Starting phenix.real_space_refine on Thu Sep 18 01:55:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cwo_45968/09_2025/9cwo_45968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cwo_45968/09_2025/9cwo_45968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cwo_45968/09_2025/9cwo_45968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cwo_45968/09_2025/9cwo_45968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cwo_45968/09_2025/9cwo_45968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cwo_45968/09_2025/9cwo_45968.map" } resolution = 3.43 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= 0.085 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8097 2.51 5 N 2179 2.21 5 O 2365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12722 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1193, 9180 Classifications: {'peptide': 1193} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1144} Chain breaks: 15 Unresolved non-hydrogen bonds: 455 Unresolved non-hydrogen angles: 553 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 20, 'ASN:plan1': 7, 'GLN:plan1': 9, 'ARG:plan': 12, 'ASP:plan': 19, 'HIS:plan': 3, 'TYR:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 303 Chain: "F" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 711 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 706 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 5, 'PHE:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "G" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 709 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 3, 'TRANS': 98} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 3, 'PHE:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "E" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1416 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 6, 'ARG:plan': 3, 'TYR:plan': 2, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 112 Time building chain proxies: 2.69, per 1000 atoms: 0.21 Number of scatterers: 12722 At special positions: 0 Unit cell: (92.02, 159.96, 167.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2365 8.00 N 2179 7.00 C 8097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1191 " - pdb=" SG CYS A1429 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 626.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 8 sheets defined 65.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.678A pdb=" N LEU A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 54 removed outlier: 4.205A pdb=" N SER A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 105 through 137 removed outlier: 3.614A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 removed outlier: 4.041A pdb=" N ASP A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 189 removed outlier: 3.505A pdb=" N LYS A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 260 through 273 removed outlier: 4.073A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 289 removed outlier: 4.104A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 309 through 325 removed outlier: 4.264A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.957A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 411 removed outlier: 3.829A pdb=" N ARG A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.611A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.641A pdb=" N GLU A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 Processing helix chain 'A' and resid 575 through 580 removed outlier: 3.705A pdb=" N PHE A 579 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 580 " --> pdb=" O GLY A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 575 through 580' Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.558A pdb=" N ASN A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.868A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 802 through 821 Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 847 through 874 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.732A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 964 Processing helix chain 'A' and resid 972 through 982 Proline residue: A 978 - end of helix removed outlier: 3.545A pdb=" N ASN A 982 " --> pdb=" O PRO A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 3.803A pdb=" N LEU A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1083 removed outlier: 3.571A pdb=" N ASN A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1110 Processing helix chain 'A' and resid 1115 through 1124 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.650A pdb=" N LEU A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1179 removed outlier: 5.502A pdb=" N ASP A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1204 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1291 through 1308 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1329 through 1337 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1391 through 1407 Processing helix chain 'F' and resid 480 through 485 removed outlier: 3.664A pdb=" N PHE F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 485 " --> pdb=" O SER F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 480 through 485' Processing helix chain 'F' and resid 492 through 497 Processing helix chain 'F' and resid 498 through 501 removed outlier: 3.882A pdb=" N ASP F 501 " --> pdb=" O TYR F 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 498 through 501' Processing helix chain 'F' and resid 510 through 541 removed outlier: 3.606A pdb=" N GLU F 514 " --> pdb=" O THR F 510 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN F 539 " --> pdb=" O HIS F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 573 removed outlier: 3.647A pdb=" N SER F 573 " --> pdb=" O GLY F 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 489 through 502 Processing helix chain 'C' and resid 507 through 533 removed outlier: 3.721A pdb=" N CYS C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU C 513 " --> pdb=" O GLU C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 543 Processing helix chain 'C' and resid 544 through 578 removed outlier: 3.927A pdb=" N ASN C 548 " --> pdb=" O PRO C 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 488 removed outlier: 3.940A pdb=" N THR G 487 " --> pdb=" O PHE G 484 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE G 488 " --> pdb=" O SER G 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 484 through 488' Processing helix chain 'G' and resid 489 through 504 Processing helix chain 'G' and resid 511 through 539 removed outlier: 3.989A pdb=" N GLN G 539 " --> pdb=" O HIS G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 574 removed outlier: 3.636A pdb=" N MET G 574 " --> pdb=" O HIS G 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 503 removed outlier: 4.168A pdb=" N LEU E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 543 Processing helix chain 'E' and resid 545 through 574 Processing helix chain 'E' and resid 605 through 609 Processing helix chain 'E' and resid 657 through 672 Processing helix chain 'E' and resid 674 through 688 Processing helix chain 'E' and resid 690 through 707 removed outlier: 3.669A pdb=" N ILE E 694 " --> pdb=" O ASN E 690 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 388 Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA4, first strand: chain 'A' and resid 554 through 555 removed outlier: 3.679A pdb=" N ILE A 764 " --> pdb=" O ILE A 791 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 715 through 716 removed outlier: 3.513A pdb=" N VAL A 715 " --> pdb=" O GLN A 840 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 718 through 720 removed outlier: 3.716A pdb=" N ILE A 883 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 897 Processing sheet with id=AA8, first strand: chain 'A' and resid 1225 through 1229 removed outlier: 3.757A pdb=" N VAL A1226 " --> pdb=" O HIS A1423 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 1.29 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: 4193 1.34 - 1.46: 2606 1.46 - 1.58: 6010 1.58 - 1.70: 0 1.70 - 1.81: 132 Bond restraints: 12941 Sorted by residual: bond pdb=" C ILE E 543 " pdb=" N PRO E 544 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.57e+00 bond pdb=" CB PRO G 480 " pdb=" CG PRO G 480 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.39e+00 bond pdb=" CG PRO G 480 " pdb=" CD PRO G 480 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.21e+00 bond pdb=" CB MET G 479 " pdb=" CG MET G 479 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CB GLU A1447 " pdb=" CG GLU A1447 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 ... (remaining 12936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 17385 1.94 - 3.89: 159 3.89 - 5.83: 34 5.83 - 7.77: 4 7.77 - 9.71: 1 Bond angle restraints: 17583 Sorted by residual: angle pdb=" CB MET G 479 " pdb=" CG MET G 479 " pdb=" SD MET G 479 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA PRO G 480 " pdb=" N PRO G 480 " pdb=" CD PRO G 480 " ideal model delta sigma weight residual 112.00 108.07 3.93 1.40e+00 5.10e-01 7.88e+00 angle pdb=" N GLY E 599 " pdb=" CA GLY E 599 " pdb=" C GLY E 599 " ideal model delta sigma weight residual 110.69 115.83 -5.14 2.05e+00 2.38e-01 6.28e+00 angle pdb=" CB MET G 577 " pdb=" CG MET G 577 " pdb=" SD MET G 577 " ideal model delta sigma weight residual 112.70 119.85 -7.15 3.00e+00 1.11e-01 5.67e+00 angle pdb=" CB GLU A1447 " pdb=" CG GLU A1447 " pdb=" CD GLU A1447 " ideal model delta sigma weight residual 112.60 116.43 -3.83 1.70e+00 3.46e-01 5.07e+00 ... (remaining 17578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6869 17.89 - 35.78: 738 35.78 - 53.67: 188 53.67 - 71.56: 42 71.56 - 89.45: 12 Dihedral angle restraints: 7849 sinusoidal: 2860 harmonic: 4989 Sorted by residual: dihedral pdb=" CB CYS A1191 " pdb=" SG CYS A1191 " pdb=" SG CYS A1429 " pdb=" CB CYS A1429 " ideal model delta sinusoidal sigma weight residual 93.00 134.28 -41.28 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CA ILE E 543 " pdb=" C ILE E 543 " pdb=" N PRO E 544 " pdb=" CA PRO E 544 " ideal model delta harmonic sigma weight residual -180.00 -157.09 -22.91 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA MET A 735 " pdb=" C MET A 735 " pdb=" N ALA A 736 " pdb=" CA ALA A 736 " ideal model delta harmonic sigma weight residual -180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1564 0.040 - 0.081: 438 0.081 - 0.121: 90 0.121 - 0.162: 13 0.162 - 0.202: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" CG LEU E 642 " pdb=" CB LEU E 642 " pdb=" CD1 LEU E 642 " pdb=" CD2 LEU E 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR A1079 " pdb=" CA THR A1079 " pdb=" OG1 THR A1079 " pdb=" CG2 THR A1079 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA VAL E 602 " pdb=" N VAL E 602 " pdb=" C VAL E 602 " pdb=" CB VAL E 602 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 2103 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 479 " 0.035 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO G 480 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 480 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 480 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 994 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 995 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 995 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 995 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 211 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 212 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.021 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 219 2.69 - 3.24: 12653 3.24 - 3.79: 21018 3.79 - 4.35: 26076 4.35 - 4.90: 43476 Nonbonded interactions: 103442 Sorted by model distance: nonbonded pdb=" OG SER A 477 " pdb=" O ASN A 536 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASN F 561 " pdb=" OG1 THR C 560 " model vdw 2.170 3.040 nonbonded pdb=" O TRP A1319 " pdb=" OG SER A1323 " model vdw 2.176 3.040 nonbonded pdb=" OD1 ASN A1364 " pdb=" OG SER A1367 " model vdw 2.199 3.040 nonbonded pdb=" O LYS A 301 " pdb=" NE2 GLN A1259 " model vdw 2.215 3.120 ... (remaining 103437 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 480 or (resid 481 through 484 and (name N or name CA or na \ me C or name O or name CB )) or resid 485 through 487 or (resid 488 through 489 \ and (name N or name CA or name C or name O or name CB )) or resid 490 through 49 \ 5 or (resid 496 through 503 and (name N or name CA or name C or name O or name C \ B )) or resid 504 or (resid 505 through 511 and (name N or name CA or name C or \ name O or name CB )) or resid 512 through 523 or (resid 524 through 525 and (nam \ e N or name CA or name C or name O or name CB )) or resid 526 or (resid 527 thro \ ugh 528 and (name N or name CA or name C or name O or name CB )) or resid 529 or \ (resid 530 through 531 and (name N or name CA or name C or name O or name CB )) \ or resid 532 through 533 or (resid 534 and (name N or name CA or name C or name \ O or name CB )) or resid 535 through 537 or (resid 538 and (name N or name CA o \ r name C or name O or name CB )) or resid 539 through 578)) selection = (chain 'F' and (resid 480 or (resid 481 through 484 and (name N or name CA or na \ me C or name O or name CB )) or resid 485 through 487 or (resid 488 through 489 \ and (name N or name CA or name C or name O or name CB )) or resid 490 through 49 \ 2 or (resid 493 through 503 and (name N or name CA or name C or name O or name C \ B )) or resid 504 or (resid 505 through 511 and (name N or name CA or name C or \ name O or name CB )) or resid 512 or (resid 513 through 514 and (name N or name \ CA or name C or name O or name CB )) or resid 515 or (resid 516 through 518 and \ (name N or name CA or name C or name O or name CB )) or resid 519 or (resid 520 \ through 521 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 2 through 527 or (resid 528 and (name N or name CA or name C or name O or name C \ B )) or resid 529 or (resid 530 through 531 and (name N or name CA or name C or \ name O or name CB )) or resid 532 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 536 or (resid 537 thro \ ugh 538 and (name N or name CA or name C or name O or name CB )) or resid 539 th \ rough 544 or (resid 545 and (name N or name CA or name C or name O or name CB )) \ or resid 546 through 578)) selection = (chain 'G' and (resid 480 through 482 or (resid 483 through 484 and (name N or n \ ame CA or name C or name O or name CB )) or resid 485 through 486 or (resid 487 \ through 489 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 0 through 492 or (resid 493 through 503 and (name N or name CA or name C or name \ O or name CB )) or (resid 504 through 511 and (name N or name CA or name C or n \ ame O or name CB )) or resid 512 or (resid 513 through 514 and (name N or name C \ A or name C or name O or name CB )) or resid 515 or (resid 516 through 518 and ( \ name N or name CA or name C or name O or name CB )) or resid 519 or (resid 520 t \ hrough 521 and (name N or name CA or name C or name O or name CB )) or resid 522 \ through 523 or (resid 524 through 525 and (name N or name CA or name C or name \ O or name CB )) or resid 526 through 536 or (resid 537 through 538 and (name N o \ r name CA or name C or name O or name CB )) or resid 539 through 544 or (resid 5 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 546 through \ 578)) } 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: 0.010 Normalize map: mean=0, sd=1: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.470 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 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 : 0.003 0.059 12942 Z= 0.118 Angle : 0.519 9.713 17585 Z= 0.270 Chirality : 0.039 0.202 2106 Planarity : 0.004 0.052 2235 Dihedral : 16.344 89.447 4582 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.54 % Allowed : 25.77 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 2.07 (0.22), residues: 1655 helix: 2.62 (0.17), residues: 988 sheet: -0.45 (0.63), residues: 79 loop : -0.57 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1295 TYR 0.013 0.001 TYR A 470 PHE 0.019 0.001 PHE A 399 TRP 0.014 0.001 TRP A 806 HIS 0.004 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00269 (12941) covalent geometry : angle 0.51893 (17583) SS BOND : bond 0.00309 ( 1) SS BOND : angle 1.70497 ( 2) hydrogen bonds : bond 0.12547 ( 805) hydrogen bonds : angle 5.12044 ( 2337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 364 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.7043 (mtp) cc_final: 0.6723 (mtt) REVERT: A 256 ILE cc_start: 0.8177 (tp) cc_final: 0.7756 (pt) REVERT: A 368 LEU cc_start: 0.7800 (mt) cc_final: 0.7597 (mp) REVERT: A 407 TYR cc_start: 0.7214 (t80) cc_final: 0.6842 (t80) REVERT: A 838 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 981 ASN cc_start: 0.8329 (m-40) cc_final: 0.8077 (m110) REVERT: A 1133 GLU cc_start: 0.7521 (tt0) cc_final: 0.6716 (mm-30) REVERT: A 1138 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7446 (tp) REVERT: A 1185 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7120 (mt) REVERT: A 1225 MET cc_start: 0.6066 (mmm) cc_final: 0.5136 (mmm) REVERT: A 1245 MET cc_start: 0.4517 (ttt) cc_final: 0.4119 (pmm) REVERT: A 1316 TYR cc_start: 0.6923 (t80) cc_final: 0.6598 (t80) REVERT: A 1319 TRP cc_start: 0.6830 (t60) cc_final: 0.6597 (t60) REVERT: A 1375 ASP cc_start: 0.8224 (t0) cc_final: 0.7746 (p0) REVERT: F 526 LEU cc_start: 0.7027 (tp) cc_final: 0.6611 (tp) REVERT: F 575 MET cc_start: 0.7597 (mmm) cc_final: 0.6738 (mtt) REVERT: C 488 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.4681 (m-80) REVERT: C 515 SER cc_start: 0.5852 (t) cc_final: 0.5570 (t) REVERT: C 559 LYS cc_start: 0.8116 (tppp) cc_final: 0.7750 (mmtt) REVERT: E 570 HIS cc_start: 0.7267 (m-70) cc_final: 0.6869 (m170) REVERT: E 665 LYS cc_start: 0.7611 (tttp) cc_final: 0.7366 (ttmt) REVERT: E 669 ARG cc_start: 0.5971 (mtt90) cc_final: 0.4765 (mtm180) REVERT: E 678 ARG cc_start: 0.6550 (ttm170) cc_final: 0.5909 (ttt180) REVERT: E 700 THR cc_start: 0.7207 (m) cc_final: 0.6829 (m) outliers start: 7 outliers final: 3 residues processed: 370 average time/residue: 0.1225 time to fit residues: 64.1715 Evaluate side-chains 255 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 248 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain E residue 576 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN A 778 HIS A1202 HIS ** G 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.222224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.189531 restraints weight = 18483.009| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.40 r_work: 0.4124 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12942 Z= 0.194 Angle : 0.624 10.950 17585 Z= 0.320 Chirality : 0.043 0.222 2106 Planarity : 0.004 0.048 2235 Dihedral : 4.565 55.478 1804 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.00 % Allowed : 24.92 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.67 (0.21), residues: 1655 helix: 2.28 (0.16), residues: 984 sheet: -0.58 (0.62), residues: 81 loop : -0.68 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1117 TYR 0.013 0.002 TYR A 765 PHE 0.020 0.002 PHE E 652 TRP 0.012 0.002 TRP A 447 HIS 0.006 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00467 (12941) covalent geometry : angle 0.62380 (17583) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.98004 ( 2) hydrogen bonds : bond 0.04096 ( 805) hydrogen bonds : angle 4.36227 ( 2337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 252 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7571 (tm-30) REVERT: A 180 MET cc_start: 0.7359 (ttp) cc_final: 0.6932 (tpt) REVERT: A 256 ILE cc_start: 0.8187 (tp) cc_final: 0.7831 (pt) REVERT: A 325 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7426 (tt0) REVERT: A 331 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: A 407 TYR cc_start: 0.7277 (t80) cc_final: 0.6947 (t80) REVERT: A 735 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6858 (tpt) REVERT: A 838 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7713 (mp) REVERT: A 880 THR cc_start: 0.6561 (OUTLIER) cc_final: 0.6319 (p) REVERT: A 977 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 981 ASN cc_start: 0.8283 (m-40) cc_final: 0.8028 (m110) REVERT: A 1133 GLU cc_start: 0.7583 (tt0) cc_final: 0.6687 (mm-30) REVERT: A 1181 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7313 (mmtm) REVERT: A 1245 MET cc_start: 0.4714 (ttt) cc_final: 0.4250 (pmm) REVERT: A 1375 ASP cc_start: 0.8168 (t0) cc_final: 0.7741 (p0) REVERT: F 575 MET cc_start: 0.7684 (mmm) cc_final: 0.6738 (mtt) REVERT: C 488 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.4675 (m-80) REVERT: C 559 LYS cc_start: 0.8200 (tppp) cc_final: 0.7921 (mptt) REVERT: E 533 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6479 (tt) REVERT: E 553 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8280 (tt) REVERT: E 557 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7222 (mp) REVERT: E 665 LYS cc_start: 0.7613 (tttp) cc_final: 0.7358 (ttmt) REVERT: E 669 ARG cc_start: 0.6158 (mtt90) cc_final: 0.4925 (mtm180) REVERT: E 695 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7631 (tm-30) outliers start: 65 outliers final: 33 residues processed: 296 average time/residue: 0.1107 time to fit residues: 47.5000 Evaluate side-chains 263 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 650 SER Chi-restraints excluded: chain E residue 679 SER Chi-restraints excluded: chain E residue 697 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 HIS A 887 HIS A 904 GLN E 699 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.223400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191139 restraints weight = 18663.603| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.41 r_work: 0.4137 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12942 Z= 0.140 Angle : 0.562 9.495 17585 Z= 0.288 Chirality : 0.040 0.206 2106 Planarity : 0.004 0.046 2235 Dihedral : 4.271 52.567 1797 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.00 % Allowed : 24.62 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.68 (0.21), residues: 1655 helix: 2.31 (0.16), residues: 987 sheet: -0.68 (0.62), residues: 81 loop : -0.73 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1117 TYR 0.014 0.002 TYR A 801 PHE 0.018 0.001 PHE A 914 TRP 0.009 0.001 TRP A1248 HIS 0.013 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00326 (12941) covalent geometry : angle 0.56170 (17583) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.72625 ( 2) hydrogen bonds : bond 0.03713 ( 805) hydrogen bonds : angle 4.16305 ( 2337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.7634 (t80) cc_final: 0.7417 (t80) REVERT: A 144 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7591 (tm-30) REVERT: A 180 MET cc_start: 0.7296 (ttp) cc_final: 0.6916 (tpt) REVERT: A 256 ILE cc_start: 0.8196 (tp) cc_final: 0.7856 (pt) REVERT: A 334 ARG cc_start: 0.7224 (mtm-85) cc_final: 0.7003 (mtm180) REVERT: A 835 SER cc_start: 0.7597 (OUTLIER) cc_final: 0.7053 (p) REVERT: A 838 ILE cc_start: 0.8047 (mp) cc_final: 0.7773 (mp) REVERT: A 977 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 981 ASN cc_start: 0.8305 (m-40) cc_final: 0.8065 (m110) REVERT: A 1133 GLU cc_start: 0.7571 (tt0) cc_final: 0.6704 (mm-30) REVERT: A 1181 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7371 (mmtm) REVERT: A 1245 MET cc_start: 0.4625 (ttt) cc_final: 0.4097 (pmm) REVERT: A 1295 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7272 (ptp-170) REVERT: A 1316 TYR cc_start: 0.6765 (t80) cc_final: 0.6497 (t80) REVERT: A 1375 ASP cc_start: 0.8209 (t0) cc_final: 0.7767 (p0) REVERT: A 1442 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7223 (mt-10) REVERT: F 575 MET cc_start: 0.7666 (mmm) cc_final: 0.6844 (mtt) REVERT: C 488 PHE cc_start: 0.6119 (OUTLIER) cc_final: 0.4645 (m-80) REVERT: C 559 LYS cc_start: 0.8184 (tppp) cc_final: 0.7913 (mptt) REVERT: G 518 MET cc_start: 0.4038 (tmt) cc_final: 0.3763 (ppp) REVERT: G 523 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8440 (p) REVERT: E 512 CYS cc_start: 0.5553 (OUTLIER) cc_final: 0.4809 (t) REVERT: E 533 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6377 (tt) REVERT: E 561 ASN cc_start: 0.7267 (t0) cc_final: 0.6788 (m-40) REVERT: E 669 ARG cc_start: 0.6146 (mtt90) cc_final: 0.4930 (mtm180) outliers start: 65 outliers final: 30 residues processed: 281 average time/residue: 0.1170 time to fit residues: 47.4157 Evaluate side-chains 250 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1423 HIS Chi-restraints excluded: chain F residue 534 ASN Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain E residue 512 CYS Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 658 ASP Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 697 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 142 optimal weight: 0.0470 chunk 125 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 108 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN G 561 ASN E 699 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.225527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.193795 restraints weight = 18532.287| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.39 r_work: 0.4168 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12942 Z= 0.112 Angle : 0.524 8.522 17585 Z= 0.268 Chirality : 0.039 0.177 2106 Planarity : 0.004 0.047 2235 Dihedral : 4.055 52.022 1795 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.08 % Allowed : 24.31 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.80 (0.21), residues: 1655 helix: 2.39 (0.16), residues: 998 sheet: -0.67 (0.63), residues: 78 loop : -0.70 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1205 TYR 0.010 0.001 TYR A 407 PHE 0.016 0.001 PHE A 458 TRP 0.010 0.001 TRP A 806 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00253 (12941) covalent geometry : angle 0.52408 (17583) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.68050 ( 2) hydrogen bonds : bond 0.03381 ( 805) hydrogen bonds : angle 3.94153 ( 2337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.5308 (OUTLIER) cc_final: 0.4995 (m-10) REVERT: A 204 LYS cc_start: 0.8022 (ptpp) cc_final: 0.7822 (ptpp) REVERT: A 256 ILE cc_start: 0.8181 (tp) cc_final: 0.7847 (pt) REVERT: A 410 ARG cc_start: 0.7523 (ptp90) cc_final: 0.7026 (ptp90) REVERT: A 835 SER cc_start: 0.7559 (OUTLIER) cc_final: 0.7246 (p) REVERT: A 838 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7711 (mp) REVERT: A 909 MET cc_start: 0.8218 (mmm) cc_final: 0.7923 (mmm) REVERT: A 977 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 981 ASN cc_start: 0.8318 (m-40) cc_final: 0.8107 (m110) REVERT: A 1133 GLU cc_start: 0.7567 (tt0) cc_final: 0.6707 (mm-30) REVERT: A 1181 LYS cc_start: 0.7843 (mtpt) cc_final: 0.7346 (mmtm) REVERT: A 1245 MET cc_start: 0.4508 (ttt) cc_final: 0.4059 (pmm) REVERT: A 1295 ARG cc_start: 0.7629 (tpt170) cc_final: 0.7233 (ptp-170) REVERT: A 1316 TYR cc_start: 0.6789 (t80) cc_final: 0.6490 (t80) REVERT: A 1366 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7198 (t) REVERT: A 1375 ASP cc_start: 0.8250 (t0) cc_final: 0.7801 (p0) REVERT: A 1442 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7230 (mt-10) REVERT: F 575 MET cc_start: 0.7662 (mmm) cc_final: 0.6960 (mtt) REVERT: C 488 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.4650 (m-80) REVERT: C 554 ASP cc_start: 0.8270 (t0) cc_final: 0.7995 (t0) REVERT: C 559 LYS cc_start: 0.8170 (tppp) cc_final: 0.7887 (mptt) REVERT: C 574 MET cc_start: 0.6542 (mtt) cc_final: 0.6179 (mtp) REVERT: G 518 MET cc_start: 0.3896 (tmt) cc_final: 0.3641 (ppp) REVERT: E 512 CYS cc_start: 0.5374 (OUTLIER) cc_final: 0.4676 (t) REVERT: E 533 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6455 (tt) REVERT: E 553 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8183 (tt) REVERT: E 669 ARG cc_start: 0.6019 (mtt90) cc_final: 0.4898 (mtm180) REVERT: E 695 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7629 (tp-100) outliers start: 66 outliers final: 27 residues processed: 287 average time/residue: 0.1098 time to fit residues: 45.4350 Evaluate side-chains 258 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 949 CYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1393 GLN Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1423 HIS Chi-restraints excluded: chain F residue 534 ASN Chi-restraints excluded: chain F residue 535 HIS Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain E residue 512 CYS Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 697 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 51 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN ** G 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 561 ASN E 708 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.217628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.184843 restraints weight = 18546.010| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.36 r_work: 0.4082 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12942 Z= 0.214 Angle : 0.644 11.344 17585 Z= 0.330 Chirality : 0.043 0.164 2106 Planarity : 0.004 0.047 2235 Dihedral : 4.428 52.433 1795 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.15 % Allowed : 23.85 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.26 (0.21), residues: 1655 helix: 1.89 (0.16), residues: 1000 sheet: -0.81 (0.65), residues: 72 loop : -0.79 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1117 TYR 0.022 0.002 TYR A 765 PHE 0.025 0.002 PHE A 458 TRP 0.011 0.002 TRP A1248 HIS 0.005 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00515 (12941) covalent geometry : angle 0.64380 (17583) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.81168 ( 2) hydrogen bonds : bond 0.04075 ( 805) hydrogen bonds : angle 4.27078 ( 2337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.5275 (OUTLIER) cc_final: 0.4934 (m-10) REVERT: A 256 ILE cc_start: 0.8197 (tp) cc_final: 0.7885 (pt) REVERT: A 289 MET cc_start: 0.8008 (tpp) cc_final: 0.7773 (tpp) REVERT: A 835 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.7213 (p) REVERT: A 964 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 968 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7880 (m-40) REVERT: A 977 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8204 (m) REVERT: A 981 ASN cc_start: 0.8316 (m-40) cc_final: 0.8043 (m110) REVERT: A 1133 GLU cc_start: 0.7660 (tt0) cc_final: 0.6729 (mm-30) REVERT: A 1180 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8378 (ttm110) REVERT: A 1181 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7475 (mmtm) REVERT: A 1245 MET cc_start: 0.4804 (ttt) cc_final: 0.4270 (pmm) REVERT: A 1295 ARG cc_start: 0.7687 (tpt170) cc_final: 0.7238 (ptp-170) REVERT: A 1366 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7154 (t) REVERT: A 1375 ASP cc_start: 0.8277 (t0) cc_final: 0.7746 (p0) REVERT: A 1442 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7251 (mt-10) REVERT: F 575 MET cc_start: 0.7851 (mmm) cc_final: 0.6996 (mtt) REVERT: C 488 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.4658 (m-80) REVERT: C 554 ASP cc_start: 0.8397 (t0) cc_final: 0.8094 (t0) REVERT: C 559 LYS cc_start: 0.8260 (tppp) cc_final: 0.7783 (mmtt) REVERT: C 574 MET cc_start: 0.6810 (mtt) cc_final: 0.6344 (mtp) REVERT: G 518 MET cc_start: 0.4251 (tmt) cc_final: 0.3925 (ppp) REVERT: G 523 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8387 (p) REVERT: E 553 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8260 (tt) REVERT: E 608 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5824 (mp) REVERT: E 669 ARG cc_start: 0.6190 (mtt90) cc_final: 0.5022 (mtm180) REVERT: E 695 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7575 (tm-30) outliers start: 80 outliers final: 46 residues processed: 288 average time/residue: 0.1016 time to fit residues: 43.1097 Evaluate side-chains 271 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 949 CYS Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1393 GLN Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain F residue 534 ASN Chi-restraints excluded: chain F residue 536 ILE Chi-restraints excluded: chain F residue 546 ILE Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain G residue 561 ASN Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 650 SER Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 696 GLU Chi-restraints excluded: chain E residue 697 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 152 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN A1011 ASN A1174 ASN A1394 GLN G 539 GLN G 561 ASN E 651 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.220713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.187926 restraints weight = 18416.785| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.49 r_work: 0.4104 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12942 Z= 0.138 Angle : 0.567 10.010 17585 Z= 0.287 Chirality : 0.040 0.176 2106 Planarity : 0.004 0.045 2235 Dihedral : 4.262 51.811 1795 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.00 % Allowed : 25.92 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.46 (0.21), residues: 1655 helix: 2.08 (0.16), residues: 1000 sheet: -0.96 (0.63), residues: 73 loop : -0.75 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1205 TYR 0.012 0.002 TYR A 539 PHE 0.016 0.001 PHE A 579 TRP 0.009 0.001 TRP A 806 HIS 0.003 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00323 (12941) covalent geometry : angle 0.56741 (17583) SS BOND : bond 0.00236 ( 1) SS BOND : angle 1.05206 ( 2) hydrogen bonds : bond 0.03627 ( 805) hydrogen bonds : angle 4.06573 ( 2337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.5347 (OUTLIER) cc_final: 0.4983 (m-10) REVERT: A 256 ILE cc_start: 0.8150 (tp) cc_final: 0.7815 (pt) REVERT: A 470 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: A 909 MET cc_start: 0.8185 (mmm) cc_final: 0.7822 (mmm) REVERT: A 977 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8169 (m) REVERT: A 981 ASN cc_start: 0.8347 (m-40) cc_final: 0.8093 (m110) REVERT: A 1133 GLU cc_start: 0.7590 (tt0) cc_final: 0.6621 (mm-30) REVERT: A 1180 ARG cc_start: 0.8591 (ttm110) cc_final: 0.8381 (ttm110) REVERT: A 1181 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7347 (mmtm) REVERT: A 1245 MET cc_start: 0.4654 (ttt) cc_final: 0.4144 (pmm) REVERT: A 1295 ARG cc_start: 0.7645 (tpt170) cc_final: 0.7186 (ptp-170) REVERT: A 1316 TYR cc_start: 0.6910 (t80) cc_final: 0.6687 (t80) REVERT: A 1366 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.7104 (t) REVERT: A 1375 ASP cc_start: 0.8344 (t0) cc_final: 0.7772 (p0) REVERT: A 1442 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7208 (mt-10) REVERT: F 575 MET cc_start: 0.7790 (mmm) cc_final: 0.6986 (mtt) REVERT: C 488 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.4600 (m-80) REVERT: C 554 ASP cc_start: 0.8396 (t0) cc_final: 0.8108 (t0) REVERT: C 559 LYS cc_start: 0.8225 (tppp) cc_final: 0.7932 (mptt) REVERT: C 574 MET cc_start: 0.6780 (mtt) cc_final: 0.6360 (mtp) REVERT: G 518 MET cc_start: 0.3991 (tmt) cc_final: 0.3687 (ppp) REVERT: G 523 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8388 (p) REVERT: E 512 CYS cc_start: 0.5264 (OUTLIER) cc_final: 0.4612 (t) REVERT: E 552 SER cc_start: 0.7671 (OUTLIER) cc_final: 0.7194 (t) REVERT: E 553 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8125 (tt) REVERT: E 608 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5835 (mt) REVERT: E 669 ARG cc_start: 0.6189 (mtt90) cc_final: 0.4969 (mtm180) REVERT: E 695 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 699 ASN cc_start: 0.8474 (m-40) cc_final: 0.8250 (m110) outliers start: 65 outliers final: 36 residues processed: 272 average time/residue: 0.1113 time to fit residues: 43.9971 Evaluate side-chains 262 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 949 CYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain F residue 534 ASN Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain E residue 512 CYS Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 697 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.0050 chunk 5 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.221228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.189428 restraints weight = 18290.818| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.37 r_work: 0.4129 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12942 Z= 0.130 Angle : 0.556 11.395 17585 Z= 0.280 Chirality : 0.040 0.157 2106 Planarity : 0.004 0.044 2235 Dihedral : 4.190 51.590 1795 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.46 % Allowed : 26.00 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.55 (0.21), residues: 1655 helix: 2.20 (0.16), residues: 994 sheet: -1.12 (0.58), residues: 85 loop : -0.73 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1205 TYR 0.012 0.001 TYR A 118 PHE 0.018 0.001 PHE A 337 TRP 0.010 0.001 TRP A 806 HIS 0.002 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00304 (12941) covalent geometry : angle 0.55547 (17583) SS BOND : bond 0.00172 ( 1) SS BOND : angle 1.13468 ( 2) hydrogen bonds : bond 0.03506 ( 805) hydrogen bonds : angle 4.01271 ( 2337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4767 (m-10) REVERT: A 256 ILE cc_start: 0.8157 (tp) cc_final: 0.7835 (pt) REVERT: A 410 ARG cc_start: 0.7727 (ptp90) cc_final: 0.7486 (ptp90) REVERT: A 909 MET cc_start: 0.8146 (mmm) cc_final: 0.7796 (mmm) REVERT: A 977 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8210 (m) REVERT: A 981 ASN cc_start: 0.8400 (m-40) cc_final: 0.8140 (m110) REVERT: A 1133 GLU cc_start: 0.7566 (tt0) cc_final: 0.6657 (mm-30) REVERT: A 1181 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7414 (mmtm) REVERT: A 1245 MET cc_start: 0.4676 (ttt) cc_final: 0.4128 (pmm) REVERT: A 1316 TYR cc_start: 0.6809 (t80) cc_final: 0.6553 (t80) REVERT: A 1366 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.7130 (t) REVERT: A 1375 ASP cc_start: 0.8294 (t0) cc_final: 0.7789 (p0) REVERT: A 1442 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7205 (mt-10) REVERT: F 575 MET cc_start: 0.7781 (mmm) cc_final: 0.7000 (mtt) REVERT: C 488 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.4577 (m-80) REVERT: C 554 ASP cc_start: 0.8358 (t0) cc_final: 0.8069 (t0) REVERT: C 559 LYS cc_start: 0.8220 (tppp) cc_final: 0.7911 (mptt) REVERT: C 574 MET cc_start: 0.6710 (mtt) cc_final: 0.6361 (mtp) REVERT: G 518 MET cc_start: 0.3974 (tmt) cc_final: 0.3673 (ppp) REVERT: G 523 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8489 (p) REVERT: E 512 CYS cc_start: 0.5287 (OUTLIER) cc_final: 0.4664 (t) REVERT: E 553 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8210 (tt) REVERT: E 608 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5795 (mt) REVERT: E 669 ARG cc_start: 0.6106 (mtt90) cc_final: 0.4930 (mtm180) REVERT: E 695 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: E 699 ASN cc_start: 0.8441 (m-40) cc_final: 0.8224 (m110) outliers start: 58 outliers final: 36 residues processed: 267 average time/residue: 0.1086 time to fit residues: 42.3649 Evaluate side-chains 265 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 949 CYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain F residue 534 ASN Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain E residue 512 CYS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 695 GLN Chi-restraints excluded: chain E residue 697 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 117 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN E 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.223130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.190824 restraints weight = 18285.476| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.48 r_work: 0.4111 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12942 Z= 0.118 Angle : 0.552 9.959 17585 Z= 0.278 Chirality : 0.040 0.167 2106 Planarity : 0.004 0.045 2235 Dihedral : 4.095 51.054 1795 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.15 % Allowed : 26.62 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.72 (0.21), residues: 1655 helix: 2.28 (0.16), residues: 1001 sheet: -1.02 (0.59), residues: 85 loop : -0.61 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1205 TYR 0.039 0.002 TYR A 523 PHE 0.015 0.001 PHE A 579 TRP 0.011 0.001 TRP A 806 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00269 (12941) covalent geometry : angle 0.55209 (17583) SS BOND : bond 0.00137 ( 1) SS BOND : angle 1.14851 ( 2) hydrogen bonds : bond 0.03385 ( 805) hydrogen bonds : angle 3.95701 ( 2337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.4998 (OUTLIER) cc_final: 0.4582 (m-10) REVERT: A 204 LYS cc_start: 0.8051 (ptpp) cc_final: 0.7830 (ptpp) REVERT: A 256 ILE cc_start: 0.8183 (tp) cc_final: 0.7877 (pt) REVERT: A 470 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6102 (m-80) REVERT: A 509 PHE cc_start: 0.6652 (t80) cc_final: 0.6438 (t80) REVERT: A 909 MET cc_start: 0.8087 (mmm) cc_final: 0.7834 (mmm) REVERT: A 977 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8220 (m) REVERT: A 981 ASN cc_start: 0.8394 (m-40) cc_final: 0.8153 (m110) REVERT: A 1133 GLU cc_start: 0.7604 (tt0) cc_final: 0.6782 (mm-30) REVERT: A 1181 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7479 (mmtm) REVERT: A 1245 MET cc_start: 0.4557 (ttt) cc_final: 0.4083 (pmm) REVERT: A 1316 TYR cc_start: 0.6760 (t80) cc_final: 0.6521 (t80) REVERT: A 1366 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7171 (t) REVERT: A 1375 ASP cc_start: 0.8309 (t0) cc_final: 0.7803 (p0) REVERT: A 1442 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7252 (mt-10) REVERT: F 575 MET cc_start: 0.7769 (mmm) cc_final: 0.7021 (mtt) REVERT: C 488 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.4484 (m-80) REVERT: C 515 SER cc_start: 0.5726 (t) cc_final: 0.5462 (t) REVERT: C 554 ASP cc_start: 0.8326 (t0) cc_final: 0.8066 (t0) REVERT: C 559 LYS cc_start: 0.8270 (tppp) cc_final: 0.7994 (mptt) REVERT: G 518 MET cc_start: 0.3981 (tmt) cc_final: 0.3704 (ppp) REVERT: G 523 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8464 (p) REVERT: E 512 CYS cc_start: 0.5419 (OUTLIER) cc_final: 0.4859 (t) REVERT: E 553 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8263 (tt) REVERT: E 593 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7270 (mm-30) REVERT: E 669 ARG cc_start: 0.6171 (mtt90) cc_final: 0.4976 (mtm180) REVERT: E 695 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7290 (tm-30) outliers start: 54 outliers final: 36 residues processed: 265 average time/residue: 0.1089 time to fit residues: 42.1382 Evaluate side-chains 263 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 949 CYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1393 GLN Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain F residue 534 ASN Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain E residue 512 CYS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 697 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 125 optimal weight: 0.3980 chunk 34 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 699 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.224026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.191654 restraints weight = 18324.003| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.50 r_work: 0.4121 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12942 Z= 0.118 Angle : 0.554 9.651 17585 Z= 0.281 Chirality : 0.040 0.171 2106 Planarity : 0.004 0.045 2235 Dihedral : 4.063 50.750 1795 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.69 % Allowed : 27.46 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.72 (0.21), residues: 1655 helix: 2.28 (0.16), residues: 996 sheet: -0.73 (0.63), residues: 73 loop : -0.63 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1180 TYR 0.030 0.002 TYR A 523 PHE 0.015 0.001 PHE A 579 TRP 0.012 0.001 TRP A1306 HIS 0.005 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00266 (12941) covalent geometry : angle 0.55348 (17583) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.08045 ( 2) hydrogen bonds : bond 0.03359 ( 805) hydrogen bonds : angle 3.96862 ( 2337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ILE cc_start: 0.8085 (tp) cc_final: 0.7784 (pt) REVERT: A 909 MET cc_start: 0.8075 (mmm) cc_final: 0.7842 (mmm) REVERT: A 977 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8186 (m) REVERT: A 981 ASN cc_start: 0.8405 (m-40) cc_final: 0.8147 (m110) REVERT: A 1090 LYS cc_start: 0.7018 (pttm) cc_final: 0.6649 (pttm) REVERT: A 1133 GLU cc_start: 0.7575 (tt0) cc_final: 0.6774 (mm-30) REVERT: A 1181 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7484 (mmtm) REVERT: A 1225 MET cc_start: 0.5866 (mmm) cc_final: 0.5371 (mmt) REVERT: A 1245 MET cc_start: 0.4562 (ttt) cc_final: 0.4020 (pmm) REVERT: A 1316 TYR cc_start: 0.6778 (t80) cc_final: 0.6557 (t80) REVERT: A 1366 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7164 (t) REVERT: A 1375 ASP cc_start: 0.8324 (t0) cc_final: 0.7817 (p0) REVERT: A 1442 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7284 (mt-10) REVERT: F 575 MET cc_start: 0.7736 (mmm) cc_final: 0.7033 (mtt) REVERT: C 515 SER cc_start: 0.5739 (t) cc_final: 0.5466 (t) REVERT: C 554 ASP cc_start: 0.8272 (t0) cc_final: 0.8041 (t0) REVERT: C 559 LYS cc_start: 0.8287 (tppp) cc_final: 0.7995 (mptt) REVERT: G 518 MET cc_start: 0.3947 (tmt) cc_final: 0.3671 (ppp) REVERT: G 523 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8475 (p) REVERT: E 512 CYS cc_start: 0.5366 (OUTLIER) cc_final: 0.4858 (t) REVERT: E 553 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8248 (tt) REVERT: E 593 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7226 (mm-30) REVERT: E 608 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5749 (mt) REVERT: E 669 ARG cc_start: 0.6163 (mtt90) cc_final: 0.4946 (mtm180) REVERT: E 695 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7708 (tm-30) outliers start: 48 outliers final: 34 residues processed: 257 average time/residue: 0.1065 time to fit residues: 39.7621 Evaluate side-chains 259 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 949 CYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain F residue 534 ASN Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain E residue 512 CYS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 695 GLN Chi-restraints excluded: chain E residue 697 ILE Chi-restraints excluded: chain E residue 699 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 152 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 18 optimal weight: 0.0040 chunk 2 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 0.0670 chunk 88 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 699 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.223975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.191578 restraints weight = 18427.928| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.49 r_work: 0.4125 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12942 Z= 0.122 Angle : 0.568 9.249 17585 Z= 0.287 Chirality : 0.041 0.423 2106 Planarity : 0.004 0.045 2235 Dihedral : 3.891 32.727 1793 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.38 % Allowed : 28.15 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.74 (0.21), residues: 1655 helix: 2.29 (0.16), residues: 996 sheet: -0.74 (0.62), residues: 73 loop : -0.61 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 555 TYR 0.029 0.002 TYR A 523 PHE 0.015 0.001 PHE A 579 TRP 0.012 0.001 TRP A1306 HIS 0.004 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00278 (12941) covalent geometry : angle 0.56753 (17583) SS BOND : bond 0.00105 ( 1) SS BOND : angle 1.08823 ( 2) hydrogen bonds : bond 0.03369 ( 805) hydrogen bonds : angle 3.94988 ( 2337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ILE cc_start: 0.8015 (tp) cc_final: 0.7722 (pt) REVERT: A 909 MET cc_start: 0.8073 (mmm) cc_final: 0.7824 (mmm) REVERT: A 977 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 981 ASN cc_start: 0.8390 (m-40) cc_final: 0.8132 (m110) REVERT: A 1090 LYS cc_start: 0.7043 (pttm) cc_final: 0.6697 (pttm) REVERT: A 1133 GLU cc_start: 0.7514 (tt0) cc_final: 0.6770 (mm-30) REVERT: A 1181 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7475 (mmtm) REVERT: A 1225 MET cc_start: 0.5769 (mmm) cc_final: 0.5273 (mmt) REVERT: A 1245 MET cc_start: 0.4520 (ttt) cc_final: 0.4012 (pmm) REVERT: A 1316 TYR cc_start: 0.6787 (t80) cc_final: 0.6554 (t80) REVERT: A 1366 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7276 (t) REVERT: A 1375 ASP cc_start: 0.8344 (t0) cc_final: 0.7841 (p0) REVERT: A 1442 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7276 (mt-10) REVERT: F 575 MET cc_start: 0.7801 (mmm) cc_final: 0.7126 (mtt) REVERT: C 515 SER cc_start: 0.5722 (t) cc_final: 0.5449 (t) REVERT: C 559 LYS cc_start: 0.8291 (tppp) cc_final: 0.8001 (mptt) REVERT: G 518 MET cc_start: 0.3960 (tmt) cc_final: 0.3663 (ppp) REVERT: G 523 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8474 (p) REVERT: E 512 CYS cc_start: 0.5385 (OUTLIER) cc_final: 0.4885 (t) REVERT: E 553 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8243 (tt) REVERT: E 593 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7226 (mm-30) REVERT: E 608 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5748 (mt) REVERT: E 669 ARG cc_start: 0.6137 (mtt90) cc_final: 0.4891 (mtm180) REVERT: E 695 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7659 (tm-30) outliers start: 44 outliers final: 36 residues processed: 259 average time/residue: 0.1133 time to fit residues: 42.6140 Evaluate side-chains 265 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 949 CYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1324 GLN Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain F residue 534 ASN Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain E residue 512 CYS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 695 GLN Chi-restraints excluded: chain E residue 699 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 699 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.222446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.189846 restraints weight = 18483.246| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.50 r_work: 0.4108 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12942 Z= 0.137 Angle : 0.574 9.501 17585 Z= 0.290 Chirality : 0.041 0.332 2106 Planarity : 0.004 0.045 2235 Dihedral : 3.921 32.486 1793 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.77 % Allowed : 27.85 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 aren not related in a simple way. whole: 1.69 (0.21), residues: 1655 helix: 2.26 (0.16), residues: 996 sheet: -0.80 (0.62), residues: 73 loop : -0.63 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1180 TYR 0.027 0.002 TYR A 523 PHE 0.016 0.001 PHE A 553 TRP 0.012 0.001 TRP A1306 HIS 0.005 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00322 (12941) covalent geometry : angle 0.57370 (17583) SS BOND : bond 0.00102 ( 1) SS BOND : angle 1.07549 ( 2) hydrogen bonds : bond 0.03438 ( 805) hydrogen bonds : angle 4.00213 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.74 seconds wall clock time: 54 minutes 28.87 seconds (3268.87 seconds total)