Starting phenix.real_space_refine on Fri Oct 23 23:24:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28mq_56646/10_2026/28mq_56646.cif Found real_map, /net/cci-nas-00/data/ceres_data/28mq_56646/10_2026/28mq_56646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28mq_56646/10_2026/28mq_56646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28mq_56646/10_2026/28mq_56646.map" model { file = "/net/cci-nas-00/data/ceres_data/28mq_56646/10_2026/28mq_56646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28mq_56646/10_2026/28mq_56646.cif" } resolution = 3.04 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 60 5.16 5 C 7142 2.51 5 N 1890 2.21 5 O 2103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11201 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2019 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 225} Chain: "B" Number of atoms: 7890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7890 Classifications: {'peptide': 996} Link IDs: {'PCIS': 4, 'PTRANS': 49, 'TRANS': 942} Chain breaks: 1 Chain: "C" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.24 Number of scatterers: 11201 At special positions: 0 Unit cell: (90.95, 102, 148.75, 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 60 16.00 P 6 15.00 O 2103 8.00 N 1890 7.00 C 7142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 637.1 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2656 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 10 sheets defined 47.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.504A pdb=" N SER A 88 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER A 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP A 90 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.595A pdb=" N LEU A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.628A pdb=" N LEU A 192 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 193' Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 220 through 225 removed outlier: 4.039A pdb=" N GLU A 225 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 252 removed outlier: 3.755A pdb=" N TYR A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 264 through 288 removed outlier: 3.548A pdb=" N VAL A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.791A pdb=" N LEU A 292 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 removed outlier: 3.510A pdb=" N MET A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 60 removed outlier: 3.968A pdb=" N TYR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N THR B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.657A pdb=" N GLY B 102 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.624A pdb=" N VAL B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 removed outlier: 4.413A pdb=" N PHE B 150 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.559A pdb=" N LEU B 256 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.765A pdb=" N LEU B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.617A pdb=" N GLU B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.803A pdb=" N GLU B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 408 removed outlier: 3.573A pdb=" N GLN B 400 " --> pdb=" O GLY B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.361A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 443 through 460 removed outlier: 3.996A pdb=" N CYS B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N THR B 453 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.807A pdb=" N CYS B 473 " --> pdb=" O GLY B 469 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 4.316A pdb=" N ARG B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.831A pdb=" N ILE B 517 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 removed outlier: 3.528A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 583 Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.618A pdb=" N THR B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 removed outlier: 3.524A pdb=" N VAL B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 779 through 788 Processing helix chain 'B' and resid 818 through 834 removed outlier: 3.712A pdb=" N ILE B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 843 removed outlier: 3.796A pdb=" N GLN B 843 " --> pdb=" O SER B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 888 Processing helix chain 'B' and resid 894 through 915 removed outlier: 3.771A pdb=" N THR B 900 " --> pdb=" O THR B 896 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 901 " --> pdb=" O THR B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 920 Processing helix chain 'B' and resid 947 through 949 No H-bonds generated for 'chain 'B' and resid 947 through 949' Processing helix chain 'B' and resid 967 through 980 Processing helix chain 'B' and resid 1002 through 1007 removed outlier: 3.792A pdb=" N LEU B1005 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1014 Processing helix chain 'C' and resid 29 through 42 removed outlier: 3.909A pdb=" N ILE C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 40 " --> pdb=" O HIS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 111 through 124 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 144 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 Processing sheet with id=AA2, first strand: chain 'B' and resid 134 through 138 removed outlier: 7.205A pdb=" N HIS B 63 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N VAL B 158 " --> pdb=" O HIS B 63 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE B 65 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR B 160 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER B 67 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA4, first strand: chain 'B' and resid 260 through 262 removed outlier: 4.526A pdb=" N PHE B 244 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B 230 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 221 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 228 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER B 272 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL B 265 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 538 through 541 removed outlier: 3.519A pdb=" N THR B 496 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 563 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 564 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER B 591 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 566 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N THR B 593 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 924 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 602 " --> pdb=" O LYS B 922 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LYS B 922 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 944 through 945 Processing sheet with id=AA7, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.845A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1027 through 1028 Processing sheet with id=AA9, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.561A pdb=" N LYS C 55 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 106 removed outlier: 8.653A pdb=" N LEU C 156 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 91 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU C 158 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 93 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE C 131 " --> pdb=" O ALA C 159 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1356 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: 2.22 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3620 1.34 - 1.46: 2358 1.46 - 1.58: 5389 1.58 - 1.70: 6 1.70 - 1.82: 89 Bond restraints: 11462 Sorted by residual: bond pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " ideal model delta sigma weight residual 1.808 1.421 0.387 3.30e-02 9.18e+02 1.38e+02 bond pdb=" CA GLY C 164 " pdb=" C GLY C 164 " ideal model delta sigma weight residual 1.520 1.554 -0.034 1.26e-02 6.30e+03 7.40e+00 bond pdb=" N ALA C 165 " pdb=" CA ALA C 165 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.62e+00 bond pdb=" CA CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.39e-02 5.18e+03 1.59e+00 bond pdb=" CA ALA C 165 " pdb=" C ALA C 165 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.10e-02 2.27e+03 1.42e+00 ... (remaining 11457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 15264 1.42 - 2.85: 222 2.85 - 4.27: 38 4.27 - 5.70: 13 5.70 - 7.12: 5 Bond angle restraints: 15542 Sorted by residual: angle pdb=" CA GLY C 164 " pdb=" C GLY C 164 " pdb=" N ALA C 165 " ideal model delta sigma weight residual 115.05 120.98 -5.93 1.65e+00 3.67e-01 1.29e+01 angle pdb=" OD1 ASN A 180 " pdb=" CG ASN A 180 " pdb=" ND2 ASN A 180 " ideal model delta sigma weight residual 122.60 119.05 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" N GLY C 164 " pdb=" CA GLY C 164 " pdb=" C GLY C 164 " ideal model delta sigma weight residual 110.29 105.96 4.33 1.28e+00 6.10e-01 1.14e+01 angle pdb=" N CYS A 188 " pdb=" CA CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sigma weight residual 110.47 105.90 4.57 1.66e+00 3.63e-01 7.59e+00 angle pdb=" CA GLY C 164 " pdb=" C GLY C 164 " pdb=" O GLY C 164 " ideal model delta sigma weight residual 120.79 118.62 2.17 8.60e-01 1.35e+00 6.36e+00 ... (remaining 15537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 6636 17.05 - 34.11: 285 34.11 - 51.16: 41 51.16 - 68.21: 13 68.21 - 85.26: 5 Dihedral angle restraints: 6980 sinusoidal: 2885 harmonic: 4095 Sorted by residual: dihedral pdb=" CA GLN B 415 " pdb=" C GLN B 415 " pdb=" N TRP B 416 " pdb=" CA TRP B 416 " ideal model delta harmonic sigma weight residual 180.00 -161.00 -19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA VAL B 995 " pdb=" C VAL B 995 " pdb=" N PRO B 996 " pdb=" CA PRO B 996 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA LEU B 461 " pdb=" C LEU B 461 " pdb=" N ASN B 462 " pdb=" CA ASN B 462 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1447 0.053 - 0.105: 250 0.105 - 0.158: 41 0.158 - 0.211: 1 0.211 - 0.263: 1 Chirality restraints: 1740 Sorted by residual: chirality pdb=" C2 IHP B1101 " pdb=" C1 IHP B1101 " pdb=" C3 IHP B1101 " pdb=" O12 IHP B1101 " both_signs ideal model delta sigma weight residual False -2.52 -2.26 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 IHP B1101 " pdb=" C2 IHP B1101 " pdb=" C6 IHP B1101 " pdb=" O11 IHP B1101 " both_signs ideal model delta sigma weight residual False 2.32 2.14 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA CYS A 188 " pdb=" N CYS A 188 " pdb=" C CYS A 188 " pdb=" CB CYS A 188 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1737 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 178 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 179 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 25 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO C 26 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 280 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 281 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " -0.022 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1473 2.76 - 3.47: 15005 3.47 - 4.19: 24131 4.19 - 4.90: 45396 Nonbonded interactions: 86007 Sorted by model distance: nonbonded pdb=" SG CYS B 625 " pdb=" C ALA C 165 " model vdw 1.328 3.630 nonbonded pdb=" SG CYS A 188 " pdb=" CB ALA C 165 " model vdw 1.824 3.820 nonbonded pdb=" SG CYS B 625 " pdb=" O ALA C 165 " model vdw 2.222 3.400 nonbonded pdb=" SG CYS B 625 " pdb=" CA ALA C 165 " model vdw 2.504 3.830 nonbonded pdb=" CB CYS B 625 " pdb=" C ALA C 165 " model vdw 2.566 3.670 ... (remaining 86002 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: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 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 : 0.004 0.387 11462 Z= 0.158 Angle : 0.485 7.125 15542 Z= 0.261 Chirality : 0.040 0.263 1740 Planarity : 0.004 0.043 1990 Dihedral : 10.061 85.264 4324 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.64 % Allowed : 3.77 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.15 (0.23), residues: 1396 helix: 2.12 (0.23), residues: 537 sheet: 0.20 (0.35), residues: 241 loop : -0.16 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 580 TYR 0.008 0.001 TYR A 158 PHE 0.009 0.001 PHE A 152 TRP 0.006 0.001 TRP B 378 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.16 (11462) covalent geometry : angle 0.48489 / 0.26 (15542) hydrogen bonds : bond 0.15600 / 10.21 ( 502) hydrogen bonds : angle 5.40709 / 3.88 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8431 (tp30) cc_final: 0.7996 (pt0) REVERT: B 508 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7211 (mpt180) REVERT: B 796 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7984 (tmtt) REVERT: B 945 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8677 (ttmm) REVERT: C 48 GLN cc_start: 0.8432 (mt0) cc_final: 0.8042 (mt0) REVERT: C 57 LEU cc_start: 0.9248 (mt) cc_final: 0.9023 (mp) REVERT: C 107 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.7980 (mtp85) outliers start: 8 outliers final: 3 residues processed: 90 average time/residue: 0.1239 time to fit residues: 15.6434 Evaluate side-chains 77 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 945 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 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 = 0.3377 r_free = 0.3377 target = 0.077731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.053557 restraints weight = 27900.485| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.41 r_work: 0.2680 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11462 Z= 0.136 Angle : 0.494 6.712 15542 Z= 0.250 Chirality : 0.042 0.272 1740 Planarity : 0.004 0.044 1990 Dihedral : 6.172 59.979 1551 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.72 % Allowed : 5.05 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.35 (0.24), residues: 1396 helix: 2.24 (0.23), residues: 541 sheet: 0.38 (0.35), residues: 239 loop : -0.04 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 151 TYR 0.011 0.001 TYR A 158 PHE 0.011 0.001 PHE B 656 TRP 0.005 0.001 TRP B 381 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11462) covalent geometry : angle 0.49404 / 0.25 (15542) hydrogen bonds : bond 0.04609 / 3.06 ( 502) hydrogen bonds : angle 4.39015 / 3.12 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8350 (tp30) cc_final: 0.8087 (tp30) REVERT: B 508 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7242 (mpt180) REVERT: B 796 LYS cc_start: 0.8208 (tmtt) cc_final: 0.7966 (tmtt) REVERT: B 945 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8625 (ttmm) REVERT: C 57 LEU cc_start: 0.9255 (mt) cc_final: 0.9043 (mp) REVERT: C 68 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7512 (mp) REVERT: C 107 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8347 (mtp85) outliers start: 9 outliers final: 4 residues processed: 80 average time/residue: 0.1340 time to fit residues: 14.7929 Evaluate side-chains 76 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 945 LYS Chi-restraints excluded: chain C residue 68 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [24, 55, 53, 112, 95, 137, 86, 89, 2, 111, 99] chunk 24 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 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 = 0.3366 r_free = 0.3366 target = 0.077015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.052869 restraints weight = 28059.295| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.42 r_work: 0.2656 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11462 Z= 0.158 Angle : 0.504 6.749 15542 Z= 0.254 Chirality : 0.042 0.277 1740 Planarity : 0.004 0.043 1990 Dihedral : 6.173 59.953 1551 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.80 % Allowed : 6.41 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.33 (0.24), residues: 1396 helix: 2.24 (0.23), residues: 539 sheet: 0.37 (0.35), residues: 243 loop : -0.08 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 151 TYR 0.012 0.001 TYR A 158 PHE 0.013 0.001 PHE B 557 TRP 0.007 0.001 TRP B 378 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (11462) covalent geometry : angle 0.50378 / 0.25 (15542) hydrogen bonds : bond 0.04538 / 3.02 ( 502) hydrogen bonds : angle 4.24117 / 3.00 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 430 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7964 (tptp) REVERT: B 508 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7069 (mtm-85) REVERT: B 945 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8633 (ttmm) REVERT: C 57 LEU cc_start: 0.9259 (mt) cc_final: 0.9052 (mp) REVERT: C 107 ARG cc_start: 0.8648 (mtt-85) cc_final: 0.8398 (mtp85) outliers start: 10 outliers final: 4 residues processed: 79 average time/residue: 0.1388 time to fit residues: 15.0672 Evaluate side-chains 76 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 945 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [53, 0, 50, 28, 4, 71, 120, 17, 13, 38, 121] chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 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 = 0.3384 r_free = 0.3384 target = 0.078213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.053956 restraints weight = 28108.673| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.44 r_work: 0.2687 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11462 Z= 0.101 Angle : 0.464 7.019 15542 Z= 0.232 Chirality : 0.041 0.261 1740 Planarity : 0.004 0.043 1990 Dihedral : 5.974 59.132 1551 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.80 % Allowed : 6.97 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.44 (0.24), residues: 1396 helix: 2.31 (0.23), residues: 546 sheet: 0.42 (0.34), residues: 243 loop : -0.02 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 151 TYR 0.009 0.001 TYR A 158 PHE 0.009 0.001 PHE B 656 TRP 0.007 0.001 TRP B 378 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (11462) covalent geometry : angle 0.46355 / 0.23 (15542) hydrogen bonds : bond 0.03645 / 2.43 ( 502) hydrogen bonds : angle 4.02821 / 2.85 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 492 MET cc_start: 0.8614 (tpt) cc_final: 0.8204 (tpt) REVERT: B 508 ARG cc_start: 0.7833 (mtm110) cc_final: 0.6995 (mtm-85) REVERT: B 796 LYS cc_start: 0.8229 (tmtt) cc_final: 0.8002 (tmtt) REVERT: B 945 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8653 (ttmm) REVERT: C 57 LEU cc_start: 0.9256 (mt) cc_final: 0.9050 (mp) REVERT: C 68 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7343 (mp) REVERT: C 107 ARG cc_start: 0.8640 (mtt-85) cc_final: 0.8398 (mtp85) REVERT: C 144 MET cc_start: 0.7520 (mmm) cc_final: 0.6955 (mmm) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.1254 time to fit residues: 13.9234 Evaluate side-chains 78 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 945 LYS Chi-restraints excluded: chain C residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [110, 72, 5, 88, 10, 29, 86, 1, 76, 32, 30] chunk 110 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 509 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.078745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054526 restraints weight = 27832.884| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.41 r_work: 0.2704 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11462 Z= 0.095 Angle : 0.449 6.899 15542 Z= 0.225 Chirality : 0.041 0.250 1740 Planarity : 0.004 0.043 1990 Dihedral : 5.792 58.353 1551 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.12 % Allowed : 6.97 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.56 (0.24), residues: 1396 helix: 2.39 (0.23), residues: 548 sheet: 0.48 (0.34), residues: 243 loop : 0.07 (0.27), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 151 TYR 0.008 0.001 TYR A 158 PHE 0.009 0.001 PHE B 656 TRP 0.006 0.001 TRP B 378 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.09 (11462) covalent geometry : angle 0.44858 / 0.23 (15542) hydrogen bonds : bond 0.03347 / 2.24 ( 502) hydrogen bonds : angle 3.90880 / 2.77 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: B 508 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7024 (mtm-85) REVERT: B 796 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7961 (tmtt) REVERT: B 945 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8678 (tttm) REVERT: B 946 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7597 (mt) REVERT: C 57 LEU cc_start: 0.9272 (mt) cc_final: 0.9072 (mp) REVERT: C 68 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7278 (mp) REVERT: C 107 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.8372 (mtp85) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.1337 time to fit residues: 15.5550 Evaluate side-chains 83 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 945 LYS Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 126 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [1, 98, 79, 68, 19, 49, 62, 35, 109, 106, 134] chunk 1 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 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 = 0.3386 r_free = 0.3386 target = 0.078364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.054056 restraints weight = 27934.171| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.43 r_work: 0.2698 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11462 Z= 0.109 Angle : 0.460 8.190 15542 Z= 0.230 Chirality : 0.041 0.249 1740 Planarity : 0.004 0.050 1990 Dihedral : 5.748 58.020 1551 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.20 % Allowed : 6.97 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.59 (0.24), residues: 1396 helix: 2.43 (0.23), residues: 548 sheet: 0.50 (0.35), residues: 239 loop : 0.07 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 151 TYR 0.009 0.001 TYR A 158 PHE 0.010 0.001 PHE B 656 TRP 0.006 0.001 TRP B 378 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (11462) covalent geometry : angle 0.45956 / 0.23 (15542) hydrogen bonds : bond 0.03525 / 2.36 ( 502) hydrogen bonds : angle 3.89278 / 2.76 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: B 47 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8207 (tp40) REVERT: B 508 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7076 (mtm-85) REVERT: B 796 LYS cc_start: 0.8176 (tmtt) cc_final: 0.7912 (tmtt) REVERT: B 852 ASP cc_start: 0.8853 (m-30) cc_final: 0.8187 (p0) REVERT: B 945 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8687 (tttm) REVERT: B 946 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7606 (mt) REVERT: B 998 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7680 (ttm) REVERT: C 68 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7366 (mp) REVERT: C 107 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.8378 (mtp85) REVERT: C 144 MET cc_start: 0.7464 (mmm) cc_final: 0.7033 (mmm) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.1208 time to fit residues: 14.6219 Evaluate side-chains 86 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 945 LYS Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 998 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 126 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [132, 128, 11, 60, 103, 54, 34, 40, 26, 112, 38] chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 11 optimal weight: 0.0000 chunk 60 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 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 = 0.3398 r_free = 0.3398 target = 0.079010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.054889 restraints weight = 27741.663| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.40 r_work: 0.2723 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11462 Z= 0.086 Angle : 0.456 8.275 15542 Z= 0.227 Chirality : 0.040 0.238 1740 Planarity : 0.004 0.054 1990 Dihedral : 5.657 57.973 1551 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.96 % Allowed : 7.77 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.68 (0.24), residues: 1396 helix: 2.49 (0.23), residues: 550 sheet: 0.53 (0.34), residues: 239 loop : 0.14 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 151 TYR 0.007 0.001 TYR A 158 PHE 0.008 0.001 PHE B 656 TRP 0.006 0.000 TRP B 378 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (11462) covalent geometry : angle 0.45551 / 0.23 (15542) hydrogen bonds : bond 0.03077 / 2.06 ( 502) hydrogen bonds : angle 3.79264 / 2.69 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 508 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7077 (mtm-85) REVERT: B 852 ASP cc_start: 0.8843 (m-30) cc_final: 0.8198 (p0) REVERT: B 945 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8638 (tttm) REVERT: B 946 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7673 (mt) REVERT: C 68 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7329 (mp) REVERT: C 107 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.8360 (mtp85) REVERT: C 144 MET cc_start: 0.7396 (mmm) cc_final: 0.6975 (mmm) outliers start: 12 outliers final: 6 residues processed: 82 average time/residue: 0.1492 time to fit residues: 16.6430 Evaluate side-chains 81 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 945 LYS Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [6, 74, 9, 105, 56, 102, 103, 126, 42, 108, 137] chunk 6 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 126 optimal weight: 0.0010 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 GLN ** B 415 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 = 0.3403 r_free = 0.3403 target = 0.079247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.055140 restraints weight = 27765.337| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.40 r_work: 0.2728 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11462 Z= 0.090 Angle : 0.465 8.725 15542 Z= 0.231 Chirality : 0.040 0.233 1740 Planarity : 0.004 0.061 1990 Dihedral : 5.587 57.730 1550 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.96 % Allowed : 7.77 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.74 (0.24), residues: 1396 helix: 2.53 (0.23), residues: 550 sheet: 0.56 (0.34), residues: 239 loop : 0.17 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 151 TYR 0.007 0.001 TYR A 158 PHE 0.009 0.001 PHE B 656 TRP 0.005 0.000 TRP B 378 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (11462) covalent geometry : angle 0.46462 / 0.23 (15542) hydrogen bonds : bond 0.03039 / 2.04 ( 502) hydrogen bonds : angle 3.76305 / 2.68 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: B 796 LYS cc_start: 0.8110 (tmtt) cc_final: 0.7786 (tmtt) REVERT: B 852 ASP cc_start: 0.8832 (m-30) cc_final: 0.8200 (p0) REVERT: B 945 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8656 (tttm) REVERT: B 946 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7633 (mt) REVERT: B 997 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8492 (p) REVERT: C 68 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7318 (mp) REVERT: C 107 ARG cc_start: 0.8639 (mtt-85) cc_final: 0.8379 (mtp85) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.1345 time to fit residues: 15.2041 Evaluate side-chains 83 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 945 LYS Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 126 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [35, 51, 75, 132, 112, 76, 85, 44, 57, 50, 105] chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 GLN ** B 415 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 = 0.3404 r_free = 0.3404 target = 0.079317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055190 restraints weight = 27730.270| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.40 r_work: 0.2724 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11462 Z= 0.092 Angle : 0.464 9.247 15542 Z= 0.230 Chirality : 0.040 0.228 1740 Planarity : 0.004 0.065 1990 Dihedral : 5.549 57.637 1550 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.88 % Allowed : 7.93 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.75 (0.24), residues: 1396 helix: 2.55 (0.23), residues: 551 sheet: 0.56 (0.34), residues: 238 loop : 0.16 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 151 TYR 0.007 0.001 TYR A 158 PHE 0.009 0.001 PHE B 656 TRP 0.005 0.000 TRP B 378 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.09 (11462) covalent geometry : angle 0.46358 / 0.23 (15542) hydrogen bonds : bond 0.03031 / 2.03 ( 502) hydrogen bonds : angle 3.73478 / 2.66 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 852 ASP cc_start: 0.8830 (m-30) cc_final: 0.8187 (p0) REVERT: B 945 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (tttm) REVERT: B 946 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7615 (mt) REVERT: C 68 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7365 (mp) REVERT: C 107 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8359 (mtp85) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.1269 time to fit residues: 14.5038 Evaluate side-chains 83 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 945 LYS Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [84, 88, 128, 93, 101, 14, 137, 74, 108, 5, 63] chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.076907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.052371 restraints weight = 28071.632| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.48 r_work: 0.2657 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11462 Z= 0.192 Angle : 0.532 10.542 15542 Z= 0.265 Chirality : 0.043 0.263 1740 Planarity : 0.004 0.070 1990 Dihedral : 5.797 58.029 1550 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.04 % Allowed : 7.85 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.53 (0.24), residues: 1396 helix: 2.41 (0.23), residues: 548 sheet: 0.40 (0.34), residues: 242 loop : 0.04 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 151 TYR 0.015 0.001 TYR A 158 PHE 0.012 0.001 PHE B 656 TRP 0.007 0.001 TRP B 381 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 (11462) covalent geometry : angle 0.53212 / 0.27 (15542) hydrogen bonds : bond 0.04461 / 2.97 ( 502) hydrogen bonds : angle 4.01610 / 2.85 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 796 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7831 (tmtt) REVERT: B 852 ASP cc_start: 0.8856 (m-30) cc_final: 0.8210 (p0) REVERT: B 945 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8600 (tttm) REVERT: B 946 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7602 (mt) REVERT: B 997 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8560 (p) REVERT: C 68 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7341 (mp) REVERT: C 144 MET cc_start: 0.7280 (mmm) cc_final: 0.6970 (mmm) outliers start: 13 outliers final: 6 residues processed: 81 average time/residue: 0.1308 time to fit residues: 14.5890 Evaluate side-chains 81 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 945 LYS Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: [111, 30, 44, 83, 19, 86, 107, 60, 108, 6, 10] chunk 111 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 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 = 0.3346 r_free = 0.3346 target = 0.078110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.053107 restraints weight = 27659.345| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.63 r_work: 0.2631 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11462 Z= 0.093 Angle : 0.470 9.895 15542 Z= 0.234 Chirality : 0.040 0.232 1740 Planarity : 0.004 0.071 1990 Dihedral : 5.649 58.109 1550 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.72 % Allowed : 8.41 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 1.68 (0.24), residues: 1396 helix: 2.52 (0.23), residues: 550 sheet: 0.49 (0.34), residues: 238 loop : 0.13 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 151 TYR 0.007 0.001 TYR B 663 PHE 0.007 0.001 PHE B 656 TRP 0.006 0.001 TRP B 378 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.09 (11462) covalent geometry : angle 0.46977 / 0.23 (15542) hydrogen bonds : bond 0.03053 / 2.04 ( 502) hydrogen bonds : angle 3.77596 / 2.68 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.84 seconds wall clock time: 44 minutes 56.29 seconds (2696.29 seconds total)