Starting phenix.real_space_refine on Sat May 10 08:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqd_43439/05_2025/8vqd_43439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqd_43439/05_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_43439/05_2025/8vqd_43439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqd_43439/05_2025/8vqd_43439.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqd_43439/05_2025/8vqd_43439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqd_43439/05_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.61, per 1000 atoms: 0.81 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: 1.22 Conformation dependent library (CDL) restraints added in 929.7 milliseconds 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: 0.80 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: 1.96 Time building geometry restraints manager: 1.50 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: 6.760 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: 0.040 Set scattering table: 0.140 Process input model: 19.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.790 ------------------------------------------------------------------------------- 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 : 0.586 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: 1.2426 time to fit residues: 100.0035 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 : 0.602 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.067450 restraints weight = 8620.650| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.63 r_work: 0.2678 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 1.12892 ( 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: 0.8925 (OUTLIER) cc_final: 0.8627 (mtpm) REVERT: C 6 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: C 87 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7448 (mtt90) REVERT: B 17 ASP cc_start: 0.8597 (t0) cc_final: 0.8108 (t0) REVERT: B 42 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8457 (mtpp) REVERT: B 45 LYS cc_start: 0.9116 (ptmt) cc_final: 0.8335 (pttm) outliers start: 27 outliers final: 10 residues processed: 76 average time/residue: 1.1783 time to fit residues: 94.0192 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 : 0.661 ------------------------------------------------------------------------------- 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: 0.5980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.091233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.068281 restraints weight = 9159.572| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.72 r_work: 0.2732 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1374 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= 0.127 Angle : 0.509 8.213 7949 Z= 0.264 Chirality : 0.043 0.171 878 Planarity : 0.004 0.033 1025 Dihedral : 4.907 52.120 840 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.06 % Allowed : 17.26 % Favored : 79.68 % 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: -0.82 (1.03), residues: 26 sheet: -0.10 (0.39), residues: 177 loop : 0.80 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 119 HIS 0.002 0.001 HIS C 35 PHE 0.008 0.001 PHE A 381 TYR 0.015 0.001 TYR C 33 ARG 0.004 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.50963 ( 3) link_BETA1-4 : bond 0.00247 ( 1) link_BETA1-4 : angle 1.08692 ( 3) hydrogen bonds : bond 0.02988 ( 141) hydrogen bonds : angle 5.23396 ( 318) SS BOND : bond 0.00214 ( 20) SS BOND : angle 0.82765 ( 40) covalent geometry : bond 0.00293 ( 5817) covalent geometry : angle 0.50557 ( 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 79 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8411 (mtp) cc_final: 0.8185 (mtp) REVERT: A 183 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 368 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8439 (mtpm) REVERT: C 86 LEU cc_start: 0.8792 (mp) cc_final: 0.8562 (mp) REVERT: B 17 ASP cc_start: 0.8533 (t0) cc_final: 0.8153 (t0) REVERT: B 42 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8331 (mtpp) REVERT: B 45 LYS cc_start: 0.8958 (ptmt) cc_final: 0.8092 (pttm) outliers start: 19 outliers final: 8 residues processed: 71 average time/residue: 1.2410 time to fit residues: 92.3149 Evaluate side-chains 68 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 B residue 5 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 78 LEU 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: 0.5980 chunk 50 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.090871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.067911 restraints weight = 9290.139| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.72 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: 0.8585 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5839 Z= 0.136 Angle : 0.503 8.543 7949 Z= 0.259 Chirality : 0.043 0.145 878 Planarity : 0.004 0.031 1025 Dihedral : 4.814 53.571 840 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.39 % Allowed : 18.23 % Favored : 78.39 % 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: 0.62 (0.31), residues: 726 helix: -0.50 (1.07), residues: 26 sheet: -0.15 (0.38), residues: 177 loop : 0.83 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 29 HIS 0.003 0.000 HIS C 35 PHE 0.019 0.001 PHE C 27 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 0.00140 ( 1) link_NAG-ASN : angle 1.46915 ( 3) link_BETA1-4 : bond 0.00161 ( 1) link_BETA1-4 : angle 1.12371 ( 3) hydrogen bonds : bond 0.02858 ( 141) hydrogen bonds : angle 5.06510 ( 318) SS BOND : bond 0.00166 ( 20) SS BOND : angle 0.65693 ( 40) covalent geometry : bond 0.00312 ( 5817) covalent geometry : angle 0.50121 ( 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 86 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8375 (t0) cc_final: 0.8161 (t0) REVERT: A 31 MET cc_start: 0.8481 (mtp) cc_final: 0.8263 (mtp) REVERT: A 183 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 305 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 368 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8500 (mtpm) REVERT: C 6 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: C 28 THR cc_start: 0.8416 (t) cc_final: 0.8170 (p) REVERT: C 77 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8300 (t0) REVERT: B 17 ASP cc_start: 0.8554 (t0) cc_final: 0.8266 (t0) REVERT: B 42 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8360 (mtpp) REVERT: B 45 LYS cc_start: 0.9001 (ptmt) cc_final: 0.8151 (pttm) REVERT: B 61 ARG cc_start: 0.8055 (ptp90) cc_final: 0.7824 (ptp-170) outliers start: 21 outliers final: 9 residues processed: 78 average time/residue: 1.2451 time to fit residues: 101.6546 Evaluate side-chains 77 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 73 ASP Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain B residue 4 MET 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=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: 0.0030 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.090609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.067627 restraints weight = 9123.950| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.75 r_work: 0.2736 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1640 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= 0.147 Angle : 0.509 9.038 7949 Z= 0.262 Chirality : 0.043 0.140 878 Planarity : 0.004 0.039 1025 Dihedral : 4.837 54.354 840 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.55 % Allowed : 19.03 % Favored : 77.42 % 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: -0.34 (1.09), residues: 26 sheet: -0.19 (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 0.009 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 0.00152 ( 1) link_NAG-ASN : angle 1.47700 ( 3) link_BETA1-4 : bond 0.00213 ( 1) link_BETA1-4 : angle 1.13753 ( 3) hydrogen bonds : bond 0.02850 ( 141) hydrogen bonds : angle 5.01569 ( 318) SS BOND : bond 0.00190 ( 20) SS BOND : angle 0.64039 ( 40) covalent geometry : bond 0.00339 ( 5817) covalent geometry : angle 0.50719 ( 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 84 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8384 (t0) cc_final: 0.8158 (t0) REVERT: A 183 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 305 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8311 (p) REVERT: A 368 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8457 (mtpm) REVERT: C 28 THR cc_start: 0.8410 (t) cc_final: 0.8132 (p) REVERT: C 77 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8168 (t0) REVERT: B 17 ASP cc_start: 0.8526 (t0) cc_final: 0.8255 (t0) REVERT: B 42 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8313 (mtpp) REVERT: B 45 LYS cc_start: 0.8945 (ptmt) cc_final: 0.8076 (pttm) REVERT: B 61 ARG cc_start: 0.8043 (ptp90) cc_final: 0.7759 (ptp-170) outliers start: 22 outliers final: 10 residues processed: 74 average time/residue: 1.2029 time to fit residues: 93.4812 Evaluate side-chains 76 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.090062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.067108 restraints weight = 9142.720| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.70 r_work: 0.2722 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5839 Z= 0.166 Angle : 0.521 9.349 7949 Z= 0.267 Chirality : 0.043 0.141 878 Planarity : 0.004 0.033 1025 Dihedral : 4.869 56.460 840 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.23 % Allowed : 19.35 % Favored : 77.42 % 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: -0.32 (1.09), residues: 26 sheet: -0.25 (0.38), residues: 179 loop : 0.81 (0.28), residues: 521 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 0.021 0.001 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.007 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 1) link_NAG-ASN : angle 1.52522 ( 3) link_BETA1-4 : bond 0.00054 ( 1) link_BETA1-4 : angle 1.10855 ( 3) hydrogen bonds : bond 0.02896 ( 141) hydrogen bonds : angle 5.01413 ( 318) SS BOND : bond 0.00247 ( 20) SS BOND : angle 0.72978 ( 40) covalent geometry : bond 0.00387 ( 5817) covalent geometry : angle 0.51816 ( 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 80 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8458 (mtp) cc_final: 0.8172 (mtp) REVERT: A 183 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 286 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8456 (mm-30) REVERT: A 305 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8309 (p) REVERT: A 368 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8553 (mtpm) REVERT: C 6 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: B 17 ASP cc_start: 0.8546 (t0) cc_final: 0.8297 (t0) REVERT: B 42 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8307 (mtpp) REVERT: B 45 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8097 (pttm) outliers start: 20 outliers final: 10 residues processed: 71 average time/residue: 1.2145 time to fit residues: 90.5694 Evaluate side-chains 73 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 286 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 6 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 32 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.0040 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.091251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.068404 restraints weight = 9109.325| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.71 r_work: 0.2730 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1763 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= 0.102 Angle : 0.499 9.484 7949 Z= 0.253 Chirality : 0.042 0.136 878 Planarity : 0.004 0.033 1025 Dihedral : 4.763 57.186 840 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.74 % Allowed : 20.00 % Favored : 77.26 % 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: 0.62 (0.31), residues: 726 helix: -0.22 (1.11), residues: 26 sheet: -0.22 (0.38), residues: 179 loop : 0.84 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 47 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 0.007 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.31808 ( 3) link_BETA1-4 : bond 0.00210 ( 1) link_BETA1-4 : angle 1.08225 ( 3) hydrogen bonds : bond 0.02579 ( 141) hydrogen bonds : angle 4.88408 ( 318) SS BOND : bond 0.00171 ( 20) SS BOND : angle 0.58996 ( 40) covalent geometry : bond 0.00232 ( 5817) covalent geometry : angle 0.49756 ( 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 79 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8453 (mtp) cc_final: 0.8173 (mtp) REVERT: A 183 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8217 (tt) REVERT: A 286 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8434 (mm-30) REVERT: A 368 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8475 (mtpm) REVERT: C 6 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6766 (mt-10) REVERT: B 42 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: B 45 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8075 (pttm) outliers start: 17 outliers final: 5 residues processed: 74 average time/residue: 1.1474 time to fit residues: 89.1518 Evaluate side-chains 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 6 GLU Chi-restraints excluded: chain C residue 63 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.065900 restraints weight = 9126.459| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.75 r_work: 0.2692 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5839 Z= 0.238 Angle : 0.567 9.831 7949 Z= 0.289 Chirality : 0.045 0.138 878 Planarity : 0.004 0.033 1025 Dihedral : 5.064 57.690 840 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.23 % Allowed : 20.48 % 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: 0.51 (0.31), residues: 726 helix: -0.36 (1.08), residues: 26 sheet: -0.34 (0.38), residues: 178 loop : 0.79 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.027 0.002 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.007 0.001 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 1) link_NAG-ASN : angle 1.75972 ( 3) link_BETA1-4 : bond 0.00075 ( 1) link_BETA1-4 : angle 1.19088 ( 3) hydrogen bonds : bond 0.03229 ( 141) hydrogen bonds : angle 5.19964 ( 318) SS BOND : bond 0.00269 ( 20) SS BOND : angle 0.82020 ( 40) covalent geometry : bond 0.00558 ( 5817) covalent geometry : angle 0.56374 ( 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 78 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8417 (mtp) cc_final: 0.8126 (mtp) REVERT: A 183 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8180 (tt) REVERT: A 286 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8469 (mm-30) REVERT: A 368 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8457 (mtpm) REVERT: B 45 LYS cc_start: 0.8959 (ptmt) cc_final: 0.8090 (pttm) outliers start: 20 outliers final: 10 residues processed: 71 average time/residue: 1.2815 time to fit residues: 95.3592 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 : 0.591 ------------------------------------------------------------------------------- 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 250 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 4 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 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 = 0.3255 r_free = 0.3255 target = 0.090574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.067686 restraints weight = 9107.208| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.72 r_work: 0.2741 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1891 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= 0.121 Angle : 0.518 9.821 7949 Z= 0.261 Chirality : 0.043 0.135 878 Planarity : 0.004 0.034 1025 Dihedral : 4.819 58.003 840 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.10 % Allowed : 22.10 % Favored : 75.81 % 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: -0.18 (1.10), residues: 26 sheet: -0.39 (0.38), residues: 178 loop : 0.81 (0.28), residues: 522 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 0.006 0.001 PHE A 381 TYR 0.013 0.001 TYR C 33 ARG 0.006 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 1.31241 ( 3) link_BETA1-4 : bond 0.00308 ( 1) link_BETA1-4 : angle 1.07458 ( 3) hydrogen bonds : bond 0.02692 ( 141) hydrogen bonds : angle 4.97103 ( 318) SS BOND : bond 0.00181 ( 20) SS BOND : angle 0.60843 ( 40) covalent geometry : bond 0.00280 ( 5817) covalent geometry : angle 0.51639 ( 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 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.692 Fit side-chains REVERT: A 31 MET cc_start: 0.8431 (mtp) cc_final: 0.8160 (mtp) REVERT: A 183 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8176 (tt) REVERT: A 185 ASP cc_start: 0.8461 (t0) cc_final: 0.8117 (t0) REVERT: A 368 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8466 (mtpm) REVERT: C 19 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7925 (tmm-80) REVERT: B 45 LYS cc_start: 0.8959 (ptmt) cc_final: 0.8095 (pttm) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 1.1864 time to fit residues: 83.5629 Evaluate side-chains 66 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 69 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: 0.5980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 0.0170 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.090369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.067843 restraints weight = 9470.459| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.82 r_work: 0.2698 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5839 Z= 0.118 Angle : 0.524 10.345 7949 Z= 0.261 Chirality : 0.043 0.157 878 Planarity : 0.004 0.034 1025 Dihedral : 4.690 55.045 840 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.26 % Allowed : 21.45 % 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: 0.55 (0.32), residues: 726 helix: -0.13 (1.10), residues: 26 sheet: -0.39 (0.39), residues: 178 loop : 0.84 (0.28), residues: 522 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 0.032 0.001 PHE C 27 TYR 0.013 0.001 TYR C 33 ARG 0.006 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 1.41115 ( 3) link_BETA1-4 : bond 0.00190 ( 1) link_BETA1-4 : angle 1.13474 ( 3) hydrogen bonds : bond 0.02621 ( 141) hydrogen bonds : angle 4.93160 ( 318) SS BOND : bond 0.00158 ( 20) SS BOND : angle 0.60124 ( 40) covalent geometry : bond 0.00275 ( 5817) covalent geometry : angle 0.52287 ( 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 73 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.656 Fit side-chains REVERT: A 31 MET cc_start: 0.8380 (mtp) cc_final: 0.8111 (mtp) REVERT: A 183 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8080 (tt) REVERT: A 185 ASP cc_start: 0.8440 (t0) cc_final: 0.8082 (t0) REVERT: A 368 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8424 (mtpm) REVERT: C 19 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8011 (tmm-80) REVERT: B 42 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8324 (mtpp) REVERT: B 45 LYS cc_start: 0.8904 (ptmt) cc_final: 0.8016 (pttm) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 1.1383 time to fit residues: 81.4323 Evaluate side-chains 68 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 69 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.0470 chunk 1 optimal weight: 0.0050 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.090955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.068450 restraints weight = 9381.974| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.81 r_work: 0.2719 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5839 Z= 0.107 Angle : 0.517 10.381 7949 Z= 0.257 Chirality : 0.043 0.189 878 Planarity : 0.004 0.034 1025 Dihedral : 4.605 53.256 840 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 : 2.26 % Allowed : 21.61 % 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: 0.57 (0.32), residues: 726 helix: 0.00 (1.11), residues: 26 sheet: -0.42 (0.38), residues: 178 loop : 0.86 (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 0.006 0.001 PHE A 258 TYR 0.012 0.001 TYR C 33 ARG 0.006 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.29032 ( 3) link_BETA1-4 : bond 0.00279 ( 1) link_BETA1-4 : angle 1.09037 ( 3) hydrogen bonds : bond 0.02518 ( 141) hydrogen bonds : angle 4.89684 ( 318) SS BOND : bond 0.00156 ( 20) SS BOND : angle 0.57692 ( 40) covalent geometry : bond 0.00251 ( 5817) covalent geometry : angle 0.51571 ( 7903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4881.97 seconds wall clock time: 85 minutes 3.83 seconds (5103.83 seconds total)