Starting phenix.real_space_refine on Wed Mar 4 20:13:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjp_33233/03_2026/7xjp_33233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjp_33233/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xjp_33233/03_2026/7xjp_33233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjp_33233/03_2026/7xjp_33233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xjp_33233/03_2026/7xjp_33233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjp_33233/03_2026/7xjp_33233.map" } 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-5986/lib/python3.9/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 dihedrals: 3 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: 2.32, per 1000 atoms: 0.26 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: 0.70 Conformation dependent library (CDL) restraints added in 483.3 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: 0.29 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: 1.37 Time building geometry restraints manager: 0.95 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 - 17.43: 5013 17.43 - 34.85: 431 34.85 - 52.28: 87 52.28 - 69.70: 7 69.70 - 87.13: 8 Dihedral angle restraints: 5546 sinusoidal: 2351 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 5543 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.570 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 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 : 13.661 87.126 3474 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 covalent geometry : bond 0.00526 ( 9132) covalent geometry : angle 0.79903 (12324) hydrogen bonds : bond 0.15513 ( 491) hydrogen bonds : angle 6.01294 ( 1434) Misc. bond : bond 0.04400 ( 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 : 0.271 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: 0.6463 time to fit residues: 123.7086 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 : 0.303 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4184 r_free = 0.4184 target = 0.123436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.101398 restraints weight = 18203.162| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.30 r_work: 0.3699 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9133 Z= 0.142 Angle : 0.604 7.468 12324 Z= 0.318 Chirality : 0.041 0.172 1334 Planarity : 0.004 0.042 1557 Dihedral : 7.795 84.808 1273 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.74 % Allowed : 13.32 % Favored : 84.94 % 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: -0.19 (0.25), residues: 1079 helix: 0.60 (0.20), residues: 637 sheet: -1.28 (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 0.019 0.002 TYR A 560 PHE 0.008 0.001 PHE A 43 TRP 0.045 0.002 TRP A 577 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9132) covalent geometry : angle 0.60445 (12324) hydrogen bonds : bond 0.04874 ( 491) hydrogen bonds : angle 4.68271 ( 1434) Misc. bond : bond 0.00057 ( 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 138 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: A 242 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 380 GLU cc_start: 0.8326 (pp20) cc_final: 0.8102 (pp20) REVERT: A 480 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8683 (mm-30) REVERT: A 599 TRP cc_start: 0.7752 (t60) cc_final: 0.7359 (t60) REVERT: B 253 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7607 (pp30) REVERT: B 338 ILE cc_start: 0.8387 (mt) cc_final: 0.8172 (mp) REVERT: B 369 ILE cc_start: 0.5934 (mm) cc_final: 0.5633 (mm) REVERT: B 474 ARG cc_start: 0.8760 (mmp-170) cc_final: 0.8447 (mmp80) REVERT: B 485 GLU cc_start: 0.8755 (pp20) cc_final: 0.8536 (pp20) outliers start: 17 outliers final: 7 residues processed: 130 average time/residue: 0.5938 time to fit residues: 82.2609 Evaluate side-chains 98 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 A residue 327 MET Chi-restraints excluded: chain A residue 480 GLU 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: 1.9990 chunk 11 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4187 r_free = 0.4187 target = 0.123081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.101524 restraints weight = 18008.215| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.21 r_work: 0.3706 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9133 Z= 0.133 Angle : 0.581 7.906 12324 Z= 0.300 Chirality : 0.040 0.151 1334 Planarity : 0.004 0.045 1557 Dihedral : 7.427 76.147 1270 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.46 % Allowed : 13.73 % Favored : 83.81 % 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: 0.35 (0.25), residues: 1079 helix: 1.02 (0.20), residues: 635 sheet: -1.04 (0.48), residues: 100 loop : -0.71 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 100 TYR 0.023 0.001 TYR A 560 PHE 0.009 0.001 PHE B 440 TRP 0.023 0.001 TRP A 577 HIS 0.003 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9132) covalent geometry : angle 0.58057 (12324) hydrogen bonds : bond 0.04506 ( 491) hydrogen bonds : angle 4.50971 ( 1434) Misc. bond : bond 0.00016 ( 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 129 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: A 109 MET cc_start: 0.9110 (tmm) cc_final: 0.8842 (tpp) REVERT: A 112 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7428 (mtm110) REVERT: A 242 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 380 GLU cc_start: 0.8275 (pp20) cc_final: 0.8000 (pp20) REVERT: A 413 SER cc_start: 0.9292 (t) cc_final: 0.8944 (p) REVERT: A 480 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8691 (tp30) REVERT: A 599 TRP cc_start: 0.7787 (t60) cc_final: 0.7420 (t60) REVERT: B 260 GLN cc_start: 0.7754 (pp30) cc_final: 0.7495 (pp30) REVERT: B 328 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8217 (mp10) REVERT: B 338 ILE cc_start: 0.8428 (mt) cc_final: 0.8190 (mp) REVERT: B 369 ILE cc_start: 0.6030 (mm) cc_final: 0.5759 (mm) REVERT: B 474 ARG cc_start: 0.8727 (mmp-170) cc_final: 0.8523 (mmp-170) REVERT: B 485 GLU cc_start: 0.8743 (pp20) cc_final: 0.8517 (pp20) outliers start: 24 outliers final: 9 residues processed: 121 average time/residue: 0.5683 time to fit residues: 73.4516 Evaluate side-chains 100 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 112 ARG 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 480 GLU Chi-restraints excluded: chain B residue 16 VAL 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: 3.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.123030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.101387 restraints weight = 18387.323| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.24 r_work: 0.3702 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9133 Z= 0.128 Angle : 0.560 7.756 12324 Z= 0.290 Chirality : 0.040 0.134 1334 Planarity : 0.004 0.062 1557 Dihedral : 7.209 70.231 1270 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.54 % Allowed : 15.68 % Favored : 82.79 % 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: 0.70 (0.26), residues: 1079 helix: 1.32 (0.21), residues: 626 sheet: -0.78 (0.50), residues: 100 loop : -0.60 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 613 TYR 0.018 0.001 TYR A 560 PHE 0.010 0.001 PHE A 166 TRP 0.016 0.001 TRP A 598 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9132) covalent geometry : angle 0.56048 (12324) hydrogen bonds : bond 0.04293 ( 491) hydrogen bonds : angle 4.42046 ( 1434) Misc. bond : bond 0.00016 ( 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 115 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: A 112 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7633 (mtm110) REVERT: A 242 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 380 GLU cc_start: 0.8345 (pp20) cc_final: 0.8033 (pp20) REVERT: A 413 SER cc_start: 0.9287 (t) cc_final: 0.8948 (p) REVERT: A 576 GLU cc_start: 0.7742 (mp0) cc_final: 0.7334 (mp0) REVERT: A 599 TRP cc_start: 0.7742 (t60) cc_final: 0.7357 (t60) REVERT: B 182 ASP cc_start: 0.7761 (p0) cc_final: 0.7392 (t0) REVERT: B 261 SER cc_start: 0.8144 (m) cc_final: 0.7807 (p) REVERT: B 328 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8334 (mp10) REVERT: B 338 ILE cc_start: 0.8361 (mt) cc_final: 0.8112 (mp) REVERT: B 369 ILE cc_start: 0.6301 (mm) cc_final: 0.6022 (mm) REVERT: B 485 GLU cc_start: 0.8740 (pp20) cc_final: 0.8482 (pp20) REVERT: B 491 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7844 (tm-30) REVERT: B 504 MET cc_start: 0.8806 (tpt) cc_final: 0.8605 (tpt) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 0.5994 time to fit residues: 71.4743 Evaluate side-chains 101 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU 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 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: 0.0970 chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.124084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.102128 restraints weight = 18216.458| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.31 r_work: 0.3721 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9133 Z= 0.117 Angle : 0.555 7.247 12324 Z= 0.288 Chirality : 0.039 0.135 1334 Planarity : 0.004 0.050 1557 Dihedral : 6.773 69.556 1268 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.84 % Allowed : 16.50 % 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: 0.91 (0.26), residues: 1079 helix: 1.49 (0.21), residues: 622 sheet: -0.44 (0.52), residues: 100 loop : -0.59 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 100 TYR 0.028 0.001 TYR A 560 PHE 0.008 0.001 PHE A 166 TRP 0.031 0.001 TRP A 598 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9132) covalent geometry : angle 0.55521 (12324) hydrogen bonds : bond 0.04088 ( 491) hydrogen bonds : angle 4.34785 ( 1434) Misc. bond : bond 0.00004 ( 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 120 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: A 112 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7837 (mtm110) REVERT: A 227 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 242 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8003 (tm-30) REVERT: A 380 GLU cc_start: 0.8350 (pp20) cc_final: 0.8017 (pp20) REVERT: A 413 SER cc_start: 0.9269 (t) cc_final: 0.8913 (p) REVERT: A 576 GLU cc_start: 0.7811 (mp0) cc_final: 0.7587 (tp30) REVERT: A 599 TRP cc_start: 0.7779 (t60) cc_final: 0.7486 (t60) REVERT: A 602 LEU cc_start: 0.8884 (mm) cc_final: 0.8659 (mm) REVERT: A 606 HIS cc_start: 0.8874 (t70) cc_final: 0.8464 (t-90) REVERT: B 158 TRP cc_start: 0.8911 (t60) cc_final: 0.8646 (t60) REVERT: B 261 SER cc_start: 0.8050 (m) cc_final: 0.7760 (p) REVERT: B 277 LYS cc_start: 0.9373 (mtpt) cc_final: 0.9160 (ptpp) REVERT: B 328 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8419 (mp10) REVERT: B 338 ILE cc_start: 0.8363 (mt) cc_final: 0.8114 (mp) REVERT: B 369 ILE cc_start: 0.6372 (mm) cc_final: 0.6068 (mm) REVERT: B 474 ARG cc_start: 0.8781 (mmp-170) cc_final: 0.8457 (mmp80) REVERT: B 485 GLU cc_start: 0.8735 (pp20) cc_final: 0.8452 (pp20) REVERT: B 491 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7799 (tm-30) outliers start: 18 outliers final: 9 residues processed: 114 average time/residue: 0.5529 time to fit residues: 67.4790 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 : 0.286 ------------------------------------------------------------------------------- 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 112 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.124717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.102741 restraints weight = 18196.206| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.31 r_work: 0.3720 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9133 Z= 0.124 Angle : 0.565 7.678 12324 Z= 0.292 Chirality : 0.040 0.164 1334 Planarity : 0.004 0.070 1557 Dihedral : 6.653 67.455 1268 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.95 % Allowed : 17.11 % Favored : 80.94 % 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: 1.56 (0.21), residues: 621 sheet: -0.35 (0.53), residues: 100 loop : -0.57 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 613 TYR 0.026 0.001 TYR A 560 PHE 0.009 0.001 PHE A 166 TRP 0.036 0.001 TRP A 598 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9132) covalent geometry : angle 0.56517 (12324) hydrogen bonds : bond 0.04085 ( 491) hydrogen bonds : angle 4.32255 ( 1434) Misc. bond : bond 0.00004 ( 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 123 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: A 227 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 242 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 380 GLU cc_start: 0.8388 (pp20) cc_final: 0.8023 (pp20) REVERT: A 386 LYS cc_start: 0.9161 (ptpp) cc_final: 0.8858 (tppt) REVERT: A 413 SER cc_start: 0.9278 (t) cc_final: 0.8918 (p) REVERT: A 576 GLU cc_start: 0.7837 (mp0) cc_final: 0.7633 (tp30) REVERT: A 599 TRP cc_start: 0.7824 (t60) cc_final: 0.7468 (t60) REVERT: B 158 TRP cc_start: 0.8934 (t60) cc_final: 0.8712 (t60) REVERT: B 182 ASP cc_start: 0.7753 (p0) cc_final: 0.7407 (t0) REVERT: B 328 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8501 (mp10) REVERT: B 338 ILE cc_start: 0.8370 (mt) cc_final: 0.8119 (mp) REVERT: B 347 GLU cc_start: 0.8183 (mp0) cc_final: 0.7883 (mp0) REVERT: B 369 ILE cc_start: 0.6524 (mm) cc_final: 0.6255 (mm) REVERT: B 474 ARG cc_start: 0.8759 (mmp-170) cc_final: 0.8418 (mmp80) REVERT: B 485 GLU cc_start: 0.8781 (pp20) cc_final: 0.8469 (pp20) REVERT: B 491 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7660 (tm-30) outliers start: 19 outliers final: 11 residues processed: 117 average time/residue: 0.5857 time to fit residues: 73.2206 Evaluate side-chains 107 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 234 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: 1.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 0.0870 chunk 94 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.125030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.103022 restraints weight = 18347.838| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.34 r_work: 0.3723 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9133 Z= 0.124 Angle : 0.574 8.271 12324 Z= 0.297 Chirality : 0.040 0.154 1334 Planarity : 0.004 0.044 1557 Dihedral : 6.564 66.742 1268 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.64 % Allowed : 17.62 % 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: 1.04 (0.26), residues: 1079 helix: 1.60 (0.21), residues: 620 sheet: -0.31 (0.53), residues: 100 loop : -0.54 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 100 TYR 0.024 0.001 TYR B 310 PHE 0.009 0.001 PHE A 254 TRP 0.033 0.001 TRP A 598 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9132) covalent geometry : angle 0.57440 (12324) hydrogen bonds : bond 0.04078 ( 491) hydrogen bonds : angle 4.32260 ( 1434) Misc. bond : bond 0.00000 ( 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 117 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: A 227 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7768 (tm-30) REVERT: A 242 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 380 GLU cc_start: 0.8393 (pp20) cc_final: 0.8019 (pp20) REVERT: A 413 SER cc_start: 0.9291 (t) cc_final: 0.8934 (p) REVERT: A 560 TYR cc_start: 0.7687 (t80) cc_final: 0.7450 (t80) REVERT: A 576 GLU cc_start: 0.7799 (mp0) cc_final: 0.7591 (tp30) REVERT: A 599 TRP cc_start: 0.7847 (t60) cc_final: 0.7446 (t60) REVERT: B 182 ASP cc_start: 0.7649 (p0) cc_final: 0.7338 (t0) REVERT: B 328 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8492 (mp10) REVERT: B 338 ILE cc_start: 0.8375 (mt) cc_final: 0.8123 (mp) REVERT: B 347 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 485 GLU cc_start: 0.8761 (pp20) cc_final: 0.8466 (pp20) REVERT: B 491 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7570 (tm-30) outliers start: 16 outliers final: 9 residues processed: 113 average time/residue: 0.6134 time to fit residues: 73.7949 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 : 0.306 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain B residue 347 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.123478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.101403 restraints weight = 18397.589| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.31 r_work: 0.3696 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9133 Z= 0.149 Angle : 0.603 8.203 12324 Z= 0.312 Chirality : 0.041 0.228 1334 Planarity : 0.004 0.062 1557 Dihedral : 6.372 66.563 1268 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.74 % Allowed : 18.14 % Favored : 80.12 % 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: 1.00 (0.26), residues: 1079 helix: 1.58 (0.21), residues: 621 sheet: -0.37 (0.52), residues: 100 loop : -0.58 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 613 TYR 0.012 0.001 TYR A 406 PHE 0.011 0.001 PHE A 43 TRP 0.037 0.001 TRP A 598 HIS 0.006 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9132) covalent geometry : angle 0.60301 (12324) hydrogen bonds : bond 0.04343 ( 491) hydrogen bonds : angle 4.41639 ( 1434) Misc. bond : bond 0.00009 ( 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 114 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: A 227 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 242 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 286 ASN cc_start: 0.8660 (t0) cc_final: 0.8273 (t0) REVERT: A 380 GLU cc_start: 0.8414 (pp20) cc_final: 0.8029 (pp20) REVERT: A 386 LYS cc_start: 0.9148 (ptpp) cc_final: 0.8871 (tppt) REVERT: A 413 SER cc_start: 0.9314 (t) cc_final: 0.8980 (p) REVERT: A 560 TYR cc_start: 0.7756 (t80) cc_final: 0.7452 (t80) REVERT: A 599 TRP cc_start: 0.7860 (t60) cc_final: 0.7465 (t60) REVERT: B 338 ILE cc_start: 0.8401 (mt) cc_final: 0.8143 (mp) REVERT: B 347 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: B 412 MET cc_start: 0.9205 (mmp) cc_final: 0.8944 (mmp) REVERT: B 474 ARG cc_start: 0.8621 (mmp-170) cc_final: 0.8227 (mmp80) REVERT: B 485 GLU cc_start: 0.8771 (pp20) cc_final: 0.8460 (pp20) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 0.6049 time to fit residues: 70.3042 Evaluate side-chains 98 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.124741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102637 restraints weight = 18270.747| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.32 r_work: 0.3718 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9133 Z= 0.132 Angle : 0.611 8.847 12324 Z= 0.317 Chirality : 0.040 0.192 1334 Planarity : 0.004 0.051 1557 Dihedral : 6.075 67.524 1268 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.23 % Allowed : 19.26 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.26), residues: 1079 helix: 1.58 (0.21), residues: 622 sheet: -0.33 (0.52), residues: 100 loop : -0.48 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 112 TYR 0.012 0.001 TYR A 406 PHE 0.012 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 covalent geometry : bond 0.00303 ( 9132) covalent geometry : angle 0.61146 (12324) hydrogen bonds : bond 0.04161 ( 491) hydrogen bonds : angle 4.38634 ( 1434) Misc. bond : bond 0.00006 ( 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 103 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: A 227 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 242 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 286 ASN cc_start: 0.8644 (t0) cc_final: 0.8273 (t0) REVERT: A 380 GLU cc_start: 0.8395 (pp20) cc_final: 0.8013 (pp20) REVERT: A 386 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8884 (tppt) REVERT: A 413 SER cc_start: 0.9303 (t) cc_final: 0.8961 (p) REVERT: A 560 TYR cc_start: 0.7753 (t80) cc_final: 0.7454 (t80) REVERT: A 599 TRP cc_start: 0.7871 (t60) cc_final: 0.7511 (t60) REVERT: B 158 TRP cc_start: 0.8849 (t60) cc_final: 0.8529 (t60) REVERT: B 338 ILE cc_start: 0.8391 (mt) cc_final: 0.8139 (mp) REVERT: B 347 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: B 474 ARG cc_start: 0.8654 (mmp-170) cc_final: 0.8330 (mmp80) REVERT: B 485 GLU cc_start: 0.8807 (pp20) cc_final: 0.8509 (pp20) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.5877 time to fit residues: 62.7259 Evaluate side-chains 97 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.124749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.102698 restraints weight = 18289.920| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.32 r_work: 0.3720 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9133 Z= 0.135 Angle : 0.631 9.391 12324 Z= 0.326 Chirality : 0.040 0.195 1334 Planarity : 0.004 0.062 1557 Dihedral : 5.968 68.254 1268 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.23 % Allowed : 19.47 % Favored : 79.30 % 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: 1.08 (0.26), residues: 1079 helix: 1.62 (0.21), residues: 620 sheet: -0.33 (0.52), residues: 100 loop : -0.51 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 112 TYR 0.013 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 covalent geometry : bond 0.00311 ( 9132) covalent geometry : angle 0.63114 (12324) hydrogen bonds : bond 0.04165 ( 491) hydrogen bonds : angle 4.38340 ( 1434) Misc. bond : bond 0.00006 ( 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 103 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: A 227 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 242 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8083 (tm-30) REVERT: A 286 ASN cc_start: 0.8631 (t0) cc_final: 0.8270 (t0) REVERT: A 386 LYS cc_start: 0.9126 (ptpp) cc_final: 0.8866 (tppt) REVERT: A 413 SER cc_start: 0.9270 (t) cc_final: 0.8915 (p) REVERT: A 560 TYR cc_start: 0.7744 (t80) cc_final: 0.7448 (t80) REVERT: A 599 TRP cc_start: 0.7813 (t60) cc_final: 0.7447 (t60) REVERT: B 158 TRP cc_start: 0.8831 (t60) cc_final: 0.8581 (t60) REVERT: B 338 ILE cc_start: 0.8434 (mt) cc_final: 0.8176 (mp) REVERT: B 347 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: B 474 ARG cc_start: 0.8684 (mmp-170) cc_final: 0.8360 (mmp80) REVERT: B 485 GLU cc_start: 0.8803 (pp20) cc_final: 0.8532 (pp20) outliers start: 12 outliers final: 8 residues processed: 100 average time/residue: 0.5784 time to fit residues: 61.9076 Evaluate side-chains 95 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 193 VAL 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: 6.9990 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 56 optimal weight: 0.0570 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN B 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.124933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.102937 restraints weight = 18141.549| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.31 r_work: 0.3728 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3439 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= 0.133 Angle : 0.645 14.456 12324 Z= 0.330 Chirality : 0.040 0.186 1334 Planarity : 0.004 0.047 1557 Dihedral : 5.890 68.705 1268 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.02 % Allowed : 19.67 % Favored : 79.30 % 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: 1.03 (0.26), residues: 1079 helix: 1.53 (0.21), residues: 627 sheet: -0.31 (0.53), residues: 100 loop : -0.48 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 112 TYR 0.012 0.001 TYR A 406 PHE 0.013 0.001 PHE B 331 TRP 0.032 0.001 TRP A 598 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9132) covalent geometry : angle 0.64548 (12324) hydrogen bonds : bond 0.04100 ( 491) hydrogen bonds : angle 4.35728 ( 1434) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3255.07 seconds wall clock time: 56 minutes 5.44 seconds (3365.44 seconds total)