Starting phenix.real_space_refine on Fri Sep 11 14:51:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xi4_66896/09_2026/9xi4_66896.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xi4_66896/09_2026/9xi4_66896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xi4_66896/09_2026/9xi4_66896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xi4_66896/09_2026/9xi4_66896.map" model { file = "/net/cci-nas-00/data/ceres_data/9xi4_66896/09_2026/9xi4_66896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xi4_66896/09_2026/9xi4_66896.cif" } resolution = 2.83 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 47 5.16 5 C 6130 2.51 5 N 1615 2.21 5 O 1861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9654 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4864 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1540 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1625 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1568 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.29, per 1000 atoms: 0.24 Number of scatterers: 9654 At special positions: 0 Unit cell: (81.984, 139.08, 133.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 47 16.00 O 1861 8.00 N 1615 7.00 C 6130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.07 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 546 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 409.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 17 sheets defined 38.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.714A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.069A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.541A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.725A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.705A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.657A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.795A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.581A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.625A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.632A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.157A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.876A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.814A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 611 through 615 removed outlier: 4.015A pdb=" N ASP A 615 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.867A pdb=" N ASN E 370 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.196A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.770A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.648A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 133 removed outlier: 3.829A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.227A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.173A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.220A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 466 through 467 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.301A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.618A pdb=" N SER H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.661A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.735A pdb=" N CYS H 151 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.617A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.653A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.653A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.654A pdb=" N SER L 119 " --> pdb=" O SER L 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER L 142 " --> pdb=" O SER L 119 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR L 182 " --> pdb=" O GLU L 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.654A pdb=" N SER L 119 " --> pdb=" O SER L 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER L 142 " --> pdb=" O SER L 119 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.302A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN L 199 " --> pdb=" O ALA L 152 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL L 211 " --> pdb=" O TYR L 196 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3042 1.34 - 1.46: 2472 1.46 - 1.59: 4327 1.59 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 9911 Sorted by residual: bond pdb=" N ILE E 434 " pdb=" CA ILE E 434 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.70e+00 bond pdb=" N CYS E 432 " pdb=" CA CYS E 432 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.26e-02 6.30e+03 7.00e+00 bond pdb=" N THR A 282 " pdb=" CA THR A 282 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 6.99e+00 bond pdb=" N LEU A 281 " pdb=" CA LEU A 281 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.27e-02 6.20e+03 5.86e+00 bond pdb=" N GLU H 62 " pdb=" CA GLU H 62 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.85e+00 ... (remaining 9906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13175 1.98 - 3.97: 268 3.97 - 5.95: 31 5.95 - 7.93: 15 7.93 - 9.92: 1 Bond angle restraints: 13490 Sorted by residual: angle pdb=" CA LEU A 266 " pdb=" C LEU A 266 " pdb=" O LEU A 266 " ideal model delta sigma weight residual 122.03 117.85 4.18 1.17e+00 7.31e-01 1.28e+01 angle pdb=" C VAL L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" CA GLU H 89 " pdb=" CB GLU H 89 " pdb=" CG GLU H 89 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" C PRO A 258 " pdb=" N ILE A 259 " pdb=" CA ILE A 259 " ideal model delta sigma weight residual 121.97 128.19 -6.22 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C LYS H 154 " pdb=" N ASP H 155 " pdb=" CA ASP H 155 " ideal model delta sigma weight residual 122.68 127.76 -5.08 1.47e+00 4.63e-01 1.19e+01 ... (remaining 13485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5125 17.98 - 35.95: 559 35.95 - 53.93: 168 53.93 - 71.90: 52 71.90 - 89.88: 14 Dihedral angle restraints: 5918 sinusoidal: 2364 harmonic: 3554 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -155.14 69.14 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 198 " pdb=" CB CYS L 198 " ideal model delta sinusoidal sigma weight residual 93.00 148.53 -55.53 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.74 34.26 1 1.00e+01 1.00e-02 1.67e+01 ... (remaining 5915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1008 0.042 - 0.083: 308 0.083 - 0.125: 126 0.125 - 0.166: 17 0.166 - 0.208: 5 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CA TYR L 51 " pdb=" N TYR L 51 " pdb=" C TYR L 51 " pdb=" CB TYR L 51 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE L 50 " pdb=" N ILE L 50 " pdb=" C ILE L 50 " pdb=" CB ILE L 50 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 1461 not shown) Planarity restraints: 1747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 336 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO E 337 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO A 500 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLY L 112 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY L 112 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN L 113 " -0.011 2.00e-02 2.50e+03 ... (remaining 1744 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 173 2.67 - 3.22: 8336 3.22 - 3.78: 15596 3.78 - 4.34: 21430 4.34 - 4.90: 35203 Nonbonded interactions: 80738 Sorted by model distance: nonbonded pdb=" NH1 ARG E 357 " pdb=" OG SER E 359 " model vdw 2.108 3.120 nonbonded pdb=" ND1 HIS L 36 " pdb=" O TYR L 51 " model vdw 2.252 3.120 nonbonded pdb=" OG SER H 108 " pdb=" NE2 HIS L 36 " model vdw 2.288 3.120 nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.292 3.040 nonbonded pdb=" OE1 GLU A 227 " pdb=" OH TYR A 454 " model vdw 2.309 3.040 ... (remaining 80733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9928 Z= 0.204 Angle : 0.678 9.915 13524 Z= 0.373 Chirality : 0.048 0.208 1464 Planarity : 0.005 0.063 1743 Dihedral : 17.553 89.878 3611 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.76 % Allowed : 25.67 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1216 helix: -0.25 (0.24), residues: 396 sheet: 1.37 (0.35), residues: 215 loop : -0.93 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 357 TYR 0.026 0.002 TYR L 51 PHE 0.014 0.002 PHE E 377 TRP 0.014 0.001 TRP A 477 HIS 0.008 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 ( 9911) covalent geometry : angle 0.67352 / 0.37 (13490) SS BOND : bond 0.01297 / 0.98 ( 11) SS BOND : angle 1.77579 / 1.06 ( 22) hydrogen bonds : bond 0.19916 / 13.74 ( 420) hydrogen bonds : angle 7.01235 / 5.13 ( 1176) metal coordination : bond 0.00316 / 0.15 ( 2) link_NAG-ASN : bond 0.00277 / 0.13 ( 4) link_NAG-ASN : angle 1.31276 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7544 (pt0) cc_final: 0.7199 (mt-10) REVERT: A 363 LYS cc_start: 0.7304 (mtmt) cc_final: 0.6760 (mmtt) REVERT: A 476 LYS cc_start: 0.7474 (tptp) cc_final: 0.7219 (tppt) REVERT: A 531 GLN cc_start: 0.7579 (tt0) cc_final: 0.7206 (mt0) REVERT: E 405 ASN cc_start: 0.7643 (m-40) cc_final: 0.7303 (m-40) REVERT: E 440 LYS cc_start: 0.7943 (mttt) cc_final: 0.7325 (mptt) REVERT: H 3 GLN cc_start: 0.7362 (tp40) cc_final: 0.6954 (mp10) REVERT: H 87 ARG cc_start: 0.7359 (ptp-170) cc_final: 0.6992 (mtm180) REVERT: L 68 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7667 (mtm180) outliers start: 8 outliers final: 1 residues processed: 135 average time/residue: 0.5649 time to fit residues: 82.0904 Evaluate side-chains 92 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 154 ASN A 194 ASN A 578 ASN E 334 ASN E 360 ASN ** E 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN L 189 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.203669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.155653 restraints weight = 9354.944| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.79 r_work: 0.3364 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9928 Z= 0.152 Angle : 0.583 10.705 13524 Z= 0.300 Chirality : 0.044 0.220 1464 Planarity : 0.004 0.062 1743 Dihedral : 4.777 45.151 1407 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.72 % Allowed : 22.81 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1216 helix: 0.50 (0.25), residues: 399 sheet: 0.94 (0.34), residues: 236 loop : -0.59 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 68 TYR 0.023 0.002 TYR L 51 PHE 0.013 0.002 PHE A 32 TRP 0.015 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9911) covalent geometry : angle 0.57977 / 0.30 (13490) SS BOND : bond 0.00541 / 0.33 ( 11) SS BOND : angle 1.06672 / 0.63 ( 22) hydrogen bonds : bond 0.04937 / 3.36 ( 420) hydrogen bonds : angle 4.87536 / 3.60 ( 1176) metal coordination : bond 0.00287 / 0.14 ( 2) link_NAG-ASN : bond 0.00189 / 0.09 ( 4) link_NAG-ASN : angle 1.66008 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.417 Fit side-chains REVERT: A 34 HIS cc_start: 0.7987 (m90) cc_final: 0.6636 (t-90) REVERT: A 37 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: A 75 GLU cc_start: 0.7800 (pt0) cc_final: 0.7400 (mt-10) REVERT: A 91 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6906 (mm) REVERT: A 148 LEU cc_start: 0.6177 (mt) cc_final: 0.5896 (mp) REVERT: A 176 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6368 (mt) REVERT: A 192 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7720 (mtt90) REVERT: A 363 LYS cc_start: 0.7516 (mtmt) cc_final: 0.6701 (mmtt) REVERT: A 367 ASP cc_start: 0.7402 (m-30) cc_final: 0.7054 (p0) REVERT: A 476 LYS cc_start: 0.7534 (tptp) cc_final: 0.7171 (tppt) REVERT: A 479 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6847 (tt0) REVERT: A 531 GLN cc_start: 0.7793 (tt0) cc_final: 0.7311 (mt0) REVERT: E 359 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8222 (p) REVERT: E 378 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8531 (mttp) REVERT: E 440 LYS cc_start: 0.7950 (mttt) cc_final: 0.7416 (mptt) REVERT: E 462 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8043 (mttp) REVERT: H 3 GLN cc_start: 0.7413 (tp40) cc_final: 0.6933 (mp10) REVERT: H 87 ARG cc_start: 0.7593 (ptp-170) cc_final: 0.7306 (ptp-170) REVERT: L 68 ARG cc_start: 0.8082 (mtm180) cc_final: 0.7864 (mtm180) outliers start: 39 outliers final: 9 residues processed: 131 average time/residue: 0.5385 time to fit residues: 76.2864 Evaluate side-chains 106 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 154 ASN E 334 ASN ** E 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.202675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.175150 restraints weight = 9366.959| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.07 r_work: 0.3606 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9928 Z= 0.143 Angle : 0.568 10.372 13524 Z= 0.290 Chirality : 0.044 0.217 1464 Planarity : 0.004 0.059 1743 Dihedral : 4.709 59.125 1405 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.10 % Allowed : 21.66 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1216 helix: 0.85 (0.26), residues: 399 sheet: 0.99 (0.34), residues: 236 loop : -0.41 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.022 0.001 TYR L 51 PHE 0.011 0.001 PHE E 371 TRP 0.012 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9911) covalent geometry : angle 0.56156 / 0.29 (13490) SS BOND : bond 0.00418 / 0.22 ( 11) SS BOND : angle 1.64299 / 0.96 ( 22) hydrogen bonds : bond 0.04736 / 3.21 ( 420) hydrogen bonds : angle 4.64333 / 3.44 ( 1176) metal coordination : bond 0.00263 / 0.13 ( 2) link_NAG-ASN : bond 0.00361 / 0.17 ( 4) link_NAG-ASN : angle 1.90948 / 1.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.340 Fit side-chains REVERT: A 34 HIS cc_start: 0.8063 (m90) cc_final: 0.6862 (t-90) REVERT: A 37 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: A 363 LYS cc_start: 0.7743 (mtmt) cc_final: 0.7156 (mmtt) REVERT: A 476 LYS cc_start: 0.7825 (tptp) cc_final: 0.7617 (tppt) REVERT: A 531 GLN cc_start: 0.7699 (tt0) cc_final: 0.7432 (mt0) REVERT: E 440 LYS cc_start: 0.7989 (mttt) cc_final: 0.7592 (mptt) REVERT: E 462 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8073 (mttp) REVERT: H 3 GLN cc_start: 0.7667 (tp40) cc_final: 0.7358 (mp10) REVERT: H 82 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8172 (tt0) outliers start: 43 outliers final: 10 residues processed: 131 average time/residue: 0.5584 time to fit residues: 78.8172 Evaluate side-chains 107 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 334 ASN E 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.201898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.174509 restraints weight = 9366.956| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.04 r_work: 0.3597 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9928 Z= 0.146 Angle : 0.571 10.250 13524 Z= 0.290 Chirality : 0.044 0.231 1464 Planarity : 0.004 0.057 1743 Dihedral : 4.347 32.189 1405 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.72 % Allowed : 23.66 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1216 helix: 0.95 (0.26), residues: 403 sheet: 0.95 (0.34), residues: 234 loop : -0.39 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.025 0.002 TYR L 51 PHE 0.011 0.001 PHE H 111 TRP 0.011 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9911) covalent geometry : angle 0.56502 / 0.29 (13490) SS BOND : bond 0.00698 / 0.50 ( 11) SS BOND : angle 1.86993 / 1.09 ( 22) hydrogen bonds : bond 0.04626 / 3.15 ( 420) hydrogen bonds : angle 4.58889 / 3.40 ( 1176) metal coordination : bond 0.00285 / 0.14 ( 2) link_NAG-ASN : bond 0.00366 / 0.17 ( 4) link_NAG-ASN : angle 1.66127 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8089 (m90) cc_final: 0.6869 (t-90) REVERT: A 37 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: A 91 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7187 (mm) REVERT: A 176 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7276 (mt) REVERT: A 363 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7150 (mmtm) REVERT: A 531 GLN cc_start: 0.7750 (tt0) cc_final: 0.7458 (mt0) REVERT: E 440 LYS cc_start: 0.8038 (mttt) cc_final: 0.7615 (mptt) REVERT: E 462 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8054 (mttp) REVERT: H 3 GLN cc_start: 0.7692 (tp40) cc_final: 0.7336 (mp10) REVERT: H 82 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: L 54 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7790 (p0) REVERT: L 120 VAL cc_start: 0.6142 (OUTLIER) cc_final: 0.5743 (t) outliers start: 39 outliers final: 11 residues processed: 123 average time/residue: 0.5297 time to fit residues: 70.4311 Evaluate side-chains 111 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 95 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 154 ASN E 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.201645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.156738 restraints weight = 9355.609| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.44 r_work: 0.3354 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9928 Z= 0.140 Angle : 0.573 11.261 13524 Z= 0.290 Chirality : 0.044 0.254 1464 Planarity : 0.004 0.056 1743 Dihedral : 4.164 19.418 1405 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.10 % Allowed : 23.00 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1216 helix: 1.08 (0.26), residues: 397 sheet: 0.92 (0.34), residues: 230 loop : -0.38 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.023 0.001 TYR L 51 PHE 0.011 0.001 PHE H 111 TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9911) covalent geometry : angle 0.56521 / 0.29 (13490) SS BOND : bond 0.00801 / 0.59 ( 11) SS BOND : angle 2.05709 / 1.21 ( 22) hydrogen bonds : bond 0.04499 / 3.07 ( 420) hydrogen bonds : angle 4.50487 / 3.34 ( 1176) metal coordination : bond 0.00259 / 0.12 ( 2) link_NAG-ASN : bond 0.00269 / 0.12 ( 4) link_NAG-ASN : angle 1.72212 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.7981 (m90) cc_final: 0.6615 (t-90) REVERT: A 37 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: A 91 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6703 (mm) REVERT: A 176 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6678 (mt) REVERT: A 192 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7730 (mtt90) REVERT: A 363 LYS cc_start: 0.7566 (mtmt) cc_final: 0.6795 (mmtm) REVERT: A 476 LYS cc_start: 0.7420 (tptp) cc_final: 0.7092 (tppt) REVERT: A 531 GLN cc_start: 0.7699 (tt0) cc_final: 0.7274 (mt0) REVERT: E 378 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8393 (mttp) REVERT: E 440 LYS cc_start: 0.8091 (mttt) cc_final: 0.7555 (mptt) REVERT: E 462 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.7918 (mttp) REVERT: H 3 GLN cc_start: 0.7479 (tp40) cc_final: 0.6945 (mp10) REVERT: H 82 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: L 54 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7643 (p0) REVERT: L 120 VAL cc_start: 0.5908 (OUTLIER) cc_final: 0.5551 (t) outliers start: 43 outliers final: 15 residues processed: 128 average time/residue: 0.4956 time to fit residues: 69.1688 Evaluate side-chains 115 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 373 HIS E 334 ASN H 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.199262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.175628 restraints weight = 9293.047| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 0.80 r_work: 0.3633 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9928 Z= 0.189 Angle : 0.631 15.548 13524 Z= 0.320 Chirality : 0.046 0.271 1464 Planarity : 0.004 0.056 1743 Dihedral : 4.444 20.710 1405 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.91 % Allowed : 23.19 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1216 helix: 0.93 (0.26), residues: 401 sheet: 0.86 (0.34), residues: 230 loop : -0.44 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 454 TYR 0.025 0.002 TYR L 51 PHE 0.013 0.002 PHE H 111 TRP 0.013 0.001 TRP A 477 HIS 0.010 0.001 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 9911) covalent geometry : angle 0.62356 / 0.32 (13490) SS BOND : bond 0.01064 / 0.78 ( 11) SS BOND : angle 2.16456 / 1.23 ( 22) hydrogen bonds : bond 0.05070 / 3.46 ( 420) hydrogen bonds : angle 4.64583 / 3.44 ( 1176) metal coordination : bond 0.00419 / 0.20 ( 2) link_NAG-ASN : bond 0.00270 / 0.13 ( 4) link_NAG-ASN : angle 1.80236 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8136 (m90) cc_final: 0.6894 (t-90) REVERT: A 91 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7116 (mm) REVERT: A 176 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7386 (mt) REVERT: A 363 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7221 (mmtm) REVERT: A 531 GLN cc_start: 0.7609 (tt0) cc_final: 0.7385 (mt0) REVERT: E 440 LYS cc_start: 0.8066 (mttt) cc_final: 0.7713 (mptt) REVERT: E 462 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8063 (mttp) REVERT: H 3 GLN cc_start: 0.7569 (tp40) cc_final: 0.7234 (mp10) REVERT: H 82 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: L 120 VAL cc_start: 0.6279 (OUTLIER) cc_final: 0.5871 (t) outliers start: 41 outliers final: 16 residues processed: 123 average time/residue: 0.5035 time to fit residues: 67.1948 Evaluate side-chains 115 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 94 optimal weight: 0.3980 chunk 113 optimal weight: 30.0000 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN E 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.200073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.171949 restraints weight = 9317.940| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.02 r_work: 0.3592 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9928 Z= 0.157 Angle : 0.603 14.497 13524 Z= 0.305 Chirality : 0.045 0.253 1464 Planarity : 0.004 0.057 1743 Dihedral : 4.356 21.817 1405 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.63 % Allowed : 23.66 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1216 helix: 1.01 (0.26), residues: 400 sheet: 0.85 (0.34), residues: 230 loop : -0.38 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 454 TYR 0.023 0.002 TYR L 51 PHE 0.012 0.002 PHE H 111 TRP 0.010 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9911) covalent geometry : angle 0.59559 / 0.30 (13490) SS BOND : bond 0.00934 / 0.69 ( 11) SS BOND : angle 2.08593 / 1.19 ( 22) hydrogen bonds : bond 0.04708 / 3.21 ( 420) hydrogen bonds : angle 4.55890 / 3.38 ( 1176) metal coordination : bond 0.00316 / 0.15 ( 2) link_NAG-ASN : bond 0.00249 / 0.12 ( 4) link_NAG-ASN : angle 1.66000 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8058 (m90) cc_final: 0.6885 (t-90) REVERT: A 37 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7112 (mm-30) REVERT: A 91 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7161 (mm) REVERT: A 176 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7435 (mt) REVERT: A 363 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7264 (mmtt) REVERT: A 531 GLN cc_start: 0.7617 (tt0) cc_final: 0.7393 (mt0) REVERT: E 440 LYS cc_start: 0.8075 (mttt) cc_final: 0.7696 (mptt) REVERT: E 462 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8052 (mttp) REVERT: H 3 GLN cc_start: 0.7622 (tp40) cc_final: 0.7247 (mp10) REVERT: H 82 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: L 120 VAL cc_start: 0.6227 (OUTLIER) cc_final: 0.5838 (t) outliers start: 38 outliers final: 15 residues processed: 119 average time/residue: 0.5058 time to fit residues: 65.2446 Evaluate side-chains 110 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 34 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 334 ASN E 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.199545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.171434 restraints weight = 9311.413| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.99 r_work: 0.3615 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9928 Z= 0.168 Angle : 0.617 14.008 13524 Z= 0.311 Chirality : 0.045 0.255 1464 Planarity : 0.004 0.057 1743 Dihedral : 4.390 21.817 1405 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.05 % Allowed : 23.95 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1216 helix: 1.03 (0.26), residues: 397 sheet: 0.87 (0.34), residues: 230 loop : -0.40 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.024 0.002 TYR L 51 PHE 0.012 0.002 PHE E 515 TRP 0.009 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 9911) covalent geometry : angle 0.61033 / 0.31 (13490) SS BOND : bond 0.00938 / 0.69 ( 11) SS BOND : angle 2.05628 / 1.18 ( 22) hydrogen bonds : bond 0.04811 / 3.29 ( 420) hydrogen bonds : angle 4.55268 / 3.38 ( 1176) metal coordination : bond 0.00357 / 0.17 ( 2) link_NAG-ASN : bond 0.00256 / 0.12 ( 4) link_NAG-ASN : angle 1.68226 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8018 (m90) cc_final: 0.6835 (t-90) REVERT: A 37 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: A 91 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7128 (mm) REVERT: A 176 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7496 (mt) REVERT: A 192 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7934 (mtt90) REVERT: A 363 LYS cc_start: 0.7777 (mtmt) cc_final: 0.7300 (mmtt) REVERT: E 343 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8048 (m-40) REVERT: E 440 LYS cc_start: 0.8035 (mttt) cc_final: 0.7692 (mptt) REVERT: E 462 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8030 (mttp) REVERT: H 3 GLN cc_start: 0.7574 (tp40) cc_final: 0.7229 (mp10) REVERT: H 82 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: L 120 VAL cc_start: 0.6212 (OUTLIER) cc_final: 0.5813 (t) outliers start: 32 outliers final: 17 residues processed: 112 average time/residue: 0.5187 time to fit residues: 62.9953 Evaluate side-chains 114 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 531 GLN E 334 ASN E 343 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.206520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.184327 restraints weight = 9263.131| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 0.88 r_work: 0.3771 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9928 Z= 0.135 Angle : 0.583 13.256 13524 Z= 0.293 Chirality : 0.044 0.245 1464 Planarity : 0.004 0.059 1743 Dihedral : 4.238 21.029 1405 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.15 % Allowed : 23.47 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1216 helix: 1.11 (0.26), residues: 400 sheet: 0.90 (0.34), residues: 230 loop : -0.33 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.022 0.001 TYR L 51 PHE 0.012 0.001 PHE A 369 TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 9911) covalent geometry : angle 0.57650 / 0.29 (13490) SS BOND : bond 0.00828 / 0.61 ( 11) SS BOND : angle 1.94195 / 1.12 ( 22) hydrogen bonds : bond 0.04430 / 3.02 ( 420) hydrogen bonds : angle 4.45645 / 3.31 ( 1176) metal coordination : bond 0.00225 / 0.11 ( 2) link_NAG-ASN : bond 0.00247 / 0.12 ( 4) link_NAG-ASN : angle 1.55326 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.7955 (m90) cc_final: 0.6845 (t-90) REVERT: A 37 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 91 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6975 (mm) REVERT: A 176 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7402 (mt) REVERT: A 192 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7951 (mtt90) REVERT: A 363 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7373 (mmtt) REVERT: E 343 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8033 (m-40) REVERT: E 440 LYS cc_start: 0.7982 (mttt) cc_final: 0.7679 (mptt) REVERT: E 462 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7904 (mttp) REVERT: H 3 GLN cc_start: 0.7521 (tp40) cc_final: 0.7271 (mp10) REVERT: H 82 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: L 54 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7659 (p0) REVERT: L 120 VAL cc_start: 0.6022 (OUTLIER) cc_final: 0.5660 (t) REVERT: L 123 PHE cc_start: 0.4202 (OUTLIER) cc_final: 0.3942 (m-80) outliers start: 33 outliers final: 18 residues processed: 115 average time/residue: 0.5018 time to fit residues: 62.5885 Evaluate side-chains 114 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 123 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 62 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 0.0970 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 531 GLN A 552 GLN E 334 ASN E 343 ASN H 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.201153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.163809 restraints weight = 9454.404| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.70 r_work: 0.3424 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9928 Z= 0.126 Angle : 0.576 12.956 13524 Z= 0.290 Chirality : 0.043 0.242 1464 Planarity : 0.004 0.055 1743 Dihedral : 4.163 20.729 1405 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.77 % Allowed : 23.95 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1216 helix: 1.19 (0.26), residues: 400 sheet: 0.90 (0.34), residues: 230 loop : -0.28 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.022 0.001 TYR L 51 PHE 0.013 0.001 PHE A 369 TRP 0.011 0.001 TRP L 37 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9911) covalent geometry : angle 0.56972 / 0.29 (13490) SS BOND : bond 0.00789 / 0.59 ( 11) SS BOND : angle 1.88456 / 1.10 ( 22) hydrogen bonds : bond 0.04304 / 2.93 ( 420) hydrogen bonds : angle 4.40608 / 3.26 ( 1176) metal coordination : bond 0.00196 / 0.09 ( 2) link_NAG-ASN : bond 0.00247 / 0.12 ( 4) link_NAG-ASN : angle 1.52317 / 0.89 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8009 (m90) cc_final: 0.6714 (t-90) REVERT: A 37 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: A 91 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6806 (mm) REVERT: A 154 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7740 (p0) REVERT: A 176 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7003 (mt) REVERT: A 192 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.7976 (mtt90) REVERT: A 363 LYS cc_start: 0.7628 (mtmt) cc_final: 0.6981 (mmtt) REVERT: E 343 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7989 (m-40) REVERT: E 440 LYS cc_start: 0.8169 (mttt) cc_final: 0.7607 (mptt) REVERT: E 462 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8025 (mttp) REVERT: H 3 GLN cc_start: 0.7450 (tp40) cc_final: 0.6896 (mp10) REVERT: H 82 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: L 54 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7651 (p0) REVERT: L 120 VAL cc_start: 0.6140 (OUTLIER) cc_final: 0.5809 (t) REVERT: L 123 PHE cc_start: 0.5066 (OUTLIER) cc_final: 0.4665 (m-80) outliers start: 29 outliers final: 16 residues processed: 107 average time/residue: 0.5217 time to fit residues: 60.2820 Evaluate side-chains 114 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 123 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 73 optimal weight: 0.0470 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.0470 chunk 6 optimal weight: 0.0770 overall best weight: 0.1912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 531 GLN E 334 ASN E 343 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.201581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164835 restraints weight = 9400.712| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.61 r_work: 0.3511 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 9928 Z= 0.208 Angle : 1.093 61.594 13524 Z= 0.601 Chirality : 0.045 0.364 1464 Planarity : 0.007 0.182 1743 Dihedral : 4.406 52.378 1405 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.48 % Allowed : 24.14 % Favored : 73.38 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1216 helix: 1.21 (0.26), residues: 400 sheet: 0.89 (0.34), residues: 230 loop : -0.30 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.043 0.002 TYR A 207 PHE 0.013 0.001 PHE A 369 TRP 0.010 0.001 TRP L 37 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.21 ( 9911) covalent geometry : angle 1.09081 / 0.60 (13490) SS BOND : bond 0.00994 / 0.65 ( 11) SS BOND : angle 2.01580 / 1.14 ( 22) hydrogen bonds : bond 0.04348 / 2.95 ( 420) hydrogen bonds : angle 4.40938 / 3.26 ( 1176) metal coordination : bond 0.00118 / 0.06 ( 2) link_NAG-ASN : bond 0.00235 / 0.11 ( 4) link_NAG-ASN : angle 1.54166 / 0.90 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3259.20 seconds wall clock time: 56 minutes 29.99 seconds (3389.99 seconds total)