Starting phenix.real_space_refine on Thu Jul 2 04:43:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sy8_25520/07_2026/7sy8_25520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy8_25520/07_2026/7sy8_25520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy8_25520/07_2026/7sy8_25520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy8_25520/07_2026/7sy8_25520.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sy8_25520/07_2026/7sy8_25520.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sy8_25520/07_2026/7sy8_25520.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sy8_25520/07_2026/7sy8_25520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy8_25520/07_2026/7sy8_25520.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 37 5.16 5 C 4190 2.51 5 N 1077 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6552 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.39, per 1000 atoms: 0.21 Number of scatterers: 6552 At special positions: 0 Unit cell: (78, 83, 123, 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 37 16.00 O 1248 8.00 N 1077 7.00 C 4190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 326.9 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 58.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.272A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.320A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.023A pdb=" N ASN E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.587A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.723A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.033A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.909A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.696A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.652A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.772A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.596A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.673A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.294A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.561A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.331A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.638A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.396A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.899A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.903A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.749A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.073A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.367A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 918 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: 0.91 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2077 1.34 - 1.47: 1790 1.47 - 1.60: 2810 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.15e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.96e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.64e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 8817 2.10 - 4.20: 296 4.20 - 6.30: 31 6.30 - 8.40: 6 8.40 - 10.50: 4 Bond angle restraints: 9154 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.46 127.96 -5.50 1.41e+00 5.03e-01 1.52e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.33 -8.93 2.30e+00 1.89e-01 1.51e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 120.68 -6.78 1.80e+00 3.09e-01 1.42e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.25 -3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CB ARG B 457 " pdb=" CG ARG B 457 " pdb=" CD ARG B 457 " ideal model delta sigma weight residual 111.30 118.77 -7.47 2.30e+00 1.89e-01 1.05e+01 ... (remaining 9149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 3538 17.02 - 34.04: 310 34.04 - 51.06: 50 51.06 - 68.08: 8 68.08 - 85.09: 11 Dihedral angle restraints: 3917 sinusoidal: 1578 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -43.35 -42.65 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 12.46 66.54 1 2.00e+01 2.50e-03 1.44e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -131.42 8.82 0 2.50e+00 1.60e-01 1.24e+01 ... (remaining 3914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 722 0.057 - 0.114: 197 0.114 - 0.171: 53 0.171 - 0.227: 5 0.227 - 0.284: 2 Chirality restraints: 979 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL B 350 " pdb=" CA VAL B 350 " pdb=" CG1 VAL B 350 " pdb=" CG2 VAL B 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 976 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 40 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C PHE E 40 " 0.072 2.00e-02 2.50e+03 pdb=" O PHE E 40 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR E 41 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO E 590 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.62e+00 pdb=" N PRO E 500 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.039 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1900 2.82 - 3.34: 5963 3.34 - 3.86: 11272 3.86 - 4.38: 12880 4.38 - 4.90: 22296 Nonbonded interactions: 54311 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.350 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.362 3.120 nonbonded pdb=" NH2 ARG B 454 " pdb=" O SER B 469 " model vdw 2.363 3.120 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.364 3.120 ... (remaining 54306 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: 4.360 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 0.064 6748 Z= 0.243 Angle : 0.903 12.371 9187 Z= 0.498 Chirality : 0.057 0.284 979 Planarity : 0.007 0.070 1176 Dihedral : 13.410 85.095 2399 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 793 helix: 0.27 (0.23), residues: 386 sheet: 0.94 (0.70), residues: 43 loop : -0.60 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 460 TYR 0.041 0.003 TYR B 495 PHE 0.028 0.003 PHE E 369 TRP 0.021 0.002 TRP E 69 HIS 0.004 0.001 HIS E 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 ( 6735) covalent geometry : angle 0.87490 / 0.49 ( 9154) SS BOND : bond 0.00552 / 0.31 ( 6) SS BOND : angle 2.69190 / 1.53 ( 12) hydrogen bonds : bond 0.14338 / 10.04 ( 323) hydrogen bonds : angle 6.28296 / 4.25 ( 918) link_NAG-ASN : bond 0.00711 / 0.41 ( 7) link_NAG-ASN : angle 4.36532 / 3.36 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8595 (m-30) cc_final: 0.8295 (m-30) REVERT: B 471 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7987 (tm-30) REVERT: E 149 ASN cc_start: 0.9152 (m-40) cc_final: 0.8933 (m-40) REVERT: E 256 ILE cc_start: 0.8944 (mp) cc_final: 0.8538 (mt) REVERT: E 455 MET cc_start: 0.8718 (tmm) cc_final: 0.8484 (ttt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1012 time to fit residues: 10.3684 Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 493 GLN E 374 HIS E 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.063603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.048883 restraints weight = 22160.192| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.55 r_work: 0.2721 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6748 Z= 0.155 Angle : 0.574 9.361 9187 Z= 0.287 Chirality : 0.042 0.205 979 Planarity : 0.005 0.042 1176 Dihedral : 4.260 14.703 866 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.71 % Allowed : 6.29 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 793 helix: 1.28 (0.25), residues: 400 sheet: 0.90 (0.74), residues: 43 loop : -0.27 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.020 0.001 TYR B 495 PHE 0.015 0.001 PHE E 369 TRP 0.016 0.001 TRP E 165 HIS 0.003 0.001 HIS E 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 6735) covalent geometry : angle 0.55477 / 0.28 ( 9154) SS BOND : bond 0.00456 / 0.26 ( 6) SS BOND : angle 2.12172 / 1.19 ( 12) hydrogen bonds : bond 0.04285 / 2.81 ( 323) hydrogen bonds : angle 4.71439 / 3.28 ( 918) link_NAG-ASN : bond 0.00364 / 0.22 ( 7) link_NAG-ASN : angle 2.76040 / 2.09 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8431 (ttmm) REVERT: B 405 ASP cc_start: 0.8959 (m-30) cc_final: 0.8678 (m-30) REVERT: B 471 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8457 (tm-30) REVERT: E 149 ASN cc_start: 0.9126 (m-40) cc_final: 0.8681 (m110) REVERT: E 249 MET cc_start: 0.9239 (ttm) cc_final: 0.8995 (mtt) REVERT: E 256 ILE cc_start: 0.8914 (mp) cc_final: 0.8492 (mt) REVERT: E 270 MET cc_start: 0.8905 (tpp) cc_final: 0.8684 (tpp) REVERT: E 332 MET cc_start: 0.8720 (tmm) cc_final: 0.8470 (tmm) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.0820 time to fit residues: 6.0206 Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 250 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.0030 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.048209 restraints weight = 22106.388| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.49 r_work: 0.2715 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6748 Z= 0.151 Angle : 0.537 9.614 9187 Z= 0.268 Chirality : 0.041 0.174 979 Planarity : 0.004 0.035 1176 Dihedral : 4.084 14.693 866 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.57 % Allowed : 6.71 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.29), residues: 793 helix: 1.67 (0.26), residues: 391 sheet: 0.63 (0.71), residues: 43 loop : 0.03 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.015 0.001 TYR B 495 PHE 0.014 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 6735) covalent geometry : angle 0.52549 / 0.26 ( 9154) SS BOND : bond 0.00263 / 0.16 ( 6) SS BOND : angle 1.17665 / 0.68 ( 12) hydrogen bonds : bond 0.04051 / 2.65 ( 323) hydrogen bonds : angle 4.51463 / 3.14 ( 918) link_NAG-ASN : bond 0.00342 / 0.21 ( 7) link_NAG-ASN : angle 2.19124 / 1.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8942 (m-30) cc_final: 0.8574 (m-30) REVERT: B 471 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8506 (tm-30) REVERT: B 484 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8863 (tptp) REVERT: E 149 ASN cc_start: 0.9222 (m-40) cc_final: 0.8922 (m-40) REVERT: E 249 MET cc_start: 0.9196 (ttm) cc_final: 0.8951 (mtt) REVERT: E 256 ILE cc_start: 0.8960 (mp) cc_final: 0.8426 (mt) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.0835 time to fit residues: 6.4590 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.048537 restraints weight = 21912.281| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.45 r_work: 0.2702 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6748 Z= 0.135 Angle : 0.520 10.028 9187 Z= 0.256 Chirality : 0.040 0.141 979 Planarity : 0.004 0.035 1176 Dihedral : 4.005 14.595 866 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 8.29 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.29), residues: 793 helix: 1.72 (0.26), residues: 397 sheet: 0.58 (0.71), residues: 43 loop : 0.14 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.014 0.001 TYR B 495 PHE 0.011 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 6735) covalent geometry : angle 0.51235 / 0.25 ( 9154) SS BOND : bond 0.00242 / 0.15 ( 6) SS BOND : angle 0.89147 / 0.54 ( 12) hydrogen bonds : bond 0.03846 / 2.52 ( 323) hydrogen bonds : angle 4.39909 / 3.07 ( 918) link_NAG-ASN : bond 0.00291 / 0.18 ( 7) link_NAG-ASN : angle 1.90415 / 1.44 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8427 (ttmm) REVERT: B 405 ASP cc_start: 0.8992 (m-30) cc_final: 0.8619 (m-30) REVERT: E 149 ASN cc_start: 0.9226 (m-40) cc_final: 0.8928 (m-40) REVERT: E 249 MET cc_start: 0.9209 (ttm) cc_final: 0.8950 (mtt) REVERT: E 256 ILE cc_start: 0.8909 (mp) cc_final: 0.8342 (mt) REVERT: E 474 MET cc_start: 0.9289 (mmp) cc_final: 0.9038 (mmm) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.0838 time to fit residues: 6.3095 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 65 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.048865 restraints weight = 21858.264| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.43 r_work: 0.2710 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6748 Z= 0.117 Angle : 0.513 12.487 9187 Z= 0.250 Chirality : 0.040 0.224 979 Planarity : 0.003 0.039 1176 Dihedral : 3.881 14.211 866 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.14 % Allowed : 9.71 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.29), residues: 793 helix: 1.95 (0.26), residues: 391 sheet: 0.67 (0.72), residues: 43 loop : 0.12 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.011 0.001 TYR B 495 PHE 0.011 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6735) covalent geometry : angle 0.50697 / 0.25 ( 9154) SS BOND : bond 0.00217 / 0.14 ( 6) SS BOND : angle 0.72733 / 0.46 ( 12) hydrogen bonds : bond 0.03682 / 2.42 ( 323) hydrogen bonds : angle 4.30585 / 3.00 ( 918) link_NAG-ASN : bond 0.00270 / 0.17 ( 7) link_NAG-ASN : angle 1.72580 / 1.29 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8418 (ttmm) REVERT: B 405 ASP cc_start: 0.8965 (m-30) cc_final: 0.8548 (m-30) REVERT: B 484 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8885 (tptp) REVERT: E 140 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8660 (tm-30) REVERT: E 149 ASN cc_start: 0.9230 (m-40) cc_final: 0.8818 (m-40) REVERT: E 249 MET cc_start: 0.9198 (ttm) cc_final: 0.8925 (mtt) REVERT: E 256 ILE cc_start: 0.8862 (mp) cc_final: 0.8212 (mt) REVERT: E 292 ASP cc_start: 0.8406 (t0) cc_final: 0.7930 (t0) REVERT: E 332 MET cc_start: 0.8629 (tmm) cc_final: 0.8407 (tmm) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.0877 time to fit residues: 6.3848 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.048835 restraints weight = 21881.414| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.45 r_work: 0.2710 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6748 Z= 0.115 Angle : 0.496 11.529 9187 Z= 0.242 Chirality : 0.040 0.232 979 Planarity : 0.003 0.042 1176 Dihedral : 3.783 13.914 866 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.14 % Allowed : 9.57 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.29), residues: 793 helix: 2.01 (0.26), residues: 391 sheet: 0.67 (0.75), residues: 43 loop : 0.18 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.011 0.001 TYR B 495 PHE 0.010 0.001 PHE E 315 TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6735) covalent geometry : angle 0.49040 / 0.24 ( 9154) SS BOND : bond 0.00230 / 0.15 ( 6) SS BOND : angle 0.67134 / 0.42 ( 12) hydrogen bonds : bond 0.03593 / 2.36 ( 323) hydrogen bonds : angle 4.24081 / 2.96 ( 918) link_NAG-ASN : bond 0.00241 / 0.15 ( 7) link_NAG-ASN : angle 1.63226 / 1.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8404 (ttmm) REVERT: B 405 ASP cc_start: 0.8948 (m-30) cc_final: 0.8545 (m-30) REVERT: E 140 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8630 (tm-30) REVERT: E 149 ASN cc_start: 0.9258 (m-40) cc_final: 0.8852 (m-40) REVERT: E 249 MET cc_start: 0.9193 (ttm) cc_final: 0.8905 (mtt) REVERT: E 256 ILE cc_start: 0.8838 (mp) cc_final: 0.8617 (mm) REVERT: E 332 MET cc_start: 0.8628 (tmm) cc_final: 0.8407 (tmm) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.0733 time to fit residues: 5.7422 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 344 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 241 HIS E 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.044776 restraints weight = 22190.589| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.31 r_work: 0.2601 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 6748 Z= 0.307 Angle : 0.634 10.590 9187 Z= 0.319 Chirality : 0.045 0.273 979 Planarity : 0.004 0.042 1176 Dihedral : 4.359 17.554 866 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.57 % Allowed : 10.14 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.29), residues: 793 helix: 1.61 (0.26), residues: 397 sheet: 0.06 (0.66), residues: 53 loop : 0.37 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.015 0.002 TYR B 495 PHE 0.016 0.002 PHE E 400 TRP 0.010 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.31 ( 6735) covalent geometry : angle 0.62752 / 0.32 ( 9154) SS BOND : bond 0.00334 / 0.22 ( 6) SS BOND : angle 1.00551 / 0.61 ( 12) hydrogen bonds : bond 0.04533 / 2.97 ( 323) hydrogen bonds : angle 4.63686 / 3.25 ( 918) link_NAG-ASN : bond 0.00337 / 0.20 ( 7) link_NAG-ASN : angle 1.93358 / 1.46 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8917 (m-30) cc_final: 0.8476 (m-30) REVERT: E 140 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8823 (tm-30) REVERT: E 249 MET cc_start: 0.9331 (ttm) cc_final: 0.8982 (mtt) REVERT: E 256 ILE cc_start: 0.9065 (mp) cc_final: 0.8583 (mt) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.0697 time to fit residues: 5.3647 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 154 ASN E 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.047169 restraints weight = 21899.991| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.36 r_work: 0.2667 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6748 Z= 0.130 Angle : 0.517 10.938 9187 Z= 0.255 Chirality : 0.041 0.263 979 Planarity : 0.003 0.044 1176 Dihedral : 3.999 14.058 866 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.00 % Allowed : 10.71 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.30), residues: 793 helix: 1.82 (0.26), residues: 397 sheet: 0.43 (0.75), residues: 43 loop : 0.34 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.010 0.001 TYR B 495 PHE 0.011 0.001 PHE E 315 TRP 0.011 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6735) covalent geometry : angle 0.51062 / 0.25 ( 9154) SS BOND : bond 0.00241 / 0.15 ( 6) SS BOND : angle 0.72045 / 0.47 ( 12) hydrogen bonds : bond 0.03772 / 2.49 ( 323) hydrogen bonds : angle 4.39914 / 3.07 ( 918) link_NAG-ASN : bond 0.00245 / 0.15 ( 7) link_NAG-ASN : angle 1.72695 / 1.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8453 (ttmm) REVERT: B 405 ASP cc_start: 0.8968 (m-30) cc_final: 0.8535 (m-30) REVERT: E 140 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8791 (tm-30) REVERT: E 249 MET cc_start: 0.9239 (ttm) cc_final: 0.8940 (mtt) REVERT: E 256 ILE cc_start: 0.9003 (mp) cc_final: 0.8765 (mm) REVERT: E 474 MET cc_start: 0.9175 (mmp) cc_final: 0.8962 (mmp) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.0693 time to fit residues: 5.0652 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.045814 restraints weight = 22320.479| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.36 r_work: 0.2630 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6748 Z= 0.197 Angle : 0.557 10.675 9187 Z= 0.277 Chirality : 0.042 0.290 979 Planarity : 0.003 0.041 1176 Dihedral : 4.069 14.879 866 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.00 % Allowed : 11.14 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.30), residues: 793 helix: 1.79 (0.26), residues: 397 sheet: 0.48 (0.76), residues: 42 loop : 0.34 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.012 0.001 TYR E 515 PHE 0.011 0.001 PHE E 369 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 6735) covalent geometry : angle 0.55033 / 0.28 ( 9154) SS BOND : bond 0.00255 / 0.17 ( 6) SS BOND : angle 0.79101 / 0.49 ( 12) hydrogen bonds : bond 0.04046 / 2.66 ( 323) hydrogen bonds : angle 4.46640 / 3.13 ( 918) link_NAG-ASN : bond 0.00244 / 0.15 ( 7) link_NAG-ASN : angle 1.79319 / 1.32 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8497 (ttmm) REVERT: B 405 ASP cc_start: 0.8995 (m-30) cc_final: 0.8548 (m-30) REVERT: E 140 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8848 (tm-30) REVERT: E 249 MET cc_start: 0.9272 (ttm) cc_final: 0.8940 (mtt) REVERT: E 256 ILE cc_start: 0.9024 (mp) cc_final: 0.8770 (mm) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.0770 time to fit residues: 5.7268 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.062161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047433 restraints weight = 21842.523| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.35 r_work: 0.2678 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6748 Z= 0.123 Angle : 0.525 10.851 9187 Z= 0.256 Chirality : 0.041 0.302 979 Planarity : 0.003 0.040 1176 Dihedral : 3.889 13.940 866 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 11.43 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.30), residues: 793 helix: 2.00 (0.26), residues: 390 sheet: 0.38 (0.76), residues: 43 loop : 0.29 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.010 0.001 TYR B 495 PHE 0.010 0.001 PHE E 315 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6735) covalent geometry : angle 0.51871 / 0.25 ( 9154) SS BOND : bond 0.00241 / 0.15 ( 6) SS BOND : angle 0.73093 / 0.45 ( 12) hydrogen bonds : bond 0.03676 / 2.43 ( 323) hydrogen bonds : angle 4.35172 / 3.03 ( 918) link_NAG-ASN : bond 0.00242 / 0.14 ( 7) link_NAG-ASN : angle 1.72029 / 1.25 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 378 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8486 (ttmm) REVERT: B 405 ASP cc_start: 0.8992 (m-30) cc_final: 0.8551 (m-30) REVERT: E 140 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8822 (tm-30) REVERT: E 249 MET cc_start: 0.9221 (ttm) cc_final: 0.8916 (mtt) REVERT: E 256 ILE cc_start: 0.8984 (mp) cc_final: 0.8738 (mm) REVERT: E 332 MET cc_start: 0.8541 (tmm) cc_final: 0.8341 (tmm) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.0653 time to fit residues: 4.8239 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.0270 chunk 10 optimal weight: 2.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.063742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.049073 restraints weight = 21704.352| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.39 r_work: 0.2721 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6748 Z= 0.099 Angle : 0.505 11.042 9187 Z= 0.246 Chirality : 0.040 0.305 979 Planarity : 0.003 0.042 1176 Dihedral : 3.668 13.662 866 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.86 % Allowed : 11.43 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.30), residues: 793 helix: 1.98 (0.26), residues: 404 sheet: 0.78 (0.77), residues: 41 loop : 0.22 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.009 0.001 TYR B 495 PHE 0.009 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 6735) covalent geometry : angle 0.49946 / 0.25 ( 9154) SS BOND : bond 0.00211 / 0.13 ( 6) SS BOND : angle 0.60039 / 0.39 ( 12) hydrogen bonds : bond 0.03408 / 2.25 ( 323) hydrogen bonds : angle 4.21772 / 2.93 ( 918) link_NAG-ASN : bond 0.00260 / 0.15 ( 7) link_NAG-ASN : angle 1.65126 / 1.19 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1452.80 seconds wall clock time: 25 minutes 38.87 seconds (1538.87 seconds total)