Starting phenix.real_space_refine on Thu Jun 27 21:06:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/06_2024/8z9q_39867_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/06_2024/8z9q_39867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/06_2024/8z9q_39867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/06_2024/8z9q_39867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/06_2024/8z9q_39867_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/06_2024/8z9q_39867_updated.pdb" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 74 5.16 5 C 7803 2.51 5 N 2153 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12362 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5020 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5190 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 33, 'TRANS': 613} Chain breaks: 4 Chain: "C" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1926 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 226 Unusual residues: {'ATP': 1} Classifications: {'RNA': 9, 'undetermined': 1} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 5, None: 1} Not linked: pdbres="ATP D 1 " pdbres=" G D 2 " Time building chain proxies: 7.31, per 1000 atoms: 0.59 Number of scatterers: 12362 At special positions: 0 Unit cell: (91.104, 100.74, 134.028, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 12 15.00 O 2320 8.00 N 2153 7.00 C 7803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.1 seconds 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2878 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 12 sheets defined 43.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 4.964A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 65 through 76 removed outlier: 4.273A pdb=" N LYS A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 76 " --> pdb=" O CYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 135 through 154 removed outlier: 4.739A pdb=" N ARG A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU A 150 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.525A pdb=" N ARG A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.502A pdb=" N THR A 275 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.616A pdb=" N ALA A 300 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 301 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.121A pdb=" N GLN A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 363 through 380 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.594A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 516 removed outlier: 3.593A pdb=" N ASN A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ARG A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL A 497 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLN A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Proline residue: A 501 - end of helix Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 560 through 580 removed outlier: 4.458A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 removed outlier: 3.844A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 615 Processing helix chain 'B' and resid 2 through 4 No H-bonds generated for 'chain 'B' and resid 2 through 4' Processing helix chain 'B' and resid 12 through 18 removed outlier: 4.362A pdb=" N GLU B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 135 through 150 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.780A pdb=" N GLU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 248 through 267 removed outlier: 4.398A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 329 through 344 Proline residue: B 338 - end of helix removed outlier: 3.541A pdb=" N SER B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 4.315A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 408 removed outlier: 3.508A pdb=" N THR B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 448 Processing helix chain 'B' and resid 497 through 513 Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 544 through 551 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 667 through 670 Processing helix chain 'B' and resid 680 through 693 Processing helix chain 'B' and resid 699 through 708 removed outlier: 3.559A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 26 Processing helix chain 'C' and resid 28 through 31 No H-bonds generated for 'chain 'C' and resid 28 through 31' Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.624A pdb=" N PHE C 41 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS C 42 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 43 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 103 through 110 removed outlier: 3.853A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 127 through 134 Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 192 through 203 Proline residue: C 202 - end of helix Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.598A pdb=" N ILE C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 238 No H-bonds generated for 'chain 'C' and resid 235 through 238' Processing helix chain 'C' and resid 241 through 244 No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing sheet with id= A, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.814A pdb=" N HIS A 115 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU A 99 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 117 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.775A pdb=" N ILE A 414 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N MET A 428 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS A 412 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 430 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 410 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.865A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER A 466 " --> pdb=" O CYS A 262 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N CYS A 262 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LYS A 468 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE A 260 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 526 through 531 Processing sheet with id= E, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.502A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 227 through 230 Processing sheet with id= G, first strand: chain 'B' and resid 460 through 462 Processing sheet with id= H, first strand: chain 'B' and resid 353 through 355 Processing sheet with id= I, first strand: chain 'B' and resid 467 through 470 Processing sheet with id= J, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.867A pdb=" N THR C 97 " --> pdb=" O MET C 69 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= L, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.605A pdb=" N LYS C 151 " --> pdb=" O LEU C 227 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1260 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: 3.44 Time building geometry restraints manager: 5.20 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: 3994 1.34 - 1.46: 1800 1.46 - 1.57: 6720 1.57 - 1.69: 22 1.69 - 1.81: 120 Bond restraints: 12656 Sorted by residual: bond pdb=" CB ARG B 315 " pdb=" CG ARG B 315 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CB ILE B 452 " pdb=" CG2 ILE B 452 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CA ARG A 147 " pdb=" CB ARG A 147 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.17e+00 bond pdb=" CG1 ILE A 606 " pdb=" CD1 ILE A 606 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.14e-01 bond pdb=" N LYS B 357 " pdb=" CA LYS B 357 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.24e-02 6.50e+03 6.12e-01 ... (remaining 12651 not shown) Histogram of bond angle deviations from ideal: 99.23 - 107.39: 593 107.39 - 115.54: 7771 115.54 - 123.69: 8412 123.69 - 131.85: 372 131.85 - 140.00: 36 Bond angle restraints: 17184 Sorted by residual: angle pdb=" C CYS A 146 " pdb=" N ARG A 147 " pdb=" CA ARG A 147 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" N ARG A 147 " pdb=" CA ARG A 147 " pdb=" CB ARG A 147 " ideal model delta sigma weight residual 110.49 115.74 -5.25 1.69e+00 3.50e-01 9.64e+00 angle pdb=" CA ARG A 147 " pdb=" CB ARG A 147 " pdb=" CG ARG A 147 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.63e+00 angle pdb=" CG1 ILE B 452 " pdb=" CB ILE B 452 " pdb=" CG2 ILE B 452 " ideal model delta sigma weight residual 110.70 102.97 7.73 3.00e+00 1.11e-01 6.63e+00 angle pdb=" CA LEU B 487 " pdb=" CB LEU B 487 " pdb=" CG LEU B 487 " ideal model delta sigma weight residual 116.30 124.66 -8.36 3.50e+00 8.16e-02 5.71e+00 ... (remaining 17179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7114 17.77 - 35.53: 493 35.53 - 53.30: 87 53.30 - 71.07: 25 71.07 - 88.83: 14 Dihedral angle restraints: 7733 sinusoidal: 3307 harmonic: 4426 Sorted by residual: dihedral pdb=" CA ARG A 147 " pdb=" C ARG A 147 " pdb=" N ALA A 148 " pdb=" CA ALA A 148 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU A 145 " pdb=" C LEU A 145 " pdb=" N CYS A 146 " pdb=" CA CYS A 146 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS C 233 " pdb=" C HIS C 233 " pdb=" N THR C 234 " pdb=" CA THR C 234 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1354 0.036 - 0.072: 417 0.072 - 0.108: 115 0.108 - 0.145: 31 0.145 - 0.181: 2 Chirality restraints: 1919 Sorted by residual: chirality pdb=" CB ILE B 452 " pdb=" CA ILE B 452 " pdb=" CG1 ILE B 452 " pdb=" CG2 ILE B 452 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CG LEU A 550 " pdb=" CB LEU A 550 " pdb=" CD1 LEU A 550 " pdb=" CD2 LEU A 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ARG A 147 " pdb=" N ARG A 147 " pdb=" C ARG A 147 " pdb=" CB ARG A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1916 not shown) Planarity restraints: 2158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 463 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 464 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 604 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 605 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 11 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B 12 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 12 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 12 " -0.023 5.00e-02 4.00e+02 ... (remaining 2155 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 236 2.67 - 3.23: 11979 3.23 - 3.79: 19939 3.79 - 4.34: 28339 4.34 - 4.90: 45333 Nonbonded interactions: 105826 Sorted by model distance: nonbonded pdb=" OG SER B 472 " pdb=" O VAL B 483 " model vdw 2.117 2.440 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.134 2.440 nonbonded pdb=" O ASN C 163 " pdb=" OG SER C 166 " model vdw 2.211 2.440 nonbonded pdb=" O THR A 269 " pdb=" OG SER A 463 " model vdw 2.238 2.440 nonbonded pdb=" OD1 ASP B 172 " pdb=" NH2 ARG B 216 " model vdw 2.243 2.520 ... (remaining 105821 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 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 5.860 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.620 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.003 0.036 12656 Z= 0.170 Angle : 0.534 11.412 17184 Z= 0.277 Chirality : 0.040 0.181 1919 Planarity : 0.005 0.042 2158 Dihedral : 13.208 88.832 4855 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1489 helix: 1.12 (0.20), residues: 688 sheet: 0.62 (0.47), residues: 124 loop : -0.35 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.006 0.001 HIS A 573 PHE 0.027 0.002 PHE A 483 TYR 0.019 0.001 TYR B 104 ARG 0.006 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.418 Fit side-chains REVERT: A 86 ASP cc_start: 0.7653 (m-30) cc_final: 0.7424 (m-30) REVERT: A 139 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 163 GLU cc_start: 0.8261 (tp30) cc_final: 0.7851 (tp30) REVERT: A 307 GLN cc_start: 0.7293 (pp30) cc_final: 0.7090 (pp30) REVERT: B 30 TYR cc_start: 0.7834 (m-80) cc_final: 0.7596 (m-80) REVERT: B 243 ILE cc_start: 0.9069 (pt) cc_final: 0.8855 (pp) REVERT: B 283 LYS cc_start: 0.8272 (tptt) cc_final: 0.8033 (tppt) REVERT: B 287 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7626 (tmtt) REVERT: B 672 GLN cc_start: 0.7878 (mt0) cc_final: 0.7360 (pt0) REVERT: C 127 ASP cc_start: 0.7121 (t0) cc_final: 0.6828 (t0) REVERT: C 201 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 210 GLU cc_start: 0.7759 (pm20) cc_final: 0.7545 (mp0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 1.7271 time to fit residues: 417.9965 Evaluate side-chains 174 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 71 ASN B 267 ASN B 302 GLN B 397 ASN B 433 HIS ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN C 154 GLN C 214 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12656 Z= 0.368 Angle : 0.618 7.794 17184 Z= 0.326 Chirality : 0.044 0.152 1919 Planarity : 0.005 0.055 2158 Dihedral : 8.940 82.857 1797 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.51 % Allowed : 8.51 % Favored : 88.98 % 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: 0.29 (0.21), residues: 1489 helix: 0.86 (0.20), residues: 694 sheet: 0.52 (0.47), residues: 118 loop : -0.49 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 336 HIS 0.011 0.002 HIS A 577 PHE 0.029 0.002 PHE C 41 TYR 0.018 0.002 TYR B 115 ARG 0.006 0.001 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.539 Fit side-chains REVERT: A 17 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7447 (tp30) REVERT: A 47 ASN cc_start: 0.7695 (t0) cc_final: 0.7472 (t0) REVERT: A 64 ASP cc_start: 0.7214 (t0) cc_final: 0.6949 (t0) REVERT: A 86 ASP cc_start: 0.7893 (m-30) cc_final: 0.7580 (m-30) REVERT: A 139 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 163 GLU cc_start: 0.8258 (tp30) cc_final: 0.7843 (tp30) REVERT: A 522 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7723 (mm-30) REVERT: B 144 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7229 (tm-30) REVERT: B 287 LYS cc_start: 0.7940 (tmtt) cc_final: 0.7684 (tmtt) REVERT: B 672 GLN cc_start: 0.7711 (mt0) cc_final: 0.7127 (pt0) REVERT: C 18 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: C 127 ASP cc_start: 0.7210 (t0) cc_final: 0.6855 (m-30) REVERT: C 201 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 210 GLU cc_start: 0.7789 (pm20) cc_final: 0.7589 (mp0) outliers start: 34 outliers final: 12 residues processed: 202 average time/residue: 1.4814 time to fit residues: 320.9101 Evaluate side-chains 192 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 156 ASN B 55 GLN B 123 GLN B 397 ASN B 433 HIS B 506 ASN C 154 GLN C 214 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12656 Z= 0.232 Angle : 0.537 6.966 17184 Z= 0.282 Chirality : 0.040 0.144 1919 Planarity : 0.005 0.051 2158 Dihedral : 8.667 79.867 1797 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.14 % Allowed : 10.58 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1489 helix: 1.02 (0.21), residues: 689 sheet: 0.37 (0.46), residues: 113 loop : -0.50 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.007 0.001 HIS C 233 PHE 0.023 0.002 PHE C 41 TYR 0.013 0.001 TYR B 533 ARG 0.008 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.404 Fit side-chains REVERT: A 64 ASP cc_start: 0.7298 (t0) cc_final: 0.6943 (t0) REVERT: A 86 ASP cc_start: 0.7914 (m-30) cc_final: 0.7578 (m-30) REVERT: A 122 GLU cc_start: 0.7751 (pm20) cc_final: 0.7493 (pm20) REVERT: A 139 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 163 GLU cc_start: 0.8263 (tp30) cc_final: 0.7834 (tp30) REVERT: B 93 ARG cc_start: 0.7293 (mtm110) cc_final: 0.6989 (mtm110) REVERT: B 144 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 576 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: B 685 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7904 (tptp) REVERT: C 18 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8191 (tp30) REVERT: C 127 ASP cc_start: 0.7187 (t0) cc_final: 0.6868 (m-30) REVERT: C 146 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7286 (mtt) REVERT: C 201 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7451 (tm-30) outliers start: 29 outliers final: 8 residues processed: 196 average time/residue: 1.5040 time to fit residues: 315.9603 Evaluate side-chains 186 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 685 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 500 GLN B 397 ASN B 433 HIS B 506 ASN B 672 GLN C 154 GLN C 163 ASN C 214 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12656 Z= 0.180 Angle : 0.504 6.148 17184 Z= 0.264 Chirality : 0.039 0.144 1919 Planarity : 0.004 0.048 2158 Dihedral : 8.369 77.302 1797 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.92 % Allowed : 11.91 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1489 helix: 1.16 (0.21), residues: 690 sheet: 0.28 (0.42), residues: 123 loop : -0.50 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS C 233 PHE 0.021 0.001 PHE C 41 TYR 0.013 0.001 TYR B 533 ARG 0.008 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.488 Fit side-chains REVERT: A 18 THR cc_start: 0.8856 (m) cc_final: 0.8570 (p) REVERT: A 64 ASP cc_start: 0.7346 (t0) cc_final: 0.6969 (t0) REVERT: A 86 ASP cc_start: 0.7884 (m-30) cc_final: 0.7532 (m-30) REVERT: A 139 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7112 (tm-30) REVERT: A 163 GLU cc_start: 0.8269 (tp30) cc_final: 0.7833 (tp30) REVERT: A 212 MET cc_start: 0.7682 (ttp) cc_final: 0.7407 (ttm) REVERT: A 579 MET cc_start: 0.8411 (mtt) cc_final: 0.8020 (mtt) REVERT: B 93 ARG cc_start: 0.7305 (mtm110) cc_final: 0.6987 (mtm110) REVERT: B 144 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 576 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: C 18 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: C 127 ASP cc_start: 0.7193 (t0) cc_final: 0.6907 (m-30) REVERT: C 146 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7336 (mtt) REVERT: C 201 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7450 (tm-30) REVERT: C 210 GLU cc_start: 0.7992 (mp0) cc_final: 0.7779 (mp0) outliers start: 26 outliers final: 12 residues processed: 198 average time/residue: 1.5479 time to fit residues: 328.4129 Evaluate side-chains 186 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 8.9990 chunk 82 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 55 GLN B 397 ASN B 506 ASN C 154 GLN C 163 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12656 Z= 0.227 Angle : 0.525 6.950 17184 Z= 0.275 Chirality : 0.040 0.144 1919 Planarity : 0.004 0.050 2158 Dihedral : 8.339 79.436 1797 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.44 % Allowed : 11.69 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1489 helix: 1.12 (0.21), residues: 689 sheet: 0.25 (0.42), residues: 123 loop : -0.50 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS C 169 PHE 0.022 0.002 PHE C 41 TYR 0.014 0.001 TYR B 533 ARG 0.008 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.728 Fit side-chains REVERT: A 18 THR cc_start: 0.8858 (m) cc_final: 0.8582 (p) REVERT: A 64 ASP cc_start: 0.7349 (t0) cc_final: 0.7010 (t0) REVERT: A 86 ASP cc_start: 0.7889 (m-30) cc_final: 0.7554 (m-30) REVERT: A 139 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7137 (tm-30) REVERT: A 163 GLU cc_start: 0.8279 (tp30) cc_final: 0.7847 (tp30) REVERT: A 205 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6210 (mm-30) REVERT: A 579 MET cc_start: 0.8483 (mtt) cc_final: 0.8052 (mtt) REVERT: B 93 ARG cc_start: 0.7326 (mtm110) cc_final: 0.6992 (mtm110) REVERT: B 144 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: B 287 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7496 (tmtt) REVERT: C 18 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: C 75 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7877 (pt) REVERT: C 127 ASP cc_start: 0.7178 (t0) cc_final: 0.6890 (m-30) REVERT: C 146 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7376 (mtt) REVERT: C 201 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7412 (tm-30) outliers start: 33 outliers final: 12 residues processed: 195 average time/residue: 1.5150 time to fit residues: 316.3256 Evaluate side-chains 191 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.0470 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 0.0470 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 0.0050 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 397 ASN B 506 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 163 ASN C 214 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12656 Z= 0.148 Angle : 0.484 6.573 17184 Z= 0.252 Chirality : 0.038 0.141 1919 Planarity : 0.004 0.043 2158 Dihedral : 8.079 75.508 1797 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.78 % Allowed : 13.24 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1489 helix: 1.27 (0.21), residues: 690 sheet: 0.26 (0.41), residues: 123 loop : -0.46 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 330 HIS 0.004 0.001 HIS A 434 PHE 0.018 0.001 PHE C 41 TYR 0.018 0.001 TYR B 104 ARG 0.008 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.454 Fit side-chains REVERT: A 18 THR cc_start: 0.8780 (m) cc_final: 0.8527 (p) REVERT: A 64 ASP cc_start: 0.7281 (t0) cc_final: 0.6977 (t0) REVERT: A 86 ASP cc_start: 0.7853 (m-30) cc_final: 0.7511 (m-30) REVERT: A 139 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 147 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7604 (ttp80) REVERT: A 163 GLU cc_start: 0.8263 (tp30) cc_final: 0.7819 (tp30) REVERT: A 212 MET cc_start: 0.7761 (ttp) cc_final: 0.7467 (ttm) REVERT: A 470 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 93 ARG cc_start: 0.7260 (mtm110) cc_final: 0.6919 (mtm110) REVERT: B 144 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 287 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7484 (tmtt) REVERT: B 576 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: C 18 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8112 (tp30) REVERT: C 127 ASP cc_start: 0.7018 (t0) cc_final: 0.6765 (m-30) REVERT: C 201 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7493 (tm-30) outliers start: 24 outliers final: 9 residues processed: 193 average time/residue: 1.5204 time to fit residues: 314.4636 Evaluate side-chains 183 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 0.0970 chunk 144 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 88 optimal weight: 0.0870 chunk 66 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 486 ASN A 507 GLN B 397 ASN B 506 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 163 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12656 Z= 0.153 Angle : 0.486 9.149 17184 Z= 0.251 Chirality : 0.038 0.141 1919 Planarity : 0.004 0.042 2158 Dihedral : 7.973 75.003 1797 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.85 % Allowed : 13.24 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1489 helix: 1.37 (0.21), residues: 689 sheet: 0.28 (0.41), residues: 123 loop : -0.44 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS A 434 PHE 0.017 0.001 PHE C 41 TYR 0.013 0.001 TYR B 533 ARG 0.007 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.434 Fit side-chains REVERT: A 18 THR cc_start: 0.8765 (m) cc_final: 0.8499 (p) REVERT: A 86 ASP cc_start: 0.7896 (m-30) cc_final: 0.7555 (m-30) REVERT: A 139 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 147 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7625 (ttp80) REVERT: A 163 GLU cc_start: 0.8263 (tp30) cc_final: 0.7819 (tp30) REVERT: A 470 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 93 ARG cc_start: 0.7238 (mtm110) cc_final: 0.6880 (mtm110) REVERT: B 144 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7237 (tm-30) REVERT: C 18 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8191 (tp30) REVERT: C 127 ASP cc_start: 0.6892 (t0) cc_final: 0.6630 (m-30) REVERT: C 201 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 25 outliers final: 12 residues processed: 198 average time/residue: 1.5253 time to fit residues: 323.4042 Evaluate side-chains 190 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 311 GLN B 397 ASN B 506 ASN C 154 GLN C 163 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12656 Z= 0.205 Angle : 0.513 6.311 17184 Z= 0.267 Chirality : 0.039 0.142 1919 Planarity : 0.004 0.046 2158 Dihedral : 8.065 78.527 1797 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.00 % Allowed : 13.24 % Favored : 84.76 % 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: 0.61 (0.22), residues: 1489 helix: 1.32 (0.21), residues: 690 sheet: 0.26 (0.41), residues: 123 loop : -0.47 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS A 434 PHE 0.020 0.001 PHE C 41 TYR 0.014 0.001 TYR B 533 ARG 0.006 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 1.463 Fit side-chains REVERT: A 18 THR cc_start: 0.8761 (m) cc_final: 0.8506 (p) REVERT: A 86 ASP cc_start: 0.7902 (m-30) cc_final: 0.7542 (m-30) REVERT: A 139 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 163 GLU cc_start: 0.8276 (tp30) cc_final: 0.7831 (tp30) REVERT: B 93 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6855 (mtm110) REVERT: B 144 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: B 682 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6518 (mt-10) REVERT: C 18 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: C 127 ASP cc_start: 0.6975 (t0) cc_final: 0.6714 (m-30) REVERT: C 201 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7497 (tm-30) outliers start: 27 outliers final: 11 residues processed: 195 average time/residue: 1.5654 time to fit residues: 327.9002 Evaluate side-chains 185 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 55 GLN B 397 ASN B 506 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 163 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12656 Z= 0.211 Angle : 0.525 8.780 17184 Z= 0.273 Chirality : 0.039 0.142 1919 Planarity : 0.004 0.045 2158 Dihedral : 8.116 80.504 1797 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.78 % Allowed : 13.91 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1489 helix: 1.28 (0.21), residues: 690 sheet: 0.30 (0.42), residues: 123 loop : -0.50 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS A 434 PHE 0.021 0.001 PHE C 41 TYR 0.021 0.001 TYR B 104 ARG 0.006 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.350 Fit side-chains REVERT: A 18 THR cc_start: 0.8779 (m) cc_final: 0.8537 (p) REVERT: A 86 ASP cc_start: 0.7910 (m-30) cc_final: 0.7553 (m-30) REVERT: A 122 GLU cc_start: 0.7812 (mp0) cc_final: 0.7584 (pm20) REVERT: A 139 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7136 (tm-30) REVERT: A 163 GLU cc_start: 0.8275 (tp30) cc_final: 0.7832 (tp30) REVERT: A 205 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6313 (mm-30) REVERT: B 93 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6866 (mtm110) REVERT: B 144 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: B 286 SER cc_start: 0.8393 (t) cc_final: 0.8008 (p) REVERT: B 576 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: B 694 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7665 (mtp85) REVERT: C 18 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: C 127 ASP cc_start: 0.6997 (t0) cc_final: 0.6746 (m-30) REVERT: C 201 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7474 (tm-30) outliers start: 24 outliers final: 12 residues processed: 183 average time/residue: 1.4907 time to fit residues: 292.1555 Evaluate side-chains 183 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 397 ASN B 506 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12656 Z= 0.242 Angle : 0.546 8.795 17184 Z= 0.284 Chirality : 0.040 0.143 1919 Planarity : 0.004 0.047 2158 Dihedral : 8.212 84.144 1797 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.63 % Allowed : 14.13 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1489 helix: 1.21 (0.21), residues: 690 sheet: 0.33 (0.43), residues: 120 loop : -0.49 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS A 434 PHE 0.023 0.002 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.006 0.000 ARG A 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 1.423 Fit side-chains REVERT: A 18 THR cc_start: 0.8868 (m) cc_final: 0.8564 (p) REVERT: A 86 ASP cc_start: 0.7923 (m-30) cc_final: 0.7542 (m-30) REVERT: A 122 GLU cc_start: 0.7700 (mp0) cc_final: 0.7452 (pm20) REVERT: A 139 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 163 GLU cc_start: 0.8282 (tp30) cc_final: 0.7841 (tp30) REVERT: A 205 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6143 (mm-30) REVERT: B 93 ARG cc_start: 0.7302 (mtm110) cc_final: 0.6951 (mtm110) REVERT: B 144 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: B 286 SER cc_start: 0.8435 (t) cc_final: 0.8030 (p) REVERT: B 576 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: C 18 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8200 (tp30) REVERT: C 127 ASP cc_start: 0.6997 (t0) cc_final: 0.6717 (t0) REVERT: C 201 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7478 (tm-30) outliers start: 22 outliers final: 10 residues processed: 186 average time/residue: 1.5459 time to fit residues: 307.5066 Evaluate side-chains 181 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 506 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099992 restraints weight = 15044.591| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.10 r_work: 0.3143 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12656 Z= 0.214 Angle : 0.538 8.593 17184 Z= 0.279 Chirality : 0.039 0.143 1919 Planarity : 0.004 0.045 2158 Dihedral : 8.182 84.612 1797 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.41 % Allowed : 14.50 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1489 helix: 1.22 (0.21), residues: 689 sheet: 0.33 (0.43), residues: 120 loop : -0.49 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS A 434 PHE 0.022 0.002 PHE C 41 TYR 0.022 0.001 TYR B 104 ARG 0.006 0.000 ARG A 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5511.47 seconds wall clock time: 96 minutes 41.28 seconds (5801.28 seconds total)