Starting phenix.real_space_refine on Tue Jul 29 19:48:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nnp_12482/07_2025/7nnp_12482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nnp_12482/07_2025/7nnp_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_12482/07_2025/7nnp_12482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nnp_12482/07_2025/7nnp_12482.map" model { file = "/net/cci-nas-00/data/ceres_data/7nnp_12482/07_2025/7nnp_12482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nnp_12482/07_2025/7nnp_12482.cif" } resolution = 3.2 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= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.50, per 1000 atoms: 0.59 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.10 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: 3.40 Time building geometry restraints manager: 3.21 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: 0.930 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.700 Find NCS groups from input model: 0.110 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- 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 (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: -0.72 (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 TRP 0.047 0.002 TRP B 245 HIS 0.009 0.001 HIS B 563 PHE 0.033 0.002 PHE A 260 TYR 0.029 0.002 TYR A 381 ARG 0.007 0.000 ARG B 402 Details of bonding type rmsd hydrogen bonds : bond 0.10322 ( 674) hydrogen bonds : angle 5.50008 ( 1959) covalent geometry : bond 0.00608 (11288) covalent geometry : angle 0.95791 (15320) *********************** 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 : 1.274 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: 0.2495 time to fit residues: 53.5626 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 : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115225 restraints weight = 11513.505| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.15 r_work: 0.3121 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11288 Z= 0.128 Angle : 0.534 6.355 15320 Z= 0.272 Chirality : 0.040 0.145 1823 Planarity : 0.004 0.052 1919 Dihedral : 13.038 89.315 1751 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.35 % Allowed : 7.36 % Favored : 92.29 % 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: 0.27 (0.21), residues: 1448 helix: 1.04 (0.17), residues: 881 sheet: -0.39 (0.63), residues: 75 loop : -1.27 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.004 0.001 HIS A 451 PHE 0.017 0.001 PHE A 373 TYR 0.022 0.001 TYR A 381 ARG 0.004 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 674) hydrogen bonds : angle 4.57404 ( 1959) covalent geometry : bond 0.00290 (11288) covalent geometry : angle 0.53351 (15320) *********************** 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 137 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 1.134 Fit side-chains REVERT: A 211 GLN cc_start: 0.8043 (tt0) cc_final: 0.7719 (mt0) REVERT: A 397 MET cc_start: 0.8630 (mtp) cc_final: 0.8409 (mtp) REVERT: C 98 ILE cc_start: 0.8777 (mt) cc_final: 0.8500 (mt) REVERT: B 339 LEU cc_start: 0.7557 (mm) cc_final: 0.7296 (mm) REVERT: B 358 GLN cc_start: 0.7837 (tt0) cc_final: 0.7198 (pt0) REVERT: B 552 ASP cc_start: 0.7770 (m-30) cc_final: 0.7497 (m-30) REVERT: B 564 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7614 (mp) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.2233 time to fit residues: 44.6041 Evaluate side-chains 126 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 SER 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 42 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112324 restraints weight = 11545.358| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.15 r_work: 0.3033 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11288 Z= 0.143 Angle : 0.533 6.082 15320 Z= 0.271 Chirality : 0.040 0.135 1823 Planarity : 0.004 0.050 1919 Dihedral : 11.659 88.970 1751 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.70 % Allowed : 10.25 % Favored : 89.05 % 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: 1448 helix: 1.27 (0.17), residues: 878 sheet: -0.22 (0.65), residues: 70 loop : -1.22 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.007 0.001 HIS A 451 PHE 0.019 0.001 PHE A 373 TYR 0.021 0.001 TYR A 381 ARG 0.003 0.000 ARG B 425 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 674) hydrogen bonds : angle 4.49581 ( 1959) covalent geometry : bond 0.00333 (11288) covalent geometry : angle 0.53332 (15320) *********************** 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 127 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 350 MET cc_start: 0.8508 (mmp) cc_final: 0.8104 (mmp) REVERT: A 430 MET cc_start: 0.8197 (mmm) cc_final: 0.7865 (mtt) REVERT: B 91 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7755 (ttmm) REVERT: B 339 LEU cc_start: 0.7531 (mm) cc_final: 0.7261 (mm) REVERT: B 358 GLN cc_start: 0.7831 (tt0) cc_final: 0.7239 (pt0) REVERT: B 463 MET cc_start: 0.8039 (mtm) cc_final: 0.7829 (mtp) REVERT: B 564 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7379 (mp) outliers start: 8 outliers final: 3 residues processed: 123 average time/residue: 0.2375 time to fit residues: 43.5858 Evaluate side-chains 123 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 91 LYS 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 1 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.150797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110684 restraints weight = 11420.251| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.08 r_work: 0.3055 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11288 Z= 0.174 Angle : 0.555 6.945 15320 Z= 0.281 Chirality : 0.041 0.151 1823 Planarity : 0.004 0.048 1919 Dihedral : 11.144 89.405 1751 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.31 % Allowed : 12.08 % Favored : 86.60 % 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: 0.49 (0.22), residues: 1448 helix: 1.21 (0.17), residues: 884 sheet: -0.36 (0.64), residues: 71 loop : -1.17 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.005 0.001 HIS A 451 PHE 0.021 0.001 PHE A 373 TYR 0.022 0.001 TYR A 381 ARG 0.003 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 674) hydrogen bonds : angle 4.56909 ( 1959) covalent geometry : bond 0.00410 (11288) covalent geometry : angle 0.55478 (15320) *********************** 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 135 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.174 Fit side-chains REVERT: A 350 MET cc_start: 0.8603 (mmp) cc_final: 0.8070 (mmp) REVERT: B 168 GLU cc_start: 0.6704 (tt0) cc_final: 0.6477 (tt0) REVERT: B 339 LEU cc_start: 0.7688 (mm) cc_final: 0.7426 (mm) REVERT: B 358 GLN cc_start: 0.7822 (tt0) cc_final: 0.7268 (pt0) REVERT: B 463 MET cc_start: 0.8137 (mtm) cc_final: 0.7854 (mtp) REVERT: B 522 ASP cc_start: 0.7233 (p0) cc_final: 0.6988 (p0) REVERT: B 564 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7693 (mt) outliers start: 15 outliers final: 7 residues processed: 130 average time/residue: 0.2196 time to fit residues: 42.6533 Evaluate side-chains 122 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 77 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.152194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111805 restraints weight = 11441.407| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.09 r_work: 0.3025 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11288 Z= 0.136 Angle : 0.527 6.444 15320 Z= 0.266 Chirality : 0.040 0.135 1823 Planarity : 0.004 0.048 1919 Dihedral : 10.724 89.607 1751 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.58 % Allowed : 12.52 % Favored : 85.90 % 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: 0.66 (0.22), residues: 1448 helix: 1.37 (0.17), residues: 885 sheet: -0.44 (0.61), residues: 71 loop : -1.13 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 245 HIS 0.005 0.001 HIS A 451 PHE 0.019 0.001 PHE A 373 TYR 0.021 0.001 TYR A 381 ARG 0.002 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 674) hydrogen bonds : angle 4.48345 ( 1959) covalent geometry : bond 0.00317 (11288) covalent geometry : angle 0.52708 (15320) *********************** 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 135 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.164 Fit side-chains REVERT: A 350 MET cc_start: 0.8448 (mmp) cc_final: 0.7954 (mmp) REVERT: B 168 GLU cc_start: 0.6630 (tt0) cc_final: 0.6351 (tt0) REVERT: B 339 LEU cc_start: 0.7571 (mm) cc_final: 0.7301 (mm) REVERT: B 358 GLN cc_start: 0.7850 (tt0) cc_final: 0.7275 (pt0) REVERT: B 463 MET cc_start: 0.8104 (mtm) cc_final: 0.7791 (mtp) REVERT: B 522 ASP cc_start: 0.7324 (p0) cc_final: 0.7017 (p0) REVERT: B 564 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7468 (mt) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 0.2180 time to fit residues: 42.6446 Evaluate side-chains 122 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.148978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108261 restraints weight = 11566.365| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.10 r_work: 0.2983 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1834 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= 0.178 Angle : 0.565 6.955 15320 Z= 0.286 Chirality : 0.041 0.150 1823 Planarity : 0.004 0.047 1919 Dihedral : 10.589 88.460 1751 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 12.96 % Favored : 85.20 % 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: 0.50 (0.22), residues: 1448 helix: 1.19 (0.17), residues: 892 sheet: -0.50 (0.61), residues: 71 loop : -1.11 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 240 HIS 0.005 0.001 HIS A 451 PHE 0.022 0.001 PHE A 373 TYR 0.021 0.002 TYR A 381 ARG 0.002 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 674) hydrogen bonds : angle 4.56982 ( 1959) covalent geometry : bond 0.00424 (11288) covalent geometry : angle 0.56469 (15320) *********************** 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 138 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.272 Fit side-chains REVERT: B 168 GLU cc_start: 0.6718 (tt0) cc_final: 0.6407 (tt0) REVERT: B 339 LEU cc_start: 0.7552 (mm) cc_final: 0.7281 (mm) REVERT: B 358 GLN cc_start: 0.7848 (tt0) cc_final: 0.7285 (pt0) REVERT: B 522 ASP cc_start: 0.7404 (p0) cc_final: 0.7051 (p0) REVERT: B 564 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7557 (mt) outliers start: 21 outliers final: 12 residues processed: 132 average time/residue: 0.2191 time to fit residues: 42.8367 Evaluate side-chains 126 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.0020 chunk 49 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 27 optimal weight: 0.0030 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.153487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113019 restraints weight = 11660.704| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.15 r_work: 0.3109 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11288 Z= 0.107 Angle : 0.508 6.917 15320 Z= 0.257 Chirality : 0.039 0.134 1823 Planarity : 0.003 0.047 1919 Dihedral : 9.957 89.123 1751 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.14 % Allowed : 14.97 % Favored : 83.89 % 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: 0.89 (0.22), residues: 1448 helix: 1.57 (0.17), residues: 885 sheet: -0.46 (0.60), residues: 70 loop : -1.04 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 245 HIS 0.004 0.000 HIS A 451 PHE 0.017 0.001 PHE A 373 TYR 0.022 0.001 TYR A 381 ARG 0.003 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 674) hydrogen bonds : angle 4.36703 ( 1959) covalent geometry : bond 0.00235 (11288) covalent geometry : angle 0.50820 (15320) *********************** 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 135 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.148 Fit side-chains REVERT: B 168 GLU cc_start: 0.6787 (tt0) cc_final: 0.6473 (tt0) REVERT: B 283 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8239 (tt) REVERT: B 302 ASP cc_start: 0.6650 (m-30) cc_final: 0.6276 (t0) REVERT: B 339 LEU cc_start: 0.7627 (mm) cc_final: 0.7359 (mm) REVERT: B 358 GLN cc_start: 0.7779 (tt0) cc_final: 0.7234 (pt0) REVERT: B 522 ASP cc_start: 0.7374 (p0) cc_final: 0.7074 (p0) REVERT: B 564 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7756 (mt) outliers start: 13 outliers final: 9 residues processed: 134 average time/residue: 0.2124 time to fit residues: 42.3680 Evaluate side-chains 127 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 283 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 100 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 116 optimal weight: 30.0000 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 40.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.150013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.109567 restraints weight = 11544.858| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.10 r_work: 0.3008 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11288 Z= 0.163 Angle : 0.552 6.944 15320 Z= 0.279 Chirality : 0.041 0.140 1823 Planarity : 0.004 0.048 1919 Dihedral : 10.049 89.440 1751 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.58 % Allowed : 14.89 % Favored : 83.54 % 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: 0.73 (0.22), residues: 1448 helix: 1.41 (0.17), residues: 887 sheet: -0.57 (0.59), residues: 71 loop : -1.05 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 240 HIS 0.004 0.001 HIS A 451 PHE 0.019 0.001 PHE A 373 TYR 0.021 0.001 TYR A 381 ARG 0.002 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 674) hydrogen bonds : angle 4.49349 ( 1959) covalent geometry : bond 0.00389 (11288) covalent geometry : angle 0.55242 (15320) *********************** 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 133 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.242 Fit side-chains REVERT: B 168 GLU cc_start: 0.6743 (tt0) cc_final: 0.6405 (tt0) REVERT: B 283 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8149 (tt) REVERT: B 339 LEU cc_start: 0.7564 (mm) cc_final: 0.7310 (mm) REVERT: B 358 GLN cc_start: 0.7791 (tt0) cc_final: 0.7220 (pt0) REVERT: B 522 ASP cc_start: 0.7423 (p0) cc_final: 0.6989 (p0) REVERT: B 564 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7545 (mt) outliers start: 18 outliers final: 13 residues processed: 131 average time/residue: 0.2084 time to fit residues: 40.9002 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 : 1.198 ------------------------------------------------------------------------------- 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 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.153586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113596 restraints weight = 11625.764| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.11 r_work: 0.3164 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11288 Z= 0.111 Angle : 0.508 7.260 15320 Z= 0.258 Chirality : 0.039 0.134 1823 Planarity : 0.003 0.047 1919 Dihedral : 9.615 89.402 1751 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.31 % Allowed : 15.59 % Favored : 83.10 % 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: 0.94 (0.22), residues: 1448 helix: 1.60 (0.17), residues: 891 sheet: -0.51 (0.59), residues: 70 loop : -1.03 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 245 HIS 0.003 0.000 HIS A 451 PHE 0.017 0.001 PHE A 373 TYR 0.022 0.001 TYR A 381 ARG 0.002 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 674) hydrogen bonds : angle 4.35843 ( 1959) covalent geometry : bond 0.00247 (11288) covalent geometry : angle 0.50770 (15320) *********************** 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 133 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.525 Fit side-chains REVERT: B 168 GLU cc_start: 0.6892 (tt0) cc_final: 0.6591 (tt0) REVERT: B 283 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8354 (tt) REVERT: B 339 LEU cc_start: 0.7713 (mm) cc_final: 0.7468 (mm) REVERT: B 358 GLN cc_start: 0.7718 (tt0) cc_final: 0.7178 (pt0) REVERT: B 522 ASP cc_start: 0.7299 (p0) cc_final: 0.6898 (p0) REVERT: B 564 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.7834 (mt) outliers start: 15 outliers final: 11 residues processed: 131 average time/residue: 0.2682 time to fit residues: 52.0779 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 : 1.170 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.0060 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 60 optimal weight: 0.0000 chunk 113 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.154853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115000 restraints weight = 11640.446| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.12 r_work: 0.3088 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11288 Z= 0.105 Angle : 0.506 7.089 15320 Z= 0.256 Chirality : 0.039 0.132 1823 Planarity : 0.003 0.048 1919 Dihedral : 9.313 89.799 1751 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.40 % Allowed : 15.76 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.22), residues: 1448 helix: 1.71 (0.17), residues: 891 sheet: -0.51 (0.60), residues: 70 loop : -1.01 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.003 0.000 HIS A 451 PHE 0.016 0.001 PHE A 373 TYR 0.021 0.001 TYR A 381 ARG 0.004 0.000 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 674) hydrogen bonds : angle 4.28962 ( 1959) covalent geometry : bond 0.00234 (11288) covalent geometry : angle 0.50552 (15320) ********************** 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 140 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.323 Fit side-chains REVERT: B 168 GLU cc_start: 0.6741 (tt0) cc_final: 0.6391 (tt0) REVERT: B 283 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8109 (tt) REVERT: B 339 LEU cc_start: 0.7609 (mm) cc_final: 0.7359 (mm) REVERT: B 358 GLN cc_start: 0.7617 (tt0) cc_final: 0.7077 (pt0) REVERT: B 522 ASP cc_start: 0.7444 (p0) cc_final: 0.6958 (p0) REVERT: B 564 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7444 (mp) outliers start: 16 outliers final: 12 residues processed: 139 average time/residue: 0.2979 time to fit residues: 62.9803 Evaluate side-chains 131 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 283 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.153151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113399 restraints weight = 11552.654| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.10 r_work: 0.3153 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1863 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= 0.125 Angle : 0.520 8.108 15320 Z= 0.263 Chirality : 0.039 0.132 1823 Planarity : 0.004 0.048 1919 Dihedral : 9.315 89.500 1751 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.23 % Allowed : 16.02 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1448 helix: 1.69 (0.17), residues: 885 sheet: -0.51 (0.60), residues: 70 loop : -0.97 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 245 HIS 0.003 0.000 HIS A 451 PHE 0.016 0.001 PHE A 373 TYR 0.021 0.001 TYR A 381 ARG 0.002 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 674) hydrogen bonds : angle 4.33111 ( 1959) covalent geometry : bond 0.00289 (11288) covalent geometry : angle 0.51958 (15320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6047.89 seconds wall clock time: 106 minutes 25.21 seconds (6385.21 seconds total)