Starting phenix.real_space_refine on Thu Jul 24 08:14:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqd_43439/07_2025/8vqd_43439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqd_43439/07_2025/8vqd_43439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vqd_43439/07_2025/8vqd_43439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqd_43439/07_2025/8vqd_43439.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqd_43439/07_2025/8vqd_43439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqd_43439/07_2025/8vqd_43439.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.016 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 47 5.16 5 C 3564 2.51 5 N 993 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5686 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3873 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 28, 'TRANS': 473} Chain breaks: 2 Chain: "C" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 977 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "B" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.12, per 1000 atoms: 0.90 Number of scatterers: 5686 At special positions: 0 Unit cell: (78.375, 93.225, 100.65, 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 47 16.00 O 1082 8.00 N 993 7.00 C 3564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 204 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 338 " distance=2.04 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 367 " distance=2.02 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 540 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 259 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 16 sheets defined 15.9% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.516A pdb=" N GLN A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.757A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.837A pdb=" N GLN A 178 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.687A pdb=" N CYS A 212 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 360 through 365 Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.975A pdb=" N PHE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.679A pdb=" N GLU A 401 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.528A pdb=" N LEU A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.913A pdb=" N GLY A 518 " --> pdb=" O CYS A 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.931A pdb=" N GLY C 31 " --> pdb=" O PHE C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.008A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.571A pdb=" N CYS A 26 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 5.154A pdb=" N GLY A 152 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 244 removed outlier: 5.137A pdb=" N ALA A 241 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS A 255 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 243 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 312 removed outlier: 6.553A pdb=" N SER A 305 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LYS A 333 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 343 removed outlier: 6.649A pdb=" N CYS A 342 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 376 removed outlier: 6.274A pdb=" N LEU A 374 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 410 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLN A 446 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 412 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR A 441 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A 467 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 443 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS A 469 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 445 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 466 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR A 496 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 468 " --> pdb=" O THR A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 534 through 536 Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.515A pdb=" N ILE C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.120A pdb=" N TYR C 118 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.487A pdb=" N LEU B 11 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.487A pdb=" N LEU B 11 " --> pdb=" O GLU B 106 " (cutoff:3.500A) 148 hydrogen bonds defined for protein. 318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1520 1.33 - 1.45: 1275 1.45 - 1.58: 2968 1.58 - 1.70: 0 1.70 - 1.83: 54 Bond restraints: 5817 Sorted by residual: bond pdb=" C LEU A 183 " pdb=" O LEU A 183 " ideal model delta sigma weight residual 1.233 1.206 0.027 1.26e-02 6.30e+03 4.73e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" N ASP A 185 " pdb=" CA ASP A 185 " ideal model delta sigma weight residual 1.456 1.480 -0.024 1.25e-02 6.40e+03 3.78e+00 bond pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.09e+00 bond pdb=" CB ASN A 284 " pdb=" CG ASN A 284 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.86e+00 ... (remaining 5812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 7497 1.68 - 3.36: 346 3.36 - 5.03: 44 5.03 - 6.71: 14 6.71 - 8.39: 2 Bond angle restraints: 7903 Sorted by residual: angle pdb=" CA MET A 45 " pdb=" CB MET A 45 " pdb=" CG MET A 45 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA ASN A 284 " pdb=" CB ASN A 284 " pdb=" CG ASN A 284 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 angle pdb=" CA LYS C 43 " pdb=" CB LYS C 43 " pdb=" CG LYS C 43 " ideal model delta sigma weight residual 114.10 120.33 -6.23 2.00e+00 2.50e-01 9.71e+00 angle pdb=" N MET A 45 " pdb=" CA MET A 45 " pdb=" CB MET A 45 " ideal model delta sigma weight residual 110.12 114.68 -4.56 1.47e+00 4.63e-01 9.62e+00 angle pdb=" CA LEU A 183 " pdb=" C LEU A 183 " pdb=" O LEU A 183 " ideal model delta sigma weight residual 120.92 117.70 3.22 1.04e+00 9.25e-01 9.57e+00 ... (remaining 7898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3072 17.92 - 35.84: 310 35.84 - 53.76: 104 53.76 - 71.69: 22 71.69 - 89.61: 13 Dihedral angle restraints: 3521 sinusoidal: 1422 harmonic: 2099 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -174.95 88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 520 " pdb=" CB CYS A 520 " ideal model delta sinusoidal sigma weight residual -86.00 -161.46 75.46 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS A 224 " pdb=" SG CYS A 224 " pdb=" SG CYS A 235 " pdb=" CB CYS A 235 " ideal model delta sinusoidal sigma weight residual -86.00 -125.31 39.31 1 1.00e+01 1.00e-02 2.17e+01 ... (remaining 3518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 511 0.041 - 0.083: 252 0.083 - 0.124: 89 0.124 - 0.166: 23 0.166 - 0.207: 3 Chirality restraints: 878 Sorted by residual: chirality pdb=" CB ILE B 2 " pdb=" CA ILE B 2 " pdb=" CG1 ILE B 2 " pdb=" CG2 ILE B 2 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU A 183 " pdb=" N LEU A 183 " pdb=" C LEU A 183 " pdb=" CB LEU A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL A 399 " pdb=" CA VAL A 399 " pdb=" CG1 VAL A 399 " pdb=" CG2 VAL A 399 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 875 not shown) Planarity restraints: 1026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 43 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C LEU A 43 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 43 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 44 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 46 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C LEU A 46 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 46 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 47 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 396 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C GLN A 396 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN A 396 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 397 " -0.014 2.00e-02 2.50e+03 ... (remaining 1023 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1312 2.79 - 3.32: 4921 3.32 - 3.85: 9796 3.85 - 4.37: 11955 4.37 - 4.90: 19990 Nonbonded interactions: 47974 Sorted by model distance: nonbonded pdb=" OH TYR A 303 " pdb=" O TYR C 107 " model vdw 2.265 3.040 nonbonded pdb=" O THR A 273 " pdb=" OG1 THR A 273 " model vdw 2.308 3.040 nonbonded pdb=" OD2 ASP A 421 " pdb=" OG SER A 423 " model vdw 2.344 3.040 nonbonded pdb=" O SER C 85 " pdb=" OG SER C 85 " model vdw 2.364 3.040 nonbonded pdb=" OG1 THR A 216 " pdb=" NH1 ARG A 226 " model vdw 2.408 3.120 ... (remaining 47969 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: 22.290 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: 0.050 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:22.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5839 Z= 0.225 Angle : 0.815 8.391 7949 Z= 0.451 Chirality : 0.054 0.207 878 Planarity : 0.006 0.046 1025 Dihedral : 16.761 89.606 2121 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.81 % Allowed : 20.32 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 726 helix: -1.96 (0.88), residues: 26 sheet: -0.06 (0.38), residues: 183 loop : 0.41 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 29 HIS 0.007 0.001 HIS A 495 PHE 0.029 0.002 PHE C 128 TYR 0.029 0.002 TYR C 52 ARG 0.007 0.001 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 1) link_NAG-ASN : angle 2.85331 ( 3) link_BETA1-4 : bond 0.00393 ( 1) link_BETA1-4 : angle 1.41739 ( 3) hydrogen bonds : bond 0.16429 ( 141) hydrogen bonds : angle 7.35903 ( 318) SS BOND : bond 0.00351 ( 20) SS BOND : angle 1.49374 ( 40) covalent geometry : bond 0.00486 ( 5817) covalent geometry : angle 0.80837 ( 7903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 286 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7784 (tm-30) REVERT: B 17 ASP cc_start: 0.8264 (t0) cc_final: 0.7985 (t0) REVERT: B 45 LYS cc_start: 0.8839 (ptmt) cc_final: 0.8593 (pttm) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 1.3403 time to fit residues: 107.8895 Evaluate side-chains 67 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.0170 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 178 GLN A 398 GLN A 478 HIS C 13 GLN C 77 ASN B 6 GLN B 90 GLN B 101 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.067390 restraints weight = 8620.644| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.65 r_work: 0.2680 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5839 Z= 0.179 Angle : 0.558 7.173 7949 Z= 0.292 Chirality : 0.045 0.172 878 Planarity : 0.004 0.034 1025 Dihedral : 5.075 50.071 840 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.35 % Allowed : 17.58 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.31), residues: 726 helix: -1.41 (1.00), residues: 26 sheet: -0.03 (0.40), residues: 169 loop : 0.76 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 29 HIS 0.003 0.001 HIS C 35 PHE 0.016 0.001 PHE C 27 TYR 0.017 0.001 TYR C 33 ARG 0.005 0.001 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 1) link_NAG-ASN : angle 1.66098 ( 3) link_BETA1-4 : bond 0.00077 ( 1) link_BETA1-4 : angle 1.12891 ( 3) hydrogen bonds : bond 0.03586 ( 141) hydrogen bonds : angle 5.61560 ( 318) SS BOND : bond 0.00226 ( 20) SS BOND : angle 0.81459 ( 40) covalent geometry : bond 0.00414 ( 5817) covalent geometry : angle 0.55509 ( 7903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 368 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8628 (mtpm) REVERT: C 6 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: C 87 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7449 (mtt90) REVERT: B 17 ASP cc_start: 0.8597 (t0) cc_final: 0.8109 (t0) REVERT: B 42 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8456 (mtpp) REVERT: B 45 LYS cc_start: 0.9117 (ptmt) cc_final: 0.8335 (pttm) outliers start: 27 outliers final: 10 residues processed: 76 average time/residue: 1.1736 time to fit residues: 93.9399 Evaluate side-chains 74 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 19 optimal weight: 0.0060 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.067970 restraints weight = 9197.652| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.70 r_work: 0.2722 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5839 Z= 0.138 Angle : 0.514 8.022 7949 Z= 0.267 Chirality : 0.043 0.172 878 Planarity : 0.004 0.033 1025 Dihedral : 4.940 52.179 840 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.39 % Allowed : 17.10 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.31), residues: 726 helix: -0.89 (1.03), residues: 26 sheet: -0.10 (0.39), residues: 177 loop : 0.79 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 29 HIS 0.002 0.001 HIS C 35 PHE 0.009 0.001 PHE A 381 TYR 0.015 0.001 TYR C 33 ARG 0.003 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 1) link_NAG-ASN : angle 1.55289 ( 3) link_BETA1-4 : bond 0.00262 ( 1) link_BETA1-4 : angle 1.11709 ( 3) hydrogen bonds : bond 0.03078 ( 141) hydrogen bonds : angle 5.27118 ( 318) SS BOND : bond 0.00177 ( 20) SS BOND : angle 0.84195 ( 40) covalent geometry : bond 0.00318 ( 5817) covalent geometry : angle 0.51090 ( 7903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.879 Fit side-chains REVERT: A 31 MET cc_start: 0.8432 (mtp) cc_final: 0.8186 (mtp) REVERT: A 368 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8439 (mtpm) REVERT: C 86 LEU cc_start: 0.8794 (mp) cc_final: 0.8561 (mp) REVERT: B 17 ASP cc_start: 0.8528 (t0) cc_final: 0.8147 (t0) REVERT: B 42 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8329 (mtpp) REVERT: B 45 LYS cc_start: 0.8954 (ptmt) cc_final: 0.8091 (pttm) outliers start: 21 outliers final: 11 residues processed: 72 average time/residue: 1.2246 time to fit residues: 92.8072 Evaluate side-chains 71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.090441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.067481 restraints weight = 9311.365| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.72 r_work: 0.2744 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5839 Z= 0.154 Angle : 0.513 8.728 7949 Z= 0.265 Chirality : 0.043 0.149 878 Planarity : 0.004 0.032 1025 Dihedral : 4.915 54.076 840 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.23 % Allowed : 18.71 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.31), residues: 726 helix: -0.54 (1.07), residues: 26 sheet: -0.18 (0.38), residues: 177 loop : 0.82 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 29 HIS 0.003 0.001 HIS C 35 PHE 0.019 0.001 PHE C 27 TYR 0.015 0.001 TYR C 33 ARG 0.003 0.000 ARG A 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 1.51711 ( 3) link_BETA1-4 : bond 0.00257 ( 1) link_BETA1-4 : angle 1.15413 ( 3) hydrogen bonds : bond 0.02978 ( 141) hydrogen bonds : angle 5.14319 ( 318) SS BOND : bond 0.00190 ( 20) SS BOND : angle 0.67882 ( 40) covalent geometry : bond 0.00356 ( 5817) covalent geometry : angle 0.51081 ( 7903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8373 (t0) cc_final: 0.8154 (t0) REVERT: A 183 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 368 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8487 (mtpm) REVERT: C 6 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6588 (mt-10) REVERT: C 28 THR cc_start: 0.8417 (t) cc_final: 0.8177 (p) REVERT: C 77 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8300 (t0) REVERT: B 17 ASP cc_start: 0.8552 (t0) cc_final: 0.8227 (t0) REVERT: B 42 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8313 (mtpp) REVERT: B 45 LYS cc_start: 0.8978 (ptmt) cc_final: 0.8120 (pttm) outliers start: 20 outliers final: 9 residues processed: 72 average time/residue: 1.4490 time to fit residues: 109.3097 Evaluate side-chains 74 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.067608 restraints weight = 9084.073| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.70 r_work: 0.2741 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5839 Z= 0.145 Angle : 0.512 9.046 7949 Z= 0.263 Chirality : 0.043 0.141 878 Planarity : 0.004 0.032 1025 Dihedral : 4.849 55.138 840 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.39 % Allowed : 18.87 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.31), residues: 726 helix: -0.35 (1.09), residues: 26 sheet: -0.24 (0.38), residues: 179 loop : 0.81 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 29 HIS 0.003 0.000 HIS C 35 PHE 0.008 0.001 PHE A 381 TYR 0.014 0.001 TYR C 33 ARG 0.004 0.000 ARG A 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 1.47415 ( 3) link_BETA1-4 : bond 0.00286 ( 1) link_BETA1-4 : angle 1.16613 ( 3) hydrogen bonds : bond 0.02868 ( 141) hydrogen bonds : angle 5.04222 ( 318) SS BOND : bond 0.00194 ( 20) SS BOND : angle 0.69705 ( 40) covalent geometry : bond 0.00335 ( 5817) covalent geometry : angle 0.50989 ( 7903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8415 (t0) cc_final: 0.8190 (t0) REVERT: A 31 MET cc_start: 0.8484 (mtp) cc_final: 0.8247 (mtp) REVERT: A 183 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 305 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8286 (p) REVERT: A 368 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8483 (mtpm) REVERT: C 28 THR cc_start: 0.8431 (t) cc_final: 0.8168 (p) REVERT: C 77 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8200 (t0) REVERT: B 17 ASP cc_start: 0.8555 (t0) cc_final: 0.8274 (t0) REVERT: B 42 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8308 (mtpp) REVERT: B 45 LYS cc_start: 0.8961 (ptmt) cc_final: 0.8096 (pttm) REVERT: B 61 ARG cc_start: 0.8047 (ptp90) cc_final: 0.7788 (ptp-170) outliers start: 21 outliers final: 11 residues processed: 73 average time/residue: 1.3101 time to fit residues: 100.2339 Evaluate side-chains 76 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.068379 restraints weight = 9108.014| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.70 r_work: 0.2756 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5839 Z= 0.109 Angle : 0.497 9.172 7949 Z= 0.254 Chirality : 0.042 0.137 878 Planarity : 0.004 0.039 1025 Dihedral : 4.810 55.525 840 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.74 % Allowed : 20.16 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.31), residues: 726 helix: -0.27 (1.10), residues: 26 sheet: -0.20 (0.38), residues: 179 loop : 0.82 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 29 HIS 0.002 0.000 HIS C 35 PHE 0.021 0.001 PHE C 27 TYR 0.013 0.001 TYR C 33 ARG 0.009 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.36216 ( 3) link_BETA1-4 : bond 0.00310 ( 1) link_BETA1-4 : angle 1.13789 ( 3) hydrogen bonds : bond 0.02652 ( 141) hydrogen bonds : angle 4.92083 ( 318) SS BOND : bond 0.00164 ( 20) SS BOND : angle 0.59382 ( 40) covalent geometry : bond 0.00248 ( 5817) covalent geometry : angle 0.49554 ( 7903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8387 (t0) cc_final: 0.8165 (t0) REVERT: A 31 MET cc_start: 0.8482 (mtp) cc_final: 0.8224 (mtp) REVERT: A 183 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8231 (tt) REVERT: A 368 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8488 (mtpm) REVERT: C 6 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6709 (mt-10) REVERT: B 42 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8353 (mtpp) REVERT: B 45 LYS cc_start: 0.8947 (ptmt) cc_final: 0.8091 (pttm) REVERT: B 61 ARG cc_start: 0.8048 (ptp90) cc_final: 0.7756 (ptp-170) outliers start: 17 outliers final: 6 residues processed: 73 average time/residue: 1.5575 time to fit residues: 119.1151 Evaluate side-chains 71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 chunk 48 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.092014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.069366 restraints weight = 9162.561| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.68 r_work: 0.2743 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5839 Z= 0.098 Angle : 0.490 9.410 7949 Z= 0.249 Chirality : 0.042 0.135 878 Planarity : 0.004 0.038 1025 Dihedral : 4.665 56.176 840 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.74 % Allowed : 20.48 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.31), residues: 726 helix: -0.19 (1.10), residues: 26 sheet: -0.14 (0.38), residues: 179 loop : 0.86 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 119 HIS 0.002 0.000 HIS C 35 PHE 0.005 0.001 PHE A 381 TYR 0.013 0.001 TYR C 33 ARG 0.009 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00010 ( 1) link_NAG-ASN : angle 1.28146 ( 3) link_BETA1-4 : bond 0.00385 ( 1) link_BETA1-4 : angle 1.14744 ( 3) hydrogen bonds : bond 0.02519 ( 141) hydrogen bonds : angle 4.78821 ( 318) SS BOND : bond 0.00147 ( 20) SS BOND : angle 0.55845 ( 40) covalent geometry : bond 0.00223 ( 5817) covalent geometry : angle 0.48908 ( 7903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.688 Fit side-chains REVERT: A 31 MET cc_start: 0.8461 (mtp) cc_final: 0.8222 (mtp) REVERT: A 183 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8272 (tt) REVERT: A 286 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8439 (mm-30) REVERT: A 368 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8509 (mtpm) REVERT: C 6 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: B 4 MET cc_start: 0.8707 (ptp) cc_final: 0.7811 (ptp) REVERT: B 42 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8375 (mtpp) REVERT: B 45 LYS cc_start: 0.8960 (ptmt) cc_final: 0.8115 (pttm) outliers start: 17 outliers final: 4 residues processed: 75 average time/residue: 1.4767 time to fit residues: 116.3274 Evaluate side-chains 68 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 38 optimal weight: 0.0670 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.068727 restraints weight = 9034.584| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.70 r_work: 0.2739 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5839 Z= 0.113 Angle : 0.502 9.598 7949 Z= 0.253 Chirality : 0.042 0.136 878 Planarity : 0.004 0.034 1025 Dihedral : 4.680 57.205 840 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.90 % Allowed : 20.48 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.31), residues: 726 helix: -0.14 (1.10), residues: 26 sheet: -0.20 (0.38), residues: 179 loop : 0.86 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 29 HIS 0.002 0.000 HIS C 35 PHE 0.027 0.001 PHE C 27 TYR 0.012 0.001 TYR C 33 ARG 0.008 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 1.32433 ( 3) link_BETA1-4 : bond 0.00262 ( 1) link_BETA1-4 : angle 1.11913 ( 3) hydrogen bonds : bond 0.02605 ( 141) hydrogen bonds : angle 4.79491 ( 318) SS BOND : bond 0.00151 ( 20) SS BOND : angle 0.57471 ( 40) covalent geometry : bond 0.00264 ( 5817) covalent geometry : angle 0.50018 ( 7903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.988 Fit side-chains REVERT: A 31 MET cc_start: 0.8385 (mtp) cc_final: 0.8136 (mtp) REVERT: A 183 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8216 (tt) REVERT: A 185 ASP cc_start: 0.8454 (t0) cc_final: 0.8131 (t0) REVERT: A 286 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8426 (mm-30) REVERT: A 368 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8474 (mtpm) REVERT: B 4 MET cc_start: 0.8691 (ptp) cc_final: 0.7747 (ptp) REVERT: B 42 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8349 (mtpp) REVERT: B 45 LYS cc_start: 0.8937 (ptmt) cc_final: 0.8082 (pttm) outliers start: 18 outliers final: 8 residues processed: 73 average time/residue: 1.5358 time to fit residues: 118.1002 Evaluate side-chains 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.066270 restraints weight = 9182.772| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.71 r_work: 0.2684 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5839 Z= 0.231 Angle : 0.572 9.859 7949 Z= 0.291 Chirality : 0.045 0.146 878 Planarity : 0.004 0.033 1025 Dihedral : 5.080 57.353 840 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.90 % Allowed : 20.97 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 726 helix: -0.29 (1.08), residues: 26 sheet: -0.35 (0.38), residues: 178 loop : 0.82 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 452 HIS 0.003 0.001 HIS C 35 PHE 0.011 0.001 PHE A 381 TYR 0.014 0.001 TYR B 49 ARG 0.008 0.001 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 1) link_NAG-ASN : angle 1.72761 ( 3) link_BETA1-4 : bond 0.00050 ( 1) link_BETA1-4 : angle 1.22476 ( 3) hydrogen bonds : bond 0.03229 ( 141) hydrogen bonds : angle 5.15060 ( 318) SS BOND : bond 0.00261 ( 20) SS BOND : angle 0.83900 ( 40) covalent geometry : bond 0.00545 ( 5817) covalent geometry : angle 0.56945 ( 7903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8376 (mtp) cc_final: 0.8078 (mtp) REVERT: A 183 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 286 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8457 (mm-30) REVERT: A 368 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8430 (mtpm) REVERT: B 45 LYS cc_start: 0.8954 (ptmt) cc_final: 0.8089 (pttm) outliers start: 18 outliers final: 9 residues processed: 67 average time/residue: 1.4820 time to fit residues: 103.9775 Evaluate side-chains 67 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN C 13 GLN C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.067006 restraints weight = 9471.348| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.81 r_work: 0.2685 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5839 Z= 0.147 Angle : 0.537 10.290 7949 Z= 0.270 Chirality : 0.043 0.134 878 Planarity : 0.004 0.034 1025 Dihedral : 4.925 57.162 840 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.61 % Allowed : 22.10 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 726 helix: -0.16 (1.09), residues: 26 sheet: -0.43 (0.38), residues: 178 loop : 0.79 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.033 0.001 PHE C 27 TYR 0.013 0.001 TYR C 33 ARG 0.007 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 1) link_NAG-ASN : angle 1.42526 ( 3) link_BETA1-4 : bond 0.00215 ( 1) link_BETA1-4 : angle 1.10053 ( 3) hydrogen bonds : bond 0.02834 ( 141) hydrogen bonds : angle 4.98918 ( 318) SS BOND : bond 0.00209 ( 20) SS BOND : angle 0.67316 ( 40) covalent geometry : bond 0.00343 ( 5817) covalent geometry : angle 0.53496 ( 7903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.697 Fit side-chains REVERT: A 31 MET cc_start: 0.8395 (mtp) cc_final: 0.8136 (mtp) REVERT: A 183 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8118 (tt) REVERT: A 185 ASP cc_start: 0.8447 (t0) cc_final: 0.8098 (t0) REVERT: A 286 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8413 (mm-30) REVERT: A 368 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8436 (mtpm) REVERT: B 45 LYS cc_start: 0.8908 (ptmt) cc_final: 0.8028 (pttm) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 1.1415 time to fit residues: 74.7120 Evaluate side-chains 64 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 0.0170 chunk 15 optimal weight: 0.0670 chunk 1 optimal weight: 0.1980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.069201 restraints weight = 9388.993| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.80 r_work: 0.2733 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.002 0.031 5839 Z= 0.096 Angle : 0.517 10.483 7949 Z= 0.257 Chirality : 0.042 0.135 878 Planarity : 0.004 0.034 1025 Dihedral : 4.630 54.764 840 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.77 % Allowed : 21.77 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.31), residues: 726 helix: -0.03 (1.10), residues: 26 sheet: -0.40 (0.38), residues: 178 loop : 0.81 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 29 HIS 0.002 0.000 HIS C 35 PHE 0.005 0.001 PHE A 258 TYR 0.013 0.001 TYR C 33 ARG 0.007 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 1.26466 ( 3) link_BETA1-4 : bond 0.00271 ( 1) link_BETA1-4 : angle 1.08388 ( 3) hydrogen bonds : bond 0.02497 ( 141) hydrogen bonds : angle 4.83531 ( 318) SS BOND : bond 0.00161 ( 20) SS BOND : angle 0.59733 ( 40) covalent geometry : bond 0.00224 ( 5817) covalent geometry : angle 0.51545 ( 7903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.60 seconds wall clock time: 97 minutes 26.38 seconds (5846.38 seconds total)