Starting phenix.real_space_refine on Wed Mar 4 06:47:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nnp_12482/03_2026/7nnp_12482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nnp_12482/03_2026/7nnp_12482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nnp_12482/03_2026/7nnp_12482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nnp_12482/03_2026/7nnp_12482.map" model { file = "/net/cci-nas-00/data/ceres_data/7nnp_12482/03_2026/7nnp_12482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nnp_12482/03_2026/7nnp_12482.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Rb 8 11.75 5 P 7 5.49 5 S 63 5.16 5 C 7167 2.51 5 N 1837 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11096 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4159 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5067 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 26, 'TRANS': 655} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {' RB': 6, 'CDL': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {' RB': 2, 'ACP': 1, 'CDL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.54, per 1000 atoms: 0.23 Number of scatterers: 11096 At special positions: 0 Unit cell: (83.996, 105.248, 153.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Rb 8 36.98 S 63 16.00 P 7 15.00 O 2014 8.00 N 1837 7.00 C 7167 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 545.9 milliseconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 63.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.541A pdb=" N ARG A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 134 through 157 removed outlier: 3.766A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.622A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.112A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 275 removed outlier: 4.477A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.604A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 305 removed outlier: 4.050A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.132A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 removed outlier: 4.139A pdb=" N LEU A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 437 removed outlier: 3.753A pdb=" N VAL A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.139A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 523 through 548 removed outlier: 4.099A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.624A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.963A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.673A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 removed outlier: 3.642A pdb=" N ILE D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 23 removed outlier: 4.339A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 56 Processing helix chain 'B' and resid 61 through 97 removed outlier: 3.696A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.753A pdb=" N PHE B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 5.726A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 361 removed outlier: 3.728A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 476 through 486 Processing helix chain 'B' and resid 495 through 509 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 557 through 582 Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.515A pdb=" N LYS B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.879A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.329A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 680 Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.486A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.501A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 108 removed outlier: 4.188A pdb=" N ASP B 119 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.586A pdb=" N ILE B 189 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 145 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AA8, first strand: chain 'B' and resid 287 through 289 removed outlier: 5.656A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 467 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU B 491 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 318 through 324 removed outlier: 5.378A pdb=" N ALA B 319 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS B 446 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 444 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 323 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N MET B 383 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE B 377 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 375 " --> pdb=" O GLY B 385 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1959 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: 1.81 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1784 1.31 - 1.44: 2758 1.44 - 1.57: 6618 1.57 - 1.70: 12 1.70 - 1.83: 116 Bond restraints: 11288 Sorted by residual: bond pdb=" CB7 CDL B 703 " pdb=" OB8 CDL B 703 " ideal model delta sigma weight residual 1.334 1.423 -0.089 1.10e-02 8.26e+03 6.59e+01 bond pdb=" CB7 CDL A 607 " pdb=" OB8 CDL A 607 " ideal model delta sigma weight residual 1.334 1.422 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CA7 CDL B 703 " pdb=" OA8 CDL B 703 " ideal model delta sigma weight residual 1.334 1.417 -0.083 1.10e-02 8.26e+03 5.66e+01 bond pdb=" CA7 CDL A 607 " pdb=" OA8 CDL A 607 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.46e+01 bond pdb=" OB2 CDL A 607 " pdb=" PB2 CDL A 607 " ideal model delta sigma weight residual 1.579 1.667 -0.088 1.50e-02 4.44e+03 3.47e+01 ... (remaining 11283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 14923 2.69 - 5.38: 341 5.38 - 8.08: 37 8.08 - 10.77: 16 10.77 - 13.46: 3 Bond angle restraints: 15320 Sorted by residual: angle pdb=" C51 CDL B 703 " pdb=" CB5 CDL B 703 " pdb=" OB6 CDL B 703 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C51 CDL A 607 " pdb=" CB5 CDL A 607 " pdb=" OB6 CDL A 607 " ideal model delta sigma weight residual 111.33 120.13 -8.80 1.32e+00 5.72e-01 4.43e+01 angle pdb=" C11 CDL B 703 " pdb=" CA5 CDL B 703 " pdb=" OA6 CDL B 703 " ideal model delta sigma weight residual 111.33 119.93 -8.60 1.32e+00 5.72e-01 4.23e+01 angle pdb=" C11 CDL A 607 " pdb=" CA5 CDL A 607 " pdb=" OA6 CDL A 607 " ideal model delta sigma weight residual 111.33 119.90 -8.57 1.32e+00 5.72e-01 4.21e+01 angle pdb=" C71 CDL B 703 " pdb=" CB7 CDL B 703 " pdb=" OB8 CDL B 703 " ideal model delta sigma weight residual 111.64 120.24 -8.60 1.65e+00 3.69e-01 2.73e+01 ... (remaining 15315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 6042 19.03 - 38.07: 570 38.07 - 57.10: 142 57.10 - 76.13: 36 76.13 - 95.17: 14 Dihedral angle restraints: 6804 sinusoidal: 2678 harmonic: 4126 Sorted by residual: dihedral pdb=" CA GLU B 364 " pdb=" C GLU B 364 " pdb=" N ARG B 365 " pdb=" CA ARG B 365 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASN A 239 " pdb=" C ASN A 239 " pdb=" N SER A 240 " pdb=" CA SER A 240 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG C 44 " pdb=" C ARG C 44 " pdb=" N GLU C 45 " pdb=" CA GLU C 45 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1249 0.040 - 0.080: 406 0.080 - 0.120: 129 0.120 - 0.160: 35 0.160 - 0.200: 4 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL B 207 " pdb=" CA VAL B 207 " pdb=" CG1 VAL B 207 " pdb=" CG2 VAL B 207 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL A 376 " pdb=" CA VAL A 376 " pdb=" CG1 VAL A 376 " pdb=" CG2 VAL A 376 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1820 not shown) Planarity restraints: 1919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 245 " -0.018 2.00e-02 2.50e+03 1.75e-02 7.65e+00 pdb=" CG TRP B 245 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 245 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 245 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 245 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 245 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 245 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 245 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 245 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 245 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 121 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 122 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 612 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO B 613 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 613 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 613 " 0.030 5.00e-02 4.00e+02 ... (remaining 1916 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.87: 3879 2.87 - 3.51: 14877 3.51 - 4.15: 24359 4.15 - 4.80: 42714 4.80 - 5.44: 53032 Nonbonded interactions: 138861 Sorted by model distance: nonbonded pdb=" O VAL C 118 " pdb=" OG1 THR C 122 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.247 3.040 nonbonded pdb=" OE2 GLU A 321 " pdb=" OG SER C 85 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP A 352 " pdb=" NE2 HIS A 451 " model vdw 2.264 3.120 nonbonded pdb=" OG1 THR A 401 " pdb=" OD2 ASP B 300 " model vdw 2.303 3.040 ... (remaining 138856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.410 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.006 0.089 11288 Z= 0.349 Angle : 0.958 13.459 15320 Z= 0.485 Chirality : 0.046 0.200 1823 Planarity : 0.005 0.066 1919 Dihedral : 16.849 95.167 4152 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1448 helix: 0.15 (0.16), residues: 879 sheet: -0.71 (0.58), residues: 90 loop : -1.44 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 402 TYR 0.029 0.002 TYR A 381 PHE 0.033 0.002 PHE A 260 TRP 0.047 0.002 TRP B 245 HIS 0.009 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00608 (11288) covalent geometry : angle 0.95791 (15320) hydrogen bonds : bond 0.10322 ( 674) hydrogen bonds : angle 5.50008 ( 1959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.382 Fit side-chains REVERT: A 350 MET cc_start: 0.8429 (mmp) cc_final: 0.8035 (mmp) REVERT: C 9 SER cc_start: 0.8684 (m) cc_final: 0.8330 (m) REVERT: B 358 GLN cc_start: 0.7537 (tt0) cc_final: 0.7025 (pt0) REVERT: B 463 MET cc_start: 0.7936 (mtp) cc_final: 0.7732 (mtp) REVERT: B 536 ASN cc_start: 0.6951 (t0) cc_final: 0.6626 (t0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1048 time to fit residues: 22.7199 Evaluate side-chains 120 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107854 restraints weight = 11574.514| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.13 r_work: 0.2970 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11288 Z= 0.239 Angle : 0.636 6.820 15320 Z= 0.323 Chirality : 0.044 0.180 1823 Planarity : 0.005 0.053 1919 Dihedral : 12.933 88.500 1751 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.79 % Allowed : 9.19 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1448 helix: 0.70 (0.17), residues: 872 sheet: -0.45 (0.62), residues: 70 loop : -1.36 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 89 TYR 0.022 0.002 TYR A 381 PHE 0.025 0.002 PHE A 373 TRP 0.013 0.002 TRP B 245 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00574 (11288) covalent geometry : angle 0.63594 (15320) hydrogen bonds : bond 0.04580 ( 674) hydrogen bonds : angle 4.85431 ( 1959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 397 MET cc_start: 0.8757 (mtp) cc_final: 0.8515 (mtp) REVERT: B 339 LEU cc_start: 0.7467 (mm) cc_final: 0.7207 (mm) REVERT: B 358 GLN cc_start: 0.7863 (tt0) cc_final: 0.7261 (pt0) REVERT: B 552 ASP cc_start: 0.7795 (m-30) cc_final: 0.7582 (m-30) REVERT: B 564 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7507 (mt) outliers start: 9 outliers final: 6 residues processed: 129 average time/residue: 0.0928 time to fit residues: 17.9154 Evaluate side-chains 126 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 8.9990 chunk 118 optimal weight: 0.0470 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.152609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112232 restraints weight = 11586.411| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.12 r_work: 0.3045 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11288 Z= 0.116 Angle : 0.524 6.068 15320 Z= 0.266 Chirality : 0.039 0.134 1823 Planarity : 0.004 0.050 1919 Dihedral : 11.898 89.372 1751 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.70 % Allowed : 11.03 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1448 helix: 1.19 (0.17), residues: 877 sheet: -0.32 (0.64), residues: 70 loop : -1.23 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.023 0.001 TYR A 381 PHE 0.019 0.001 PHE A 373 TRP 0.015 0.001 TRP B 186 HIS 0.004 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00257 (11288) covalent geometry : angle 0.52402 (15320) hydrogen bonds : bond 0.03743 ( 674) hydrogen bonds : angle 4.53970 ( 1959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.381 Fit side-chains REVERT: A 413 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: B 186 TRP cc_start: 0.7077 (p-90) cc_final: 0.6843 (p-90) REVERT: B 339 LEU cc_start: 0.7601 (mm) cc_final: 0.7325 (mm) REVERT: B 358 GLN cc_start: 0.7813 (tt0) cc_final: 0.7233 (pt0) REVERT: B 564 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7518 (mt) outliers start: 8 outliers final: 1 residues processed: 125 average time/residue: 0.0943 time to fit residues: 17.4383 Evaluate side-chains 122 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 506 TYR Chi-restraints excluded: chain B residue 564 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 109 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111409 restraints weight = 11618.146| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.22 r_work: 0.3058 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11288 Z= 0.209 Angle : 0.590 7.049 15320 Z= 0.299 Chirality : 0.043 0.171 1823 Planarity : 0.004 0.049 1919 Dihedral : 11.616 89.080 1751 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.75 % Allowed : 11.82 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1448 helix: 0.97 (0.17), residues: 891 sheet: -0.52 (0.63), residues: 71 loop : -1.22 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.021 0.002 TYR A 381 PHE 0.024 0.002 PHE A 373 TRP 0.011 0.001 TRP B 240 HIS 0.009 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00503 (11288) covalent geometry : angle 0.59028 (15320) hydrogen bonds : bond 0.04284 ( 674) hydrogen bonds : angle 4.69875 ( 1959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.403 Fit side-chains REVERT: B 339 LEU cc_start: 0.7754 (mm) cc_final: 0.7484 (mm) REVERT: B 358 GLN cc_start: 0.7850 (tt0) cc_final: 0.7262 (pt0) REVERT: B 564 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.7959 (mt) outliers start: 20 outliers final: 12 residues processed: 129 average time/residue: 0.0918 time to fit residues: 17.9098 Evaluate side-chains 128 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 506 TYR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113498 restraints weight = 11490.334| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.09 r_work: 0.3166 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11288 Z= 0.115 Angle : 0.513 6.216 15320 Z= 0.260 Chirality : 0.039 0.135 1823 Planarity : 0.004 0.048 1919 Dihedral : 10.862 88.502 1751 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.14 % Allowed : 13.75 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1448 helix: 1.38 (0.17), residues: 885 sheet: -0.50 (0.61), residues: 71 loop : -1.14 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.022 0.001 TYR A 381 PHE 0.018 0.001 PHE A 373 TRP 0.012 0.001 TRP B 245 HIS 0.005 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00258 (11288) covalent geometry : angle 0.51256 (15320) hydrogen bonds : bond 0.03575 ( 674) hydrogen bonds : angle 4.46040 ( 1959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.383 Fit side-chains REVERT: B 168 GLU cc_start: 0.6764 (tt0) cc_final: 0.6482 (tt0) REVERT: B 302 ASP cc_start: 0.6561 (m-30) cc_final: 0.6238 (t0) REVERT: B 339 LEU cc_start: 0.7679 (mm) cc_final: 0.7403 (mm) REVERT: B 358 GLN cc_start: 0.7824 (tt0) cc_final: 0.7276 (pt0) REVERT: B 522 ASP cc_start: 0.7160 (p0) cc_final: 0.6888 (p0) REVERT: B 564 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7791 (mt) outliers start: 13 outliers final: 5 residues processed: 132 average time/residue: 0.0891 time to fit residues: 17.8933 Evaluate side-chains 121 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 506 TYR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 68 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 49 optimal weight: 0.0570 chunk 100 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 126 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 44 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115296 restraints weight = 11642.179| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.13 r_work: 0.3087 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11288 Z= 0.103 Angle : 0.496 6.563 15320 Z= 0.251 Chirality : 0.039 0.138 1823 Planarity : 0.003 0.048 1919 Dihedral : 10.054 88.529 1751 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.05 % Allowed : 14.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1448 helix: 1.61 (0.17), residues: 890 sheet: -0.50 (0.59), residues: 70 loop : -1.10 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.022 0.001 TYR A 381 PHE 0.016 0.001 PHE A 373 TRP 0.013 0.001 TRP B 245 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00224 (11288) covalent geometry : angle 0.49650 (15320) hydrogen bonds : bond 0.03306 ( 674) hydrogen bonds : angle 4.31065 ( 1959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.397 Fit side-chains REVERT: B 168 GLU cc_start: 0.6667 (tt0) cc_final: 0.6337 (tt0) REVERT: B 302 ASP cc_start: 0.6488 (m-30) cc_final: 0.6021 (t0) REVERT: B 339 LEU cc_start: 0.7550 (mm) cc_final: 0.7297 (mm) REVERT: B 358 GLN cc_start: 0.7820 (tt0) cc_final: 0.7228 (pt0) REVERT: B 522 ASP cc_start: 0.7294 (p0) cc_final: 0.7024 (p0) REVERT: B 564 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7489 (mt) outliers start: 12 outliers final: 6 residues processed: 140 average time/residue: 0.0969 time to fit residues: 20.1113 Evaluate side-chains 124 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 137 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.0000 chunk 109 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108475 restraints weight = 11499.634| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.14 r_work: 0.2989 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11288 Z= 0.186 Angle : 0.568 6.875 15320 Z= 0.287 Chirality : 0.042 0.147 1823 Planarity : 0.004 0.048 1919 Dihedral : 10.272 87.215 1751 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.75 % Allowed : 14.62 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1448 helix: 1.35 (0.17), residues: 887 sheet: -0.55 (0.59), residues: 71 loop : -1.10 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.021 0.002 TYR A 381 PHE 0.021 0.001 PHE A 373 TRP 0.009 0.001 TRP B 240 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00442 (11288) covalent geometry : angle 0.56791 (15320) hydrogen bonds : bond 0.04000 ( 674) hydrogen bonds : angle 4.52334 ( 1959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.407 Fit side-chains REVERT: A 350 MET cc_start: 0.8506 (mmp) cc_final: 0.8076 (mmp) REVERT: A 430 MET cc_start: 0.8278 (mmm) cc_final: 0.7820 (mtt) REVERT: B 168 GLU cc_start: 0.6692 (tt0) cc_final: 0.6351 (tt0) REVERT: B 283 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8120 (tt) REVERT: B 339 LEU cc_start: 0.7543 (mm) cc_final: 0.7287 (mm) REVERT: B 358 GLN cc_start: 0.7814 (tt0) cc_final: 0.7227 (pt0) REVERT: B 522 ASP cc_start: 0.7525 (p0) cc_final: 0.7090 (p0) REVERT: B 564 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7490 (mt) outliers start: 20 outliers final: 13 residues processed: 133 average time/residue: 0.0900 time to fit residues: 18.1551 Evaluate side-chains 128 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 16 optimal weight: 0.0980 chunk 76 optimal weight: 0.4980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113368 restraints weight = 11554.643| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.09 r_work: 0.3180 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11288 Z= 0.112 Angle : 0.512 7.047 15320 Z= 0.260 Chirality : 0.039 0.140 1823 Planarity : 0.003 0.048 1919 Dihedral : 9.862 87.341 1751 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.40 % Allowed : 16.02 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.22), residues: 1448 helix: 1.53 (0.17), residues: 887 sheet: -0.48 (0.59), residues: 70 loop : -1.03 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.021 0.001 TYR A 381 PHE 0.015 0.001 PHE A 373 TRP 0.011 0.001 TRP B 245 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00244 (11288) covalent geometry : angle 0.51153 (15320) hydrogen bonds : bond 0.03489 ( 674) hydrogen bonds : angle 4.39235 ( 1959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.416 Fit side-chains REVERT: A 350 MET cc_start: 0.8670 (mmp) cc_final: 0.8296 (mmp) REVERT: A 430 MET cc_start: 0.8238 (mmm) cc_final: 0.7937 (mtt) REVERT: B 168 GLU cc_start: 0.6809 (tt0) cc_final: 0.6459 (tt0) REVERT: B 339 LEU cc_start: 0.7667 (mm) cc_final: 0.7422 (mm) REVERT: B 358 GLN cc_start: 0.7759 (tt0) cc_final: 0.7185 (pt0) REVERT: B 522 ASP cc_start: 0.7295 (p0) cc_final: 0.6954 (p0) REVERT: B 564 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7752 (mt) outliers start: 16 outliers final: 14 residues processed: 133 average time/residue: 0.0908 time to fit residues: 18.1613 Evaluate side-chains 129 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 59 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108832 restraints weight = 11529.953| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.15 r_work: 0.3117 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.004 0.044 11288 Z= 0.149 Angle : 0.538 7.203 15320 Z= 0.273 Chirality : 0.040 0.135 1823 Planarity : 0.004 0.048 1919 Dihedral : 9.791 86.842 1751 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.84 % Allowed : 15.67 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1448 helix: 1.46 (0.17), residues: 888 sheet: -0.53 (0.59), residues: 70 loop : -1.02 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.022 0.001 TYR A 381 PHE 0.018 0.001 PHE A 373 TRP 0.008 0.001 TRP B 245 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00350 (11288) covalent geometry : angle 0.53831 (15320) hydrogen bonds : bond 0.03746 ( 674) hydrogen bonds : angle 4.46223 ( 1959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.312 Fit side-chains REVERT: A 350 MET cc_start: 0.8677 (mmp) cc_final: 0.8282 (mmp) REVERT: A 430 MET cc_start: 0.8338 (mmm) cc_final: 0.8074 (mtt) REVERT: B 168 GLU cc_start: 0.6846 (tt0) cc_final: 0.6502 (tt0) REVERT: B 283 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8417 (tt) REVERT: B 339 LEU cc_start: 0.7694 (mm) cc_final: 0.7449 (mm) REVERT: B 358 GLN cc_start: 0.7769 (tt0) cc_final: 0.7212 (pt0) REVERT: B 522 ASP cc_start: 0.7354 (p0) cc_final: 0.6899 (p0) REVERT: B 564 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7815 (mt) outliers start: 21 outliers final: 17 residues processed: 132 average time/residue: 0.0839 time to fit residues: 16.6911 Evaluate side-chains 132 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112965 restraints weight = 11590.018| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.10 r_work: 0.3162 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11288 Z= 0.121 Angle : 0.520 7.445 15320 Z= 0.264 Chirality : 0.039 0.135 1823 Planarity : 0.004 0.048 1919 Dihedral : 9.627 86.884 1751 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.66 % Allowed : 15.76 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.22), residues: 1448 helix: 1.52 (0.17), residues: 888 sheet: -0.55 (0.58), residues: 70 loop : -0.99 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.022 0.001 TYR A 381 PHE 0.016 0.001 PHE A 373 TRP 0.012 0.001 TRP B 245 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00277 (11288) covalent geometry : angle 0.52016 (15320) hydrogen bonds : bond 0.03579 ( 674) hydrogen bonds : angle 4.41159 ( 1959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.394 Fit side-chains REVERT: A 350 MET cc_start: 0.8649 (mmp) cc_final: 0.8248 (mmp) REVERT: A 430 MET cc_start: 0.8270 (mmm) cc_final: 0.8014 (mtt) REVERT: B 168 GLU cc_start: 0.6837 (tt0) cc_final: 0.6482 (tt0) REVERT: B 283 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 339 LEU cc_start: 0.7707 (mm) cc_final: 0.7465 (mm) REVERT: B 358 GLN cc_start: 0.7733 (tt0) cc_final: 0.7178 (pt0) REVERT: B 522 ASP cc_start: 0.7348 (p0) cc_final: 0.6890 (p0) REVERT: B 564 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7775 (mt) outliers start: 19 outliers final: 16 residues processed: 132 average time/residue: 0.0924 time to fit residues: 18.4211 Evaluate side-chains 132 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 0.5980 chunk 135 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113654 restraints weight = 11615.925| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.10 r_work: 0.3187 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11288 Z= 0.109 Angle : 0.510 8.059 15320 Z= 0.259 Chirality : 0.039 0.136 1823 Planarity : 0.004 0.048 1919 Dihedral : 9.378 86.871 1751 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 15.76 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.22), residues: 1448 helix: 1.63 (0.17), residues: 886 sheet: -0.52 (0.59), residues: 70 loop : -0.96 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 359 TYR 0.022 0.001 TYR A 381 PHE 0.016 0.001 PHE A 373 TRP 0.015 0.001 TRP B 245 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00241 (11288) covalent geometry : angle 0.50972 (15320) hydrogen bonds : bond 0.03423 ( 674) hydrogen bonds : angle 4.35760 ( 1959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2528.79 seconds wall clock time: 44 minutes 4.87 seconds (2644.87 seconds total)