Starting phenix.real_space_refine on Fri Jul 3 20:35:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xjp_33233/07_2026/7xjp_33233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjp_33233/07_2026/7xjp_33233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xjp_33233/07_2026/7xjp_33233.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xjp_33233/07_2026/7xjp_33233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xjp_33233/07_2026/7xjp_33233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjp_33233/07_2026/7xjp_33233.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjp_33233/07_2026/7xjp_33233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjp_33233/07_2026/7xjp_33233.cif" } resolution = 2.71 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8627 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 39 5.16 5 C 5693 2.51 5 N 1518 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8930 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4720 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 4140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4140 Classifications: {'peptide': 509} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 492} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'APR': 1, 'IPA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8930 At special positions: 0 Unit cell: (84.435, 122.322, 97.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 5 15.00 O 1675 8.00 N 1518 7.00 C 5693 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 250.0 milliseconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 5 sheets defined 64.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 87 through 98 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.593A pdb=" N SER A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 3.652A pdb=" N ALA A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 188 through 193 removed outlier: 4.602A pdb=" N MET A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.715A pdb=" N VAL A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.502A pdb=" N VAL A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 246 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.732A pdb=" N PHE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 307 through 317 removed outlier: 4.603A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'A' and resid 351 through 380 Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.931A pdb=" N ILE A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.531A pdb=" N LYS A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 415 through 442 removed outlier: 3.578A pdb=" N PHE A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 removed outlier: 4.383A pdb=" N GLY A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 476 Proline residue: A 467 - end of helix removed outlier: 3.681A pdb=" N HIS A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.722A pdb=" N ARG A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.815A pdb=" N ILE A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.552A pdb=" N GLU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 581 removed outlier: 3.580A pdb=" N VAL A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 593 through 601 removed outlier: 3.926A pdb=" N THR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.900A pdb=" N GLY B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 110 through 136 removed outlier: 4.913A pdb=" N THR B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 160 removed outlier: 3.868A pdb=" N VAL B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.638A pdb=" N VAL B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 317 removed outlier: 3.679A pdb=" N ILE B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 334 through 343 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.654A pdb=" N GLU B 347 " --> pdb=" O HIS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 396 removed outlier: 3.516A pdb=" N PHE B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) Proline residue: B 387 - end of helix Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.693A pdb=" N VAL B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 420 " --> pdb=" O TRP B 416 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 Processing helix chain 'B' and resid 466 through 489 Processing helix chain 'B' and resid 493 through 498 removed outlier: 3.766A pdb=" N LEU B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 514 Processing helix chain 'B' and resid 519 through 527 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.600A pdb=" N GLY A 121 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N CYS A 153 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE A 182 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 155 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N SER A 184 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A 179 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL A 274 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN A 181 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N SER A 276 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 183 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 283 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 61 removed outlier: 6.199A pdb=" N THR B 66 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR B 143 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 68 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE B 198 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU B 220 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS B 200 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N CYS B 222 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 202 " --> pdb=" O CYS B 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 182 removed outlier: 4.121A pdb=" N GLY B 181 " --> pdb=" O LYS B 214 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1434 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: 1.39 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2726 1.34 - 1.45: 1418 1.45 - 1.57: 4918 1.57 - 1.69: 9 1.69 - 1.81: 61 Bond restraints: 9132 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.59e+01 bond pdb=" C8 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.21e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 1.98e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.333 0.041 1.00e-02 1.00e+04 1.70e+01 ... (remaining 9127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 12248 3.60 - 7.19: 67 7.19 - 10.79: 7 10.79 - 14.39: 1 14.39 - 17.98: 1 Bond angle restraints: 12324 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.89 17.98 1.00e+00 1.00e+00 3.23e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 122.91 13.92 1.00e+00 1.00e+00 1.94e+02 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.63e+01 angle pdb=" N3 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 127.04 135.04 -8.00 1.15e+00 7.59e-01 4.85e+01 angle pdb=" N1 ATP B 601 " pdb=" C2 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 128.69 123.63 5.06 1.00e+00 1.00e+00 2.56e+01 ... (remaining 12319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 4943 16.58 - 33.16: 426 33.16 - 49.74: 87 49.74 - 66.31: 10 66.31 - 82.89: 6 Dihedral angle restraints: 5472 sinusoidal: 2277 harmonic: 3195 Sorted by residual: dihedral pdb=" CA HIS A 122 " pdb=" C HIS A 122 " pdb=" N SER A 123 " pdb=" CA SER A 123 " ideal model delta harmonic sigma weight residual -180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LEU A 464 " pdb=" C LEU A 464 " pdb=" N VAL A 465 " pdb=" CA VAL A 465 " ideal model delta harmonic sigma weight residual 180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ARG A 280 " pdb=" C ARG A 280 " pdb=" N LEU A 281 " pdb=" CA LEU A 281 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 944 0.045 - 0.090: 283 0.090 - 0.134: 81 0.134 - 0.179: 17 0.179 - 0.224: 9 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA LEU B 370 " pdb=" N LEU B 370 " pdb=" C LEU B 370 " pdb=" CB LEU B 370 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 369 " pdb=" N ILE B 369 " pdb=" C ILE B 369 " pdb=" CB ILE B 369 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE A 578 " pdb=" N ILE A 578 " pdb=" C ILE A 578 " pdb=" CB ILE A 578 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1331 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 573 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C MET A 573 " -0.045 2.00e-02 2.50e+03 pdb=" O MET A 573 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 574 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 189 " -0.030 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 190 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 386 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 387 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 387 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 387 " 0.024 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1339 2.75 - 3.29: 9215 3.29 - 3.83: 15088 3.83 - 4.36: 18187 4.36 - 4.90: 29975 Nonbonded interactions: 73804 Sorted by model distance: nonbonded pdb=" OD2 ASP A 187 " pdb=" OH TYR A 320 " model vdw 2.215 3.040 nonbonded pdb=" O SER B 80 " pdb=" NE2 HIS B 109 " model vdw 2.250 3.120 nonbonded pdb=" O ILE B 75 " pdb=" NH1 ARG B 77 " model vdw 2.256 3.120 nonbonded pdb=" NE1 TRP B 26 " pdb=" OG SER B 252 " model vdw 2.256 3.120 nonbonded pdb=" O THR B 133 " pdb=" OG SER B 136 " model vdw 2.258 3.040 ... (remaining 73799 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 9133 Z= 0.356 Angle : 0.799 17.982 12324 Z= 0.549 Chirality : 0.050 0.224 1334 Planarity : 0.004 0.045 1557 Dihedral : 13.010 82.892 3400 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 0.82 % Allowed : 1.84 % Favored : 97.34 % 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: -1.81 (0.23), residues: 1079 helix: -0.73 (0.19), residues: 633 sheet: -1.72 (0.48), residues: 100 loop : -1.64 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 596 TYR 0.013 0.001 TYR A 30 PHE 0.013 0.001 PHE B 444 TRP 0.015 0.001 TRP B 507 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.35 ( 9132) covalent geometry : angle 0.79903 / 0.55 (12324) hydrogen bonds : bond 0.15513 / 10.40 ( 491) hydrogen bonds : angle 6.01294 / 4.19 ( 1434) Misc. bond : bond 0.04400 / 2.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 181 average time/residue: 0.6250 time to fit residues: 119.8728 Evaluate side-chains 105 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 523 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 GLN A 381 GLN A 606 HIS B 200 HIS B 253 GLN B 256 ASN B 287 ASN B 342 ASN B 517 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.123350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.101303 restraints weight = 18188.538| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.30 r_work: 0.3698 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9133 Z= 0.142 Angle : 0.603 7.429 12324 Z= 0.316 Chirality : 0.041 0.167 1334 Planarity : 0.004 0.042 1557 Dihedral : 5.445 58.973 1199 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.95 % Allowed : 13.22 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.25), residues: 1079 helix: 0.58 (0.20), residues: 637 sheet: -1.29 (0.48), residues: 100 loop : -0.97 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 613 TYR 0.020 0.002 TYR A 560 PHE 0.008 0.001 PHE A 43 TRP 0.046 0.002 TRP A 577 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9132) covalent geometry : angle 0.60293 / 0.32 (12324) hydrogen bonds : bond 0.04904 / 3.16 ( 491) hydrogen bonds : angle 4.69097 / 3.27 ( 1434) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: A 242 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 380 GLU cc_start: 0.8319 (pp20) cc_final: 0.8101 (pp20) REVERT: A 599 TRP cc_start: 0.7763 (t60) cc_final: 0.7366 (t60) REVERT: B 253 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7603 (pp30) REVERT: B 338 ILE cc_start: 0.8393 (mt) cc_final: 0.8178 (mp) REVERT: B 369 ILE cc_start: 0.5971 (mm) cc_final: 0.5661 (mm) REVERT: B 474 ARG cc_start: 0.8709 (mmp-170) cc_final: 0.8397 (mmp80) REVERT: B 485 GLU cc_start: 0.8754 (pp20) cc_final: 0.8525 (pp20) REVERT: B 491 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7860 (mm-30) outliers start: 19 outliers final: 7 residues processed: 131 average time/residue: 0.5981 time to fit residues: 83.4595 Evaluate side-chains 99 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 ASN A 606 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.121191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.099523 restraints weight = 18093.524| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.22 r_work: 0.3673 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9133 Z= 0.167 Angle : 0.604 8.576 12324 Z= 0.313 Chirality : 0.042 0.151 1334 Planarity : 0.004 0.042 1557 Dihedral : 5.281 59.966 1196 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.05 % Allowed : 14.24 % Favored : 83.71 % 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 (0.25), residues: 1079 helix: 0.91 (0.20), residues: 639 sheet: -1.11 (0.49), residues: 99 loop : -0.73 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 100 TYR 0.022 0.002 TYR A 560 PHE 0.010 0.001 PHE A 43 TRP 0.022 0.002 TRP A 577 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 9132) covalent geometry : angle 0.60445 / 0.31 (12324) hydrogen bonds : bond 0.04860 / 3.15 ( 491) hydrogen bonds : angle 4.61761 / 3.22 ( 1434) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: A 109 MET cc_start: 0.9132 (tmm) cc_final: 0.8862 (tmm) REVERT: A 112 ARG cc_start: 0.7961 (mtm110) cc_final: 0.7615 (mtm110) REVERT: A 242 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 380 GLU cc_start: 0.8288 (pp20) cc_final: 0.8036 (pp20) REVERT: A 413 SER cc_start: 0.9309 (t) cc_final: 0.8957 (p) REVERT: A 599 TRP cc_start: 0.7808 (t60) cc_final: 0.7425 (t60) REVERT: B 260 GLN cc_start: 0.7671 (pp30) cc_final: 0.7423 (pp30) REVERT: B 328 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8200 (mp10) REVERT: B 338 ILE cc_start: 0.8467 (mt) cc_final: 0.8236 (mp) REVERT: B 369 ILE cc_start: 0.6373 (mm) cc_final: 0.6099 (mm) REVERT: B 474 ARG cc_start: 0.8716 (mmp-170) cc_final: 0.8486 (mmp-170) REVERT: B 485 GLU cc_start: 0.8786 (pp20) cc_final: 0.8535 (pp20) outliers start: 20 outliers final: 11 residues processed: 112 average time/residue: 0.5406 time to fit residues: 64.8801 Evaluate side-chains 98 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 1.9990 chunk 37 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 80 optimal weight: 0.0070 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 0.0770 chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 overall best weight: 0.1772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 ASN A 606 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.125151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.103314 restraints weight = 18302.600| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.31 r_work: 0.3738 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9133 Z= 0.109 Angle : 0.547 7.606 12324 Z= 0.283 Chirality : 0.039 0.129 1334 Planarity : 0.004 0.057 1557 Dihedral : 4.892 56.930 1196 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.54 % Allowed : 15.57 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 1079 helix: 1.30 (0.21), residues: 631 sheet: -0.77 (0.49), residues: 102 loop : -0.55 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 100 TYR 0.017 0.001 TYR A 406 PHE 0.009 0.001 PHE B 331 TRP 0.022 0.001 TRP A 598 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 9132) covalent geometry : angle 0.54711 / 0.28 (12324) hydrogen bonds : bond 0.03985 / 2.61 ( 491) hydrogen bonds : angle 4.34264 / 3.04 ( 1434) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7886 (m-30) cc_final: 0.7595 (m-30) REVERT: A 94 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: A 109 MET cc_start: 0.9150 (tmm) cc_final: 0.8940 (mmm) REVERT: A 112 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7676 (mtm110) REVERT: A 242 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 380 GLU cc_start: 0.8340 (pp20) cc_final: 0.8021 (pp20) REVERT: A 413 SER cc_start: 0.9275 (t) cc_final: 0.8924 (p) REVERT: A 576 GLU cc_start: 0.7695 (mp0) cc_final: 0.7300 (mp0) REVERT: A 599 TRP cc_start: 0.7703 (t60) cc_final: 0.7293 (t60) REVERT: A 602 LEU cc_start: 0.8970 (mm) cc_final: 0.8756 (mm) REVERT: B 182 ASP cc_start: 0.7666 (p0) cc_final: 0.7294 (t0) REVERT: B 261 SER cc_start: 0.8150 (m) cc_final: 0.7749 (p) REVERT: B 328 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8370 (mp10) REVERT: B 338 ILE cc_start: 0.8350 (mt) cc_final: 0.8101 (mp) REVERT: B 369 ILE cc_start: 0.6056 (mm) cc_final: 0.5769 (mm) REVERT: B 485 GLU cc_start: 0.8773 (pp20) cc_final: 0.8515 (pp20) REVERT: B 504 MET cc_start: 0.8795 (tpt) cc_final: 0.8582 (tpt) outliers start: 15 outliers final: 6 residues processed: 120 average time/residue: 0.5088 time to fit residues: 65.3592 Evaluate side-chains 103 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 0.0670 chunk 69 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.124305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.102278 restraints weight = 18266.410| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.31 r_work: 0.3720 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9133 Z= 0.126 Angle : 0.570 7.270 12324 Z= 0.295 Chirality : 0.040 0.140 1334 Planarity : 0.004 0.049 1557 Dihedral : 4.898 57.758 1196 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.64 % Allowed : 16.70 % Favored : 81.66 % 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: 0.84 (0.26), residues: 1079 helix: 1.44 (0.21), residues: 628 sheet: -0.47 (0.51), residues: 100 loop : -0.66 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 100 TYR 0.028 0.001 TYR A 560 PHE 0.009 0.001 PHE A 166 TRP 0.028 0.001 TRP A 598 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9132) covalent geometry : angle 0.57041 / 0.29 (12324) hydrogen bonds : bond 0.04136 / 2.72 ( 491) hydrogen bonds : angle 4.34866 / 3.05 ( 1434) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: A 97 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 112 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7728 (mtm110) REVERT: A 242 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 380 GLU cc_start: 0.8369 (pp20) cc_final: 0.8046 (pp20) REVERT: A 413 SER cc_start: 0.9264 (t) cc_final: 0.8881 (p) REVERT: A 576 GLU cc_start: 0.7765 (mp0) cc_final: 0.7372 (mp0) REVERT: A 599 TRP cc_start: 0.7752 (t60) cc_final: 0.7452 (t60) REVERT: A 602 LEU cc_start: 0.8899 (mm) cc_final: 0.8650 (mm) REVERT: B 261 SER cc_start: 0.8007 (m) cc_final: 0.7772 (p) REVERT: B 328 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8444 (mp10) REVERT: B 338 ILE cc_start: 0.8378 (mt) cc_final: 0.8127 (mp) REVERT: B 369 ILE cc_start: 0.6346 (mm) cc_final: 0.6028 (mm) REVERT: B 485 GLU cc_start: 0.8775 (pp20) cc_final: 0.8496 (pp20) outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.4841 time to fit residues: 58.2814 Evaluate side-chains 102 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.124448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.102521 restraints weight = 18231.935| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.34 r_work: 0.3717 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9133 Z= 0.128 Angle : 0.578 7.987 12324 Z= 0.299 Chirality : 0.040 0.160 1334 Planarity : 0.004 0.068 1557 Dihedral : 4.815 57.043 1194 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.74 % Allowed : 17.52 % Favored : 80.74 % 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: 0.93 (0.26), residues: 1079 helix: 1.49 (0.21), residues: 629 sheet: -0.37 (0.53), residues: 100 loop : -0.61 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 613 TYR 0.013 0.001 TYR A 406 PHE 0.009 0.001 PHE A 166 TRP 0.038 0.001 TRP A 598 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9132) covalent geometry : angle 0.57751 / 0.30 (12324) hydrogen bonds : bond 0.04155 / 2.73 ( 491) hydrogen bonds : angle 4.32931 / 3.03 ( 1434) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: A 97 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8018 (mm) REVERT: A 112 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7770 (mtm110) REVERT: A 227 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 242 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8030 (tm-30) REVERT: A 380 GLU cc_start: 0.8403 (pp20) cc_final: 0.8040 (pp20) REVERT: A 386 LYS cc_start: 0.9160 (ptpp) cc_final: 0.8841 (tppt) REVERT: A 413 SER cc_start: 0.9276 (t) cc_final: 0.8918 (p) REVERT: A 576 GLU cc_start: 0.7835 (mp0) cc_final: 0.7622 (tp30) REVERT: A 599 TRP cc_start: 0.7739 (t60) cc_final: 0.7416 (t60) REVERT: A 602 LEU cc_start: 0.8888 (mm) cc_final: 0.8632 (mm) REVERT: A 606 HIS cc_start: 0.8855 (t70) cc_final: 0.8486 (t-90) REVERT: B 158 TRP cc_start: 0.8942 (t60) cc_final: 0.8718 (t60) REVERT: B 182 ASP cc_start: 0.7755 (p0) cc_final: 0.7331 (t0) REVERT: B 338 ILE cc_start: 0.8389 (mt) cc_final: 0.8136 (mp) REVERT: B 347 GLU cc_start: 0.8179 (mp0) cc_final: 0.7885 (mp0) REVERT: B 369 ILE cc_start: 0.6544 (mm) cc_final: 0.6280 (mm) REVERT: B 474 ARG cc_start: 0.8775 (mmp-170) cc_final: 0.8395 (mmp80) REVERT: B 485 GLU cc_start: 0.8804 (pp20) cc_final: 0.8517 (pp20) outliers start: 17 outliers final: 9 residues processed: 112 average time/residue: 0.5441 time to fit residues: 65.2443 Evaluate side-chains 104 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 0.0570 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.123909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.101758 restraints weight = 18421.555| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.32 r_work: 0.3705 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9133 Z= 0.138 Angle : 0.587 8.009 12324 Z= 0.305 Chirality : 0.040 0.154 1334 Planarity : 0.004 0.040 1557 Dihedral : 4.889 59.240 1194 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.84 % Allowed : 17.52 % Favored : 80.64 % 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: 0.90 (0.26), residues: 1079 helix: 1.44 (0.21), residues: 633 sheet: -0.42 (0.53), residues: 100 loop : -0.59 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 613 TYR 0.011 0.001 TYR A 406 PHE 0.010 0.001 PHE A 166 TRP 0.039 0.002 TRP A 598 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9132) covalent geometry : angle 0.58662 / 0.30 (12324) hydrogen bonds : bond 0.04257 / 2.79 ( 491) hydrogen bonds : angle 4.35693 / 3.05 ( 1434) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: A 227 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 242 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 413 SER cc_start: 0.9313 (t) cc_final: 0.8978 (p) REVERT: A 599 TRP cc_start: 0.7786 (t60) cc_final: 0.7437 (t60) REVERT: A 607 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8453 (ptpp) REVERT: B 182 ASP cc_start: 0.7717 (p0) cc_final: 0.7343 (t0) REVERT: B 328 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8500 (mp10) REVERT: B 338 ILE cc_start: 0.8410 (mt) cc_final: 0.8160 (mp) REVERT: B 347 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: B 474 ARG cc_start: 0.8713 (mmp-170) cc_final: 0.8385 (mmp80) REVERT: B 485 GLU cc_start: 0.8804 (pp20) cc_final: 0.8517 (pp20) outliers start: 18 outliers final: 10 residues processed: 114 average time/residue: 0.5660 time to fit residues: 69.0633 Evaluate side-chains 106 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.124407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.102240 restraints weight = 18305.158| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.34 r_work: 0.3710 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9133 Z= 0.133 Angle : 0.596 7.455 12324 Z= 0.309 Chirality : 0.040 0.220 1334 Planarity : 0.004 0.062 1557 Dihedral : 4.863 59.771 1194 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.54 % Allowed : 18.55 % Favored : 79.92 % 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: 0.91 (0.26), residues: 1079 helix: 1.45 (0.21), residues: 633 sheet: -0.41 (0.52), residues: 100 loop : -0.58 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 613 TYR 0.031 0.001 TYR B 310 PHE 0.009 0.001 PHE A 43 TRP 0.038 0.001 TRP A 598 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9132) covalent geometry : angle 0.59570 / 0.31 (12324) hydrogen bonds : bond 0.04210 / 2.74 ( 491) hydrogen bonds : angle 4.38909 / 3.08 ( 1434) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: A 112 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7573 (mtm110) REVERT: A 227 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 242 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 286 ASN cc_start: 0.8653 (t0) cc_final: 0.8259 (t0) REVERT: A 386 LYS cc_start: 0.9148 (ptpp) cc_final: 0.8877 (tppt) REVERT: A 413 SER cc_start: 0.9300 (t) cc_final: 0.8951 (p) REVERT: A 599 TRP cc_start: 0.7832 (t60) cc_final: 0.7491 (t60) REVERT: A 607 LYS cc_start: 0.8623 (ptpp) cc_final: 0.8299 (ptpp) REVERT: B 182 ASP cc_start: 0.7604 (p0) cc_final: 0.7289 (t0) REVERT: B 328 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8490 (mp10) REVERT: B 338 ILE cc_start: 0.8449 (mt) cc_final: 0.8185 (mp) REVERT: B 347 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: B 412 MET cc_start: 0.9185 (mmp) cc_final: 0.8922 (mmp) REVERT: B 474 ARG cc_start: 0.8721 (mmp-170) cc_final: 0.8371 (mmp80) REVERT: B 485 GLU cc_start: 0.8814 (pp20) cc_final: 0.8522 (pp20) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.6007 time to fit residues: 67.2741 Evaluate side-chains 102 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 347 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.2980 chunk 89 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 99 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 overall best weight: 0.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.125992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.104065 restraints weight = 18159.858| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.32 r_work: 0.3741 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9133 Z= 0.120 Angle : 0.598 8.298 12324 Z= 0.310 Chirality : 0.039 0.194 1334 Planarity : 0.004 0.040 1557 Dihedral : 4.730 57.504 1194 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.43 % Allowed : 19.16 % Favored : 79.41 % 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 (0.26), residues: 1079 helix: 1.50 (0.21), residues: 633 sheet: -0.28 (0.52), residues: 100 loop : -0.56 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 100 TYR 0.014 0.001 TYR A 406 PHE 0.010 0.001 PHE B 331 TRP 0.037 0.002 TRP A 598 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9132) covalent geometry : angle 0.59841 / 0.31 (12324) hydrogen bonds : bond 0.03933 / 2.57 ( 491) hydrogen bonds : angle 4.31568 / 3.04 ( 1434) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: A 227 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 242 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 286 ASN cc_start: 0.8585 (t0) cc_final: 0.8224 (t0) REVERT: A 386 LYS cc_start: 0.9134 (ptpp) cc_final: 0.8860 (tppt) REVERT: A 413 SER cc_start: 0.9253 (t) cc_final: 0.8872 (p) REVERT: A 599 TRP cc_start: 0.7773 (t60) cc_final: 0.7456 (t60) REVERT: B 158 TRP cc_start: 0.8843 (t60) cc_final: 0.8562 (t60) REVERT: B 338 ILE cc_start: 0.8432 (mt) cc_final: 0.8173 (mp) REVERT: B 347 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: B 474 ARG cc_start: 0.8728 (mmp-170) cc_final: 0.8364 (mmp80) REVERT: B 485 GLU cc_start: 0.8790 (pp20) cc_final: 0.8504 (pp20) outliers start: 14 outliers final: 10 residues processed: 115 average time/residue: 0.6070 time to fit residues: 74.3342 Evaluate side-chains 105 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 GLN ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.124721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.102680 restraints weight = 18199.379| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.32 r_work: 0.3722 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9133 Z= 0.144 Angle : 0.638 9.201 12324 Z= 0.332 Chirality : 0.041 0.195 1334 Planarity : 0.004 0.047 1557 Dihedral : 4.834 58.168 1194 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.43 % Allowed : 19.88 % Favored : 78.69 % 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: 1.01 (0.26), residues: 1079 helix: 1.51 (0.21), residues: 628 sheet: -0.32 (0.52), residues: 100 loop : -0.48 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 112 TYR 0.012 0.001 TYR A 406 PHE 0.011 0.001 PHE B 331 TRP 0.036 0.001 TRP A 598 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9132) covalent geometry : angle 0.63828 / 0.33 (12324) hydrogen bonds : bond 0.04289 / 2.82 ( 491) hydrogen bonds : angle 4.41134 / 3.10 ( 1434) Misc. bond : bond 0.00015 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: A 109 MET cc_start: 0.9044 (mmm) cc_final: 0.8835 (tpp) REVERT: A 193 MET cc_start: 0.9197 (mmm) cc_final: 0.8957 (mmm) REVERT: A 227 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 242 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 286 ASN cc_start: 0.8618 (t0) cc_final: 0.8251 (t0) REVERT: A 386 LYS cc_start: 0.9137 (ptpp) cc_final: 0.8866 (tppt) REVERT: A 413 SER cc_start: 0.9294 (t) cc_final: 0.8942 (p) REVERT: A 599 TRP cc_start: 0.7813 (t60) cc_final: 0.7496 (t60) REVERT: B 158 TRP cc_start: 0.8857 (t60) cc_final: 0.8592 (t60) REVERT: B 182 ASP cc_start: 0.7815 (p0) cc_final: 0.7416 (t0) REVERT: B 328 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8499 (mp10) REVERT: B 338 ILE cc_start: 0.8445 (mt) cc_final: 0.8185 (mp) REVERT: B 347 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: B 474 ARG cc_start: 0.8757 (mmp-170) cc_final: 0.8394 (mmp80) REVERT: B 485 GLU cc_start: 0.8805 (pp20) cc_final: 0.8507 (pp20) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 0.5381 time to fit residues: 62.6692 Evaluate side-chains 99 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.123976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.101785 restraints weight = 18173.803| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.33 r_work: 0.3705 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9133 Z= 0.155 Angle : 0.648 9.113 12324 Z= 0.337 Chirality : 0.042 0.203 1334 Planarity : 0.004 0.056 1557 Dihedral : 4.895 55.568 1194 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.13 % Allowed : 20.39 % Favored : 78.48 % 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: 0.98 (0.26), residues: 1079 helix: 1.49 (0.21), residues: 627 sheet: -0.37 (0.52), residues: 100 loop : -0.47 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 112 TYR 0.011 0.001 TYR A 406 PHE 0.012 0.001 PHE B 331 TRP 0.035 0.001 TRP A 598 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 9132) covalent geometry : angle 0.64832 / 0.34 (12324) hydrogen bonds : bond 0.04369 / 2.84 ( 491) hydrogen bonds : angle 4.45209 / 3.12 ( 1434) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.75 seconds wall clock time: 56 minutes 33.54 seconds (3393.54 seconds total)