.4068 (t80) REVERT: B 101 GLN cc_start: 0.6951 (mt0) cc_final: 0.6228 (tm-30) REVERT: B 102 LEU cc_start: 0.8568 (mt) cc_final: 0.8270 (tt) REVERT: B 108 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 127 MET cc_start: 0.5917 (mtp) cc_final: 0.5629 (mtm) REVERT: B 129 TYR cc_start: 0.7339 (m-10) cc_final: 0.6536 (m-80) REVERT: C 22 ILE cc_start: 0.7416 (mt) cc_final: 0.7206 (mp) REVERT: C 112 CYS cc_start: 0.4762 (t) cc_final: 0.4471 (t) REVERT: C 116 LYS cc_start: 0.7015 (tttt) cc_final: 0.6421 (mttt) outliers start: 1 outliers final: 1 residues processed: 218 average time/residue: 0.1900 time to fit residues: 53.1537 Evaluate side-chains 133 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.0070 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 0.0170 chunk 38 optimal weight: 0.0170 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 overall best weight: 0.7876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 202 ASN A 254 GLN B 25 GLN B 58 GLN C 51 ASN C 100 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6326 Z= 0.158 Angle : 0.660 11.377 8614 Z= 0.320 Chirality : 0.043 0.264 959 Planarity : 0.005 0.050 1050 Dihedral : 10.232 145.291 974 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.26 % Allowed : 10.23 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.26), residues: 762 helix: -2.81 (0.21), residues: 318 sheet: -1.98 (0.51), residues: 87 loop : -2.37 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 541 HIS 0.003 0.001 HIS A 223 PHE 0.033 0.001 PHE A 454 TYR 0.017 0.001 TYR A 495 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8498 (t80) cc_final: 0.8022 (t80) REVERT: A 205 ASN cc_start: 0.6492 (t0) cc_final: 0.6283 (t0) REVERT: A 272 LYS cc_start: 0.6346 (mmtt) cc_final: 0.6070 (pttt) REVERT: A 526 LYS cc_start: 0.7612 (mttt) cc_final: 0.7152 (ttmm) REVERT: A 548 PHE cc_start: 0.7690 (m-80) cc_final: 0.7225 (t80) REVERT: A 558 MET cc_start: 0.4410 (tpt) cc_final: 0.3428 (mtt) REVERT: B 38 ARG cc_start: 0.7948 (ttt90) cc_final: 0.7721 (ttt90) REVERT: B 50 TYR cc_start: 0.4189 (t80) cc_final: 0.3545 (t80) REVERT: B 101 GLN cc_start: 0.7210 (mt0) cc_final: 0.6654 (pt0) REVERT: B 102 LEU cc_start: 0.8537 (mt) cc_final: 0.8227 (tt) REVERT: B 129 TYR cc_start: 0.7528 (m-10) cc_final: 0.7077 (m-10) REVERT: C 22 ILE cc_start: 0.7400 (mt) cc_final: 0.7106 (mp) REVERT: C 44 ARG cc_start: 0.6314 (mmt-90) cc_final: 0.5198 (mmm160) REVERT: C 86 PHE cc_start: 0.5504 (m-80) cc_final: 0.5261 (m-10) REVERT: C 116 LYS cc_start: 0.7029 (tttt) cc_final: 0.6294 (ptpt) outliers start: 21 outliers final: 17 residues processed: 139 average time/residue: 0.1836 time to fit residues: 34.2364 Evaluate side-chains 125 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6326 Z= 0.150 Angle : 0.589 9.364 8614 Z= 0.287 Chirality : 0.041 0.261 959 Planarity : 0.005 0.044 1050 Dihedral : 9.105 155.316 974 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.88 % Allowed : 12.40 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.28), residues: 762 helix: -1.66 (0.26), residues: 326 sheet: -1.38 (0.57), residues: 83 loop : -2.18 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 541 HIS 0.003 0.001 HIS C 100 PHE 0.024 0.001 PHE A 454 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.6469 (t0) cc_final: 0.6216 (t0) REVERT: A 272 LYS cc_start: 0.6388 (mmtt) cc_final: 0.6057 (pttt) REVERT: A 375 SER cc_start: 0.8748 (m) cc_final: 0.8132 (t) REVERT: A 526 LYS cc_start: 0.7688 (mttt) cc_final: 0.7254 (ttmm) REVERT: A 548 PHE cc_start: 0.7651 (m-80) cc_final: 0.7198 (t80) REVERT: A 558 MET cc_start: 0.4420 (tpt) cc_final: 0.3448 (mtt) REVERT: B 50 TYR cc_start: 0.4221 (t80) cc_final: 0.3533 (t80) REVERT: B 101 GLN cc_start: 0.7221 (mt0) cc_final: 0.6733 (pt0) REVERT: B 102 LEU cc_start: 0.8544 (mt) cc_final: 0.8228 (tt) REVERT: C 116 LYS cc_start: 0.6990 (tttt) cc_final: 0.6210 (ptpt) outliers start: 25 outliers final: 19 residues processed: 135 average time/residue: 0.1810 time to fit residues: 32.4216 Evaluate side-chains 127 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 35 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6326 Z= 0.203 Angle : 0.611 9.390 8614 Z= 0.302 Chirality : 0.042 0.266 959 Planarity : 0.005 0.055 1050 Dihedral : 7.865 122.788 974 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.74 % Allowed : 13.33 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.29), residues: 762 helix: -1.02 (0.28), residues: 320 sheet: -1.13 (0.55), residues: 88 loop : -1.87 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 541 HIS 0.003 0.001 HIS C 100 PHE 0.017 0.001 PHE A 454 TYR 0.017 0.002 TYR A 592 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.6590 (t0) cc_final: 0.6309 (t0) REVERT: A 375 SER cc_start: 0.8684 (m) cc_final: 0.8101 (t) REVERT: A 526 LYS cc_start: 0.7717 (mttt) cc_final: 0.7092 (tmtt) REVERT: A 528 MET cc_start: 0.7773 (ptp) cc_final: 0.7431 (pmm) REVERT: A 558 MET cc_start: 0.4455 (tpt) cc_final: 0.3553 (mtt) REVERT: B 38 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7783 (tpt170) REVERT: B 69 ARG cc_start: 0.7947 (ptm160) cc_final: 0.7227 (ptm160) REVERT: B 101 GLN cc_start: 0.7398 (mt0) cc_final: 0.7066 (pt0) REVERT: B 102 LEU cc_start: 0.8692 (mt) cc_final: 0.8363 (tt) REVERT: C 44 ARG cc_start: 0.6024 (mmt180) cc_final: 0.5505 (mmm160) REVERT: C 116 LYS cc_start: 0.7075 (tttt) cc_final: 0.6114 (ptpt) outliers start: 37 outliers final: 27 residues processed: 132 average time/residue: 0.1690 time to fit residues: 29.9765 Evaluate side-chains 131 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 537 TRP Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6326 Z= 0.135 Angle : 0.559 9.308 8614 Z= 0.274 Chirality : 0.040 0.254 959 Planarity : 0.004 0.044 1050 Dihedral : 5.980 61.478 974 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.57 % Allowed : 15.81 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.31), residues: 762 helix: -0.48 (0.30), residues: 311 sheet: -1.21 (0.53), residues: 92 loop : -1.59 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 197 HIS 0.002 0.000 HIS C 100 PHE 0.017 0.001 PHE A 454 TYR 0.013 0.001 TYR B 71 ARG 0.003 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.6520 (t0) cc_final: 0.6238 (t0) REVERT: A 215 GLU cc_start: 0.6986 (mp0) cc_final: 0.6478 (mp0) REVERT: A 375 SER cc_start: 0.8711 (m) cc_final: 0.8106 (t) REVERT: A 526 LYS cc_start: 0.7752 (mttt) cc_final: 0.7122 (tmtt) REVERT: A 528 MET cc_start: 0.7761 (ptp) cc_final: 0.7411 (pmm) REVERT: A 558 MET cc_start: 0.4483 (tpt) cc_final: 0.3544 (mtt) REVERT: B 38 ARG cc_start: 0.8043 (ttt90) cc_final: 0.7840 (ttt90) REVERT: B 101 GLN cc_start: 0.7345 (mt0) cc_final: 0.6929 (pt0) REVERT: B 102 LEU cc_start: 0.8670 (mt) cc_final: 0.8298 (tt) REVERT: C 44 ARG cc_start: 0.5956 (mmt180) cc_final: 0.5697 (mmm160) REVERT: C 105 ASP cc_start: 0.8457 (t0) cc_final: 0.7983 (t0) REVERT: C 116 LYS cc_start: 0.6876 (tttt) cc_final: 0.6178 (ptpt) outliers start: 23 outliers final: 16 residues processed: 129 average time/residue: 0.1711 time to fit residues: 29.5800 Evaluate side-chains 123 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 10.0000 chunk 66 optimal weight: 0.0030 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN B 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6326 Z= 0.133 Angle : 0.532 9.362 8614 Z= 0.262 Chirality : 0.040 0.261 959 Planarity : 0.004 0.039 1050 Dihedral : 5.270 58.817 974 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.88 % Allowed : 15.66 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.31), residues: 762 helix: -0.27 (0.30), residues: 319 sheet: -1.14 (0.53), residues: 93 loop : -1.54 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 541 HIS 0.001 0.000 HIS C 100 PHE 0.014 0.001 PHE A 454 TYR 0.015 0.001 TYR B 129 ARG 0.003 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.7993 (ttp) cc_final: 0.7769 (ttt) REVERT: A 205 ASN cc_start: 0.6531 (t0) cc_final: 0.6250 (t0) REVERT: A 215 GLU cc_start: 0.6969 (mp0) cc_final: 0.6449 (mp0) REVERT: A 375 SER cc_start: 0.8709 (m) cc_final: 0.8105 (t) REVERT: A 475 PHE cc_start: 0.6066 (m-80) cc_final: 0.5821 (m-80) REVERT: A 526 LYS cc_start: 0.7787 (mttt) cc_final: 0.7148 (tmtt) REVERT: A 528 MET cc_start: 0.7724 (ptp) cc_final: 0.7353 (pmm) REVERT: A 558 MET cc_start: 0.4511 (tpt) cc_final: 0.3587 (mtt) REVERT: B 38 ARG cc_start: 0.8082 (ttt90) cc_final: 0.7581 (ttt90) REVERT: B 101 GLN cc_start: 0.7349 (mt0) cc_final: 0.6932 (pt0) REVERT: B 102 LEU cc_start: 0.8652 (mt) cc_final: 0.8299 (tt) REVERT: B 125 PHE cc_start: 0.4883 (p90) cc_final: 0.4670 (p90) REVERT: C 44 ARG cc_start: 0.5932 (mmt180) cc_final: 0.5484 (mmm160) REVERT: C 116 LYS cc_start: 0.6818 (tttt) cc_final: 0.6127 (ptpt) outliers start: 25 outliers final: 23 residues processed: 124 average time/residue: 0.1861 time to fit residues: 30.8314 Evaluate side-chains 128 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 44 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6326 Z= 0.135 Angle : 0.562 11.245 8614 Z= 0.271 Chirality : 0.040 0.262 959 Planarity : 0.004 0.046 1050 Dihedral : 5.180 58.883 974 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.57 % Allowed : 17.21 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.31), residues: 762 helix: -0.13 (0.30), residues: 323 sheet: -1.07 (0.52), residues: 93 loop : -1.52 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 541 HIS 0.001 0.000 HIS A 235 PHE 0.013 0.001 PHE A 454 TYR 0.011 0.001 TYR A 592 ARG 0.004 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8008 (ttp) cc_final: 0.7776 (ttt) REVERT: A 205 ASN cc_start: 0.6531 (t0) cc_final: 0.6250 (t0) REVERT: A 215 GLU cc_start: 0.6952 (mp0) cc_final: 0.6422 (mp0) REVERT: A 286 THR cc_start: 0.6116 (p) cc_final: 0.5899 (p) REVERT: A 302 LEU cc_start: 0.8736 (tp) cc_final: 0.8147 (tp) REVERT: A 375 SER cc_start: 0.8706 (m) cc_final: 0.8144 (t) REVERT: A 475 PHE cc_start: 0.6099 (m-80) cc_final: 0.5818 (m-80) REVERT: A 526 LYS cc_start: 0.7692 (mttt) cc_final: 0.7057 (tmtt) REVERT: A 528 MET cc_start: 0.7716 (ptp) cc_final: 0.7321 (pmm) REVERT: A 558 MET cc_start: 0.4617 (tpt) cc_final: 0.3697 (mtt) REVERT: B 38 ARG cc_start: 0.8097 (ttt90) cc_final: 0.7784 (tpt170) REVERT: B 101 GLN cc_start: 0.7355 (mt0) cc_final: 0.7032 (pt0) REVERT: B 102 LEU cc_start: 0.8624 (mt) cc_final: 0.8279 (tt) REVERT: B 125 PHE cc_start: 0.4923 (p90) cc_final: 0.4699 (p90) REVERT: B 129 TYR cc_start: 0.7393 (m-10) cc_final: 0.6863 (m-80) REVERT: C 44 ARG cc_start: 0.5916 (mmt180) cc_final: 0.5483 (mmm160) REVERT: C 116 LYS cc_start: 0.6814 (tttt) cc_final: 0.6097 (ptpt) outliers start: 23 outliers final: 21 residues processed: 124 average time/residue: 0.1930 time to fit residues: 31.5599 Evaluate side-chains 127 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 0.0000 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.175 Angle : 0.580 9.619 8614 Z= 0.283 Chirality : 0.041 0.267 959 Planarity : 0.004 0.043 1050 Dihedral : 5.231 58.631 974 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.03 % Allowed : 17.21 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.31), residues: 762 helix: -0.11 (0.29), residues: 326 sheet: -1.02 (0.52), residues: 92 loop : -1.52 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 541 HIS 0.001 0.000 HIS C 100 PHE 0.012 0.001 PHE A 454 TYR 0.013 0.001 TYR A 592 ARG 0.010 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7675 (tpt) cc_final: 0.7405 (tpt) REVERT: A 135 MET cc_start: 0.8117 (ttp) cc_final: 0.7884 (ttt) REVERT: A 205 ASN cc_start: 0.6583 (t0) cc_final: 0.6336 (t0) REVERT: A 375 SER cc_start: 0.8677 (m) cc_final: 0.8188 (t) REVERT: A 475 PHE cc_start: 0.6253 (m-80) cc_final: 0.5915 (m-80) REVERT: A 526 LYS cc_start: 0.7772 (mttt) cc_final: 0.7147 (tmtt) REVERT: A 558 MET cc_start: 0.4644 (tpt) cc_final: 0.3661 (mtt) REVERT: B 38 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7791 (tpt170) REVERT: B 101 GLN cc_start: 0.7383 (mt0) cc_final: 0.7079 (pt0) REVERT: B 102 LEU cc_start: 0.8731 (mt) cc_final: 0.8392 (tt) REVERT: B 129 TYR cc_start: 0.7587 (m-10) cc_final: 0.6988 (m-80) REVERT: C 44 ARG cc_start: 0.5913 (mmt180) cc_final: 0.5440 (mmm160) REVERT: C 69 LYS cc_start: 0.7446 (tmtt) cc_final: 0.6453 (ptpt) REVERT: C 102 MET cc_start: 0.7722 (pmm) cc_final: 0.7073 (pmm) REVERT: C 116 LYS cc_start: 0.6925 (tttt) cc_final: 0.6037 (ptpt) outliers start: 26 outliers final: 24 residues processed: 127 average time/residue: 0.1711 time to fit residues: 28.9954 Evaluate side-chains 130 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 34 optimal weight: 0.0970 chunk 50 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6326 Z= 0.149 Angle : 0.568 9.714 8614 Z= 0.278 Chirality : 0.040 0.260 959 Planarity : 0.004 0.040 1050 Dihedral : 5.176 58.311 974 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.03 % Allowed : 17.98 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.31), residues: 762 helix: 0.13 (0.30), residues: 321 sheet: -0.89 (0.52), residues: 92 loop : -1.52 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 541 HIS 0.000 0.000 HIS A 235 PHE 0.012 0.001 PHE A 454 TYR 0.011 0.001 TYR A 592 ARG 0.009 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7746 (tpt) cc_final: 0.7530 (tpt) REVERT: A 135 MET cc_start: 0.8096 (ttp) cc_final: 0.7819 (ttt) REVERT: A 205 ASN cc_start: 0.6567 (t0) cc_final: 0.6327 (t0) REVERT: A 375 SER cc_start: 0.8713 (m) cc_final: 0.8226 (t) REVERT: A 526 LYS cc_start: 0.7748 (mttt) cc_final: 0.7136 (tmtt) REVERT: A 528 MET cc_start: 0.7596 (ptp) cc_final: 0.7305 (pmm) REVERT: A 558 MET cc_start: 0.4664 (tpt) cc_final: 0.3680 (mtt) REVERT: A 570 TYR cc_start: 0.5192 (OUTLIER) cc_final: 0.4481 (m-80) REVERT: B 38 ARG cc_start: 0.8103 (ttt90) cc_final: 0.7743 (tpt170) REVERT: B 101 GLN cc_start: 0.7414 (mt0) cc_final: 0.7044 (pt0) REVERT: B 102 LEU cc_start: 0.8731 (mt) cc_final: 0.8388 (tt) REVERT: C 44 ARG cc_start: 0.5948 (mmt180) cc_final: 0.5528 (mmm160) REVERT: C 69 LYS cc_start: 0.7414 (tmtt) cc_final: 0.6451 (ptpt) REVERT: C 102 MET cc_start: 0.7475 (pmm) cc_final: 0.7146 (pmm) REVERT: C 116 LYS cc_start: 0.6887 (tttt) cc_final: 0.5932 (ptpt) outliers start: 26 outliers final: 24 residues processed: 122 average time/residue: 0.1774 time to fit residues: 28.7148 Evaluate side-chains 128 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.0030 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.0370 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6326 Z= 0.168 Angle : 0.592 10.040 8614 Z= 0.288 Chirality : 0.041 0.269 959 Planarity : 0.004 0.039 1050 Dihedral : 5.306 58.504 974 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.19 % Allowed : 17.83 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.31), residues: 762 helix: 0.07 (0.30), residues: 329 sheet: -0.76 (0.52), residues: 92 loop : -1.48 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 151 HIS 0.001 0.000 HIS C 100 PHE 0.025 0.001 PHE A 341 TYR 0.025 0.001 TYR B 129 ARG 0.020 0.001 ARG A 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7797 (tpt) cc_final: 0.7587 (tpt) REVERT: A 135 MET cc_start: 0.8103 (ttp) cc_final: 0.7852 (ttt) REVERT: A 205 ASN cc_start: 0.6629 (t0) cc_final: 0.6377 (t0) REVERT: A 375 SER cc_start: 0.8752 (m) cc_final: 0.8307 (t) REVERT: A 475 PHE cc_start: 0.6290 (m-80) cc_final: 0.6073 (m-80) REVERT: A 526 LYS cc_start: 0.7754 (mttt) cc_final: 0.7146 (tmtt) REVERT: A 528 MET cc_start: 0.7677 (ptp) cc_final: 0.7343 (pmm) REVERT: A 570 TYR cc_start: 0.5260 (OUTLIER) cc_final: 0.4454 (m-80) REVERT: B 38 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7733 (tpt170) REVERT: B 101 GLN cc_start: 0.7421 (mt0) cc_final: 0.7080 (pt0) REVERT: B 102 LEU cc_start: 0.8715 (mt) cc_final: 0.8388 (tt) REVERT: B 129 TYR cc_start: 0.7489 (m-10) cc_final: 0.7045 (m-80) REVERT: C 44 ARG cc_start: 0.5896 (mmt180) cc_final: 0.5467 (mmm160) REVERT: C 69 LYS cc_start: 0.7463 (tmtt) cc_final: 0.6485 (ptpt) REVERT: C 102 MET cc_start: 0.7700 (pmm) cc_final: 0.7303 (pmm) REVERT: C 116 LYS cc_start: 0.6901 (tttt) cc_final: 0.5932 (ptpt) outliers start: 27 outliers final: 25 residues processed: 126 average time/residue: 0.1799 time to fit residues: 30.3678 Evaluate side-chains 133 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.0770 chunk 25 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 51 optimal weight: 6.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** 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 = 0.4174 r_free = 0.4174 target = 0.153133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.135224 restraints weight = 13400.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.139042 restraints weight = 7005.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.141614 restraints weight = 4458.462| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6326 Z= 0.142 Angle : 0.573 10.179 8614 Z= 0.278 Chirality : 0.041 0.259 959 Planarity : 0.004 0.038 1050 Dihedral : 5.233 58.271 974 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.41 % Allowed : 18.91 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.31), residues: 762 helix: 0.16 (0.30), residues: 329 sheet: -0.65 (0.53), residues: 93 loop : -1.45 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 458 HIS 0.001 0.000 HIS C 100 PHE 0.024 0.001 PHE A 341 TYR 0.018 0.001 TYR B 129 ARG 0.012 0.001 ARG A 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.45 seconds wall clock time: 32 minutes 51.22 seconds (1971.22 seconds total)