Starting phenix.real_space_refine on Thu Jul 2 04:45:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sy4_25516/07_2026/7sy4_25516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy4_25516/07_2026/7sy4_25516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sy4_25516/07_2026/7sy4_25516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy4_25516/07_2026/7sy4_25516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sy4_25516/07_2026/7sy4_25516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy4_25516/07_2026/7sy4_25516.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sy4_25516/07_2026/7sy4_25516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sy4_25516/07_2026/7sy4_25516.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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 4192 2.51 5 N 1078 2.21 5 O 1247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 6554 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1594 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: 1.56, per 1000 atoms: 0.24 Number of scatterers: 6554 At special positions: 0 Unit cell: (82, 84, 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 1247 8.00 N 1078 7.00 C 4192 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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: 0.51 Conformation dependent library (CDL) restraints added in 371.1 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: 38 helices and 7 sheets defined 57.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.754A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.006A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.516A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.775A 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: 4.056A 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: 3.944A 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: 3.726A 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: 3.658A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.775A 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: 3.768A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.610A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.709A 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: 4.279A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.558A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.375A 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: 3.719A 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: 4.509A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.917A 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: 3.945A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.834A 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: 3.753A 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: 6.050A 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: 6.333A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 906 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: 0.88 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2079 1.35 - 1.47: 1776 1.47 - 1.59: 2824 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6737 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.27e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.09e+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 4.98e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 ... (remaining 6732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8787 1.96 - 3.93: 314 3.93 - 5.89: 42 5.89 - 7.85: 8 7.85 - 9.82: 4 Bond angle restraints: 9155 Sorted by residual: angle pdb=" N PHE E 32 " pdb=" CA PHE E 32 " pdb=" C PHE E 32 " ideal model delta sigma weight residual 111.04 103.72 7.32 1.55e+00 4.16e-01 2.23e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 128.97 -6.15 1.42e+00 4.96e-01 1.88e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.24 -8.84 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 120.23 -6.33 1.80e+00 3.09e-01 1.24e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 118.06 -4.90 1.42e+00 4.96e-01 1.19e+01 ... (remaining 9150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3557 17.13 - 34.26: 300 34.26 - 51.39: 44 51.39 - 68.52: 7 68.52 - 85.65: 12 Dihedral angle restraints: 3920 sinusoidal: 1581 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 -43.96 -42.04 1 1.00e+01 1.00e-02 2.47e+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 14.88 64.12 1 2.00e+01 2.50e-03 1.35e+01 dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 714 0.052 - 0.105: 197 0.105 - 0.157: 55 0.157 - 0.210: 10 0.210 - 0.262: 2 Chirality restraints: 978 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 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 103 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 975 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ARG E 169 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG E 169 " -0.021 2.00e-02 2.50e+03 pdb=" N SER E 170 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 29 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.46e+00 pdb=" C LEU E 29 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU E 29 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP E 30 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C ALA E 36 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA E 36 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 37 " -0.017 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 2205 2.86 - 3.37: 5969 3.37 - 3.88: 11213 3.88 - 4.39: 12524 4.39 - 4.90: 21658 Nonbonded interactions: 53569 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.345 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.352 3.120 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.364 3.040 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.369 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.369 3.120 ... (remaining 53564 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: 5.830 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: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.260 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.055 6750 Z= 0.228 Angle : 0.880 12.114 9188 Z= 0.469 Chirality : 0.055 0.262 978 Planarity : 0.007 0.063 1176 Dihedral : 13.471 85.655 2402 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -0.68 (0.26), residues: 793 helix: -0.29 (0.23), residues: 387 sheet: 0.99 (0.73), residues: 43 loop : -0.68 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 460 TYR 0.028 0.002 TYR B 495 PHE 0.030 0.002 PHE E 369 TRP 0.019 0.002 TRP E 165 HIS 0.005 0.001 HIS E 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 ( 6737) covalent geometry : angle 0.84592 / 0.46 ( 9155) SS BOND : bond 0.00517 / 0.30 ( 6) SS BOND : angle 2.62702 / 1.51 ( 12) hydrogen bonds : bond 0.13994 / 9.69 ( 319) hydrogen bonds : angle 6.06874 / 4.19 ( 906) link_NAG-ASN : bond 0.00762 / 0.35 ( 7) link_NAG-ASN : angle 4.81526 / 3.47 ( 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 108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 414 GLN cc_start: 0.9364 (mm-40) cc_final: 0.9059 (mm-40) REVERT: B 420 ASP cc_start: 0.9060 (m-30) cc_final: 0.8777 (m-30) REVERT: E 37 GLU cc_start: 0.8226 (tt0) cc_final: 0.7840 (tp30) REVERT: E 82 MET cc_start: 0.8690 (mtp) cc_final: 0.8253 (ttm) REVERT: E 323 MET cc_start: 0.9194 (mmp) cc_final: 0.8738 (mmm) REVERT: E 367 ASP cc_start: 0.9374 (m-30) cc_final: 0.9156 (p0) REVERT: E 368 ASP cc_start: 0.8701 (m-30) cc_final: 0.8037 (m-30) REVERT: E 409 SER cc_start: 0.9539 (t) cc_final: 0.9193 (p) REVERT: E 429 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8157 (tm-30) REVERT: E 435 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8766 (mm-30) REVERT: E 471 ASP cc_start: 0.8880 (p0) cc_final: 0.8603 (t0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1087 time to fit residues: 14.8058 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.061819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.045867 restraints weight = 22734.354| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.90 r_work: 0.2565 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6750 Z= 0.209 Angle : 0.616 6.809 9188 Z= 0.316 Chirality : 0.043 0.183 978 Planarity : 0.005 0.038 1176 Dihedral : 4.486 17.479 866 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.71 % Allowed : 8.29 % Favored : 91.00 % 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: 0.76 (0.28), residues: 793 helix: 1.13 (0.25), residues: 388 sheet: 0.80 (0.74), residues: 43 loop : -0.13 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 466 TYR 0.025 0.001 TYR E 50 PHE 0.016 0.001 PHE E 523 TRP 0.018 0.001 TRP E 165 HIS 0.003 0.001 HIS E 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 ( 6737) covalent geometry : angle 0.59461 / 0.31 ( 9155) SS BOND : bond 0.00415 / 0.23 ( 6) SS BOND : angle 2.27952 / 1.30 ( 12) hydrogen bonds : bond 0.04427 / 2.88 ( 319) hydrogen bonds : angle 4.56874 / 3.18 ( 906) link_NAG-ASN : bond 0.00323 / 0.17 ( 7) link_NAG-ASN : angle 2.99572 / 2.18 ( 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 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8623 (mt-10) REVERT: B 467 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8093 (p0) REVERT: B 498 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8749 (mm-40) REVERT: E 37 GLU cc_start: 0.8676 (tt0) cc_final: 0.8455 (tp30) REVERT: E 270 MET cc_start: 0.9210 (tpp) cc_final: 0.8815 (tpp) REVERT: E 323 MET cc_start: 0.9417 (mmp) cc_final: 0.9081 (mmm) REVERT: E 332 MET cc_start: 0.8912 (ptm) cc_final: 0.8656 (ttp) REVERT: E 360 MET cc_start: 0.8461 (tpt) cc_final: 0.8169 (tmm) REVERT: E 368 ASP cc_start: 0.9031 (m-30) cc_final: 0.8554 (t0) REVERT: E 429 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8039 (tm-30) REVERT: E 462 MET cc_start: 0.9601 (mtm) cc_final: 0.9236 (mtm) REVERT: E 471 ASP cc_start: 0.9055 (p0) cc_final: 0.8781 (t0) outliers start: 5 outliers final: 1 residues processed: 60 average time/residue: 0.0478 time to fit residues: 4.4687 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain E residue 447 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.061983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.046298 restraints weight = 22466.629| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.83 r_work: 0.2581 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6750 Z= 0.148 Angle : 0.528 5.863 9188 Z= 0.271 Chirality : 0.041 0.155 978 Planarity : 0.004 0.037 1176 Dihedral : 4.194 16.579 866 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.86 % Allowed : 8.86 % Favored : 90.29 % 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: 1.24 (0.29), residues: 793 helix: 1.69 (0.26), residues: 381 sheet: 0.48 (0.71), residues: 43 loop : 0.03 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 466 TYR 0.016 0.001 TYR E 50 PHE 0.016 0.001 PHE E 369 TRP 0.015 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6737) covalent geometry : angle 0.50953 / 0.27 ( 9155) SS BOND : bond 0.00420 / 0.21 ( 6) SS BOND : angle 2.11815 / 1.20 ( 12) hydrogen bonds : bond 0.04022 / 2.64 ( 319) hydrogen bonds : angle 4.31988 / 3.01 ( 906) link_NAG-ASN : bond 0.00317 / 0.16 ( 7) link_NAG-ASN : angle 2.47740 / 1.81 ( 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 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8794 (mt-10) REVERT: B 467 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8027 (p0) REVERT: B 498 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8844 (mm-40) REVERT: E 37 GLU cc_start: 0.8714 (tt0) cc_final: 0.8453 (tp30) REVERT: E 270 MET cc_start: 0.9080 (tpp) cc_final: 0.8520 (tpp) REVERT: E 323 MET cc_start: 0.9533 (mmp) cc_final: 0.9057 (mmm) REVERT: E 462 MET cc_start: 0.9627 (mtm) cc_final: 0.9187 (mtt) outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 0.0494 time to fit residues: 4.4668 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain E residue 447 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.061708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.045907 restraints weight = 22798.086| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.86 r_work: 0.2570 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6750 Z= 0.143 Angle : 0.501 5.462 9188 Z= 0.258 Chirality : 0.040 0.143 978 Planarity : 0.003 0.036 1176 Dihedral : 4.075 15.900 866 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.57 % Allowed : 10.57 % Favored : 88.86 % 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: 1.50 (0.29), residues: 793 helix: 1.83 (0.26), residues: 381 sheet: 0.30 (0.70), residues: 43 loop : 0.29 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.016 0.001 TYR E 50 PHE 0.012 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6737) covalent geometry : angle 0.48862 / 0.26 ( 9155) SS BOND : bond 0.00276 / 0.14 ( 6) SS BOND : angle 1.49419 / 0.85 ( 12) hydrogen bonds : bond 0.03862 / 2.52 ( 319) hydrogen bonds : angle 4.20300 / 2.94 ( 906) link_NAG-ASN : bond 0.00261 / 0.15 ( 7) link_NAG-ASN : angle 2.14535 / 1.55 ( 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 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8801 (mt-10) REVERT: B 467 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.7927 (p0) REVERT: E 37 GLU cc_start: 0.8734 (tt0) cc_final: 0.8483 (tp30) REVERT: E 270 MET cc_start: 0.8953 (tpp) cc_final: 0.8342 (tpp) REVERT: E 332 MET cc_start: 0.9029 (ttp) cc_final: 0.8399 (ppp) REVERT: E 360 MET cc_start: 0.8090 (tmm) cc_final: 0.7541 (tmm) REVERT: E 366 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8915 (ttm) REVERT: E 368 ASP cc_start: 0.9049 (m-30) cc_final: 0.8571 (t0) REVERT: E 462 MET cc_start: 0.9626 (mtm) cc_final: 0.9145 (mtt) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.0456 time to fit residues: 3.6529 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 15 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.061523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.045709 restraints weight = 22960.538| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.89 r_work: 0.2563 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6750 Z= 0.145 Angle : 0.497 5.432 9188 Z= 0.254 Chirality : 0.040 0.150 978 Planarity : 0.003 0.036 1176 Dihedral : 3.999 15.481 866 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.14 % Allowed : 9.86 % Favored : 89.00 % 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: 1.68 (0.30), residues: 793 helix: 1.97 (0.26), residues: 380 sheet: 0.23 (0.69), residues: 43 loop : 0.44 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.015 0.001 TYR E 50 PHE 0.013 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6737) covalent geometry : angle 0.48584 / 0.25 ( 9155) SS BOND : bond 0.00233 / 0.12 ( 6) SS BOND : angle 1.16598 / 0.68 ( 12) hydrogen bonds : bond 0.03814 / 2.48 ( 319) hydrogen bonds : angle 4.16843 / 2.92 ( 906) link_NAG-ASN : bond 0.00256 / 0.15 ( 7) link_NAG-ASN : angle 2.05047 / 1.45 ( 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.9179 (m-30) cc_final: 0.8954 (p0) REVERT: B 406 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8776 (mt-10) REVERT: B 467 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.7911 (p0) REVERT: B 498 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8840 (mm-40) REVERT: E 37 GLU cc_start: 0.8757 (tt0) cc_final: 0.8498 (tp30) REVERT: E 267 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9239 (mm) REVERT: E 270 MET cc_start: 0.8881 (tpp) cc_final: 0.8241 (tpp) REVERT: E 332 MET cc_start: 0.9101 (ttp) cc_final: 0.8301 (ppp) REVERT: E 366 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8975 (ttm) REVERT: E 368 ASP cc_start: 0.9012 (m-30) cc_final: 0.8433 (t0) REVERT: E 462 MET cc_start: 0.9630 (mtm) cc_final: 0.9167 (mtt) outliers start: 8 outliers final: 1 residues processed: 56 average time/residue: 0.0514 time to fit residues: 4.6424 Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.044856 restraints weight = 22956.072| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.79 r_work: 0.2536 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6750 Z= 0.184 Angle : 0.525 5.716 9188 Z= 0.268 Chirality : 0.041 0.160 978 Planarity : 0.003 0.035 1176 Dihedral : 4.071 16.293 866 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.14 % Allowed : 9.86 % Favored : 89.00 % 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: 1.73 (0.30), residues: 793 helix: 1.90 (0.26), residues: 391 sheet: 0.16 (0.69), residues: 43 loop : 0.56 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.016 0.001 TYR E 50 PHE 0.013 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 6737) covalent geometry : angle 0.51501 / 0.27 ( 9155) SS BOND : bond 0.00222 / 0.12 ( 6) SS BOND : angle 1.12805 / 0.68 ( 12) hydrogen bonds : bond 0.03990 / 2.59 ( 319) hydrogen bonds : angle 4.22399 / 2.95 ( 906) link_NAG-ASN : bond 0.00213 / 0.13 ( 7) link_NAG-ASN : angle 2.02823 / 1.43 ( 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8831 (mt-10) REVERT: B 442 ASP cc_start: 0.9047 (m-30) cc_final: 0.8775 (m-30) REVERT: B 467 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.7856 (p0) REVERT: B 498 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.8778 (mm-40) REVERT: B 518 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7213 (tt) REVERT: E 37 GLU cc_start: 0.8795 (tt0) cc_final: 0.8519 (tp30) REVERT: E 82 MET cc_start: 0.9335 (mtp) cc_final: 0.8875 (ttm) REVERT: E 270 MET cc_start: 0.8763 (tpp) cc_final: 0.8059 (tpp) REVERT: E 332 MET cc_start: 0.9187 (ttp) cc_final: 0.8426 (ppp) REVERT: E 366 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8993 (ttm) REVERT: E 368 ASP cc_start: 0.9051 (m-30) cc_final: 0.8458 (t0) REVERT: E 462 MET cc_start: 0.9626 (mtm) cc_final: 0.9107 (mtt) outliers start: 8 outliers final: 2 residues processed: 54 average time/residue: 0.0521 time to fit residues: 4.5299 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 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.061017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.045475 restraints weight = 22654.663| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.78 r_work: 0.2558 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6750 Z= 0.142 Angle : 0.497 5.953 9188 Z= 0.254 Chirality : 0.040 0.144 978 Planarity : 0.003 0.035 1176 Dihedral : 3.965 15.574 866 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.43 % Allowed : 10.14 % Favored : 88.43 % 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: 1.66 (0.30), residues: 793 helix: 1.89 (0.26), residues: 392 sheet: 0.14 (0.70), residues: 43 loop : 0.46 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.017 0.001 TYR E 50 PHE 0.012 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 0.00313 / 0.14 ( 6737) covalent geometry : angle 0.48779 / 0.25 ( 9155) SS BOND : bond 0.00204 / 0.11 ( 6) SS BOND : angle 1.01977 / 0.62 ( 12) hydrogen bonds : bond 0.03795 / 2.47 ( 319) hydrogen bonds : angle 4.14528 / 2.91 ( 906) link_NAG-ASN : bond 0.00236 / 0.13 ( 7) link_NAG-ASN : angle 1.96093 / 1.39 ( 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 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.9176 (m-30) cc_final: 0.8958 (p0) REVERT: B 406 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8799 (mt-10) REVERT: B 442 ASP cc_start: 0.9000 (m-30) cc_final: 0.8745 (m-30) REVERT: B 467 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.7897 (p0) REVERT: B 498 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.8837 (mm-40) REVERT: B 518 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7194 (tt) REVERT: E 23 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9177 (mp0) REVERT: E 37 GLU cc_start: 0.8770 (tt0) cc_final: 0.8516 (tp30) REVERT: E 82 MET cc_start: 0.9338 (mtp) cc_final: 0.8852 (ttm) REVERT: E 86 GLN cc_start: 0.9140 (pm20) cc_final: 0.8795 (pm20) REVERT: E 267 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9247 (mm) REVERT: E 270 MET cc_start: 0.8693 (tpp) cc_final: 0.7988 (tpp) REVERT: E 332 MET cc_start: 0.9148 (ttp) cc_final: 0.8396 (ppp) REVERT: E 360 MET cc_start: 0.8064 (tmm) cc_final: 0.7336 (tmm) REVERT: E 368 ASP cc_start: 0.9029 (m-30) cc_final: 0.8502 (t0) REVERT: E 462 MET cc_start: 0.9653 (mtm) cc_final: 0.9392 (mtm) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.0563 time to fit residues: 5.0527 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 : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.061301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.045732 restraints weight = 22716.804| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.81 r_work: 0.2566 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6750 Z= 0.135 Angle : 0.510 8.319 9188 Z= 0.259 Chirality : 0.041 0.141 978 Planarity : 0.003 0.035 1176 Dihedral : 3.932 15.080 866 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: 1.64 (0.30), residues: 793 helix: 1.86 (0.26), residues: 392 sheet: 0.12 (0.71), residues: 43 loop : 0.46 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.020 0.001 TYR E 50 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 0.00301 / 0.14 ( 6737) covalent geometry : angle 0.50146 / 0.26 ( 9155) SS BOND : bond 0.00194 / 0.10 ( 6) SS BOND : angle 1.04520 / 0.63 ( 12) hydrogen bonds : bond 0.03758 / 2.45 ( 319) hydrogen bonds : angle 4.15032 / 2.92 ( 906) link_NAG-ASN : bond 0.00219 / 0.13 ( 7) link_NAG-ASN : angle 1.94163 / 1.37 ( 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8787 (mt-10) REVERT: B 442 ASP cc_start: 0.8991 (m-30) cc_final: 0.8734 (m-30) REVERT: B 467 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.7910 (p0) REVERT: B 498 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8843 (mm-40) REVERT: B 518 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7206 (tt) REVERT: E 23 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9138 (mp0) REVERT: E 37 GLU cc_start: 0.8757 (tt0) cc_final: 0.8518 (tp30) REVERT: E 82 MET cc_start: 0.9340 (mtp) cc_final: 0.8870 (ttm) REVERT: E 86 GLN cc_start: 0.9141 (pm20) cc_final: 0.8795 (pm20) REVERT: E 267 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9247 (mm) REVERT: E 270 MET cc_start: 0.8653 (tpp) cc_final: 0.7957 (tpp) REVERT: E 332 MET cc_start: 0.9142 (ttp) cc_final: 0.8403 (ppp) REVERT: E 360 MET cc_start: 0.7975 (tmm) cc_final: 0.7052 (tmm) REVERT: E 368 ASP cc_start: 0.9008 (m-30) cc_final: 0.8691 (t0) outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 0.0533 time to fit residues: 4.7015 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.3404 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.060062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.044454 restraints weight = 23132.121| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.81 r_work: 0.2528 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6750 Z= 0.202 Angle : 0.589 16.439 9188 Z= 0.290 Chirality : 0.042 0.151 978 Planarity : 0.004 0.035 1176 Dihedral : 4.083 15.890 866 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.00 % Allowed : 11.71 % Favored : 87.29 % 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: 1.69 (0.30), residues: 793 helix: 1.83 (0.26), residues: 391 sheet: 0.04 (0.72), residues: 43 loop : 0.60 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 403 TYR 0.016 0.001 TYR E 50 PHE 0.012 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 0.00450 / 0.20 ( 6737) covalent geometry : angle 0.58106 / 0.29 ( 9155) SS BOND : bond 0.00189 / 0.10 ( 6) SS BOND : angle 1.06652 / 0.66 ( 12) hydrogen bonds : bond 0.04079 / 2.64 ( 319) hydrogen bonds : angle 4.31900 / 3.05 ( 906) link_NAG-ASN : bond 0.00215 / 0.13 ( 7) link_NAG-ASN : angle 2.03514 / 1.43 ( 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 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8864 (mt-10) REVERT: B 442 ASP cc_start: 0.9013 (m-30) cc_final: 0.8756 (m-30) REVERT: B 467 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.7795 (p0) REVERT: B 498 GLN cc_start: 0.9413 (OUTLIER) cc_final: 0.8782 (mm-40) REVERT: B 518 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7292 (tt) REVERT: E 23 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9182 (mp0) REVERT: E 37 GLU cc_start: 0.8810 (tt0) cc_final: 0.8521 (tp30) REVERT: E 82 MET cc_start: 0.9324 (mtp) cc_final: 0.8882 (ttm) REVERT: E 267 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9299 (mm) REVERT: E 270 MET cc_start: 0.8647 (tpp) cc_final: 0.7920 (tpp) REVERT: E 332 MET cc_start: 0.9216 (ttp) cc_final: 0.8503 (ppp) REVERT: E 360 MET cc_start: 0.8047 (tmm) cc_final: 0.7103 (tmm) REVERT: E 368 ASP cc_start: 0.9029 (m-30) cc_final: 0.8708 (t0) REVERT: E 462 MET cc_start: 0.9593 (mtm) cc_final: 0.9347 (mtm) REVERT: E 480 MET cc_start: 0.9233 (mtp) cc_final: 0.8960 (mtp) REVERT: E 613 TYR cc_start: 0.8633 (t80) cc_final: 0.8250 (t80) outliers start: 7 outliers final: 1 residues processed: 54 average time/residue: 0.0550 time to fit residues: 4.7004 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3152 r_free = 0.3152 target = 0.061348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.045716 restraints weight = 22550.961| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.82 r_work: 0.2595 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6750 Z= 0.128 Angle : 0.551 15.523 9188 Z= 0.269 Chirality : 0.041 0.138 978 Planarity : 0.003 0.034 1176 Dihedral : 3.952 15.032 866 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.86 % Allowed : 12.29 % Favored : 86.86 % 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: 1.64 (0.30), residues: 793 helix: 1.86 (0.26), residues: 389 sheet: -0.24 (0.70), residues: 45 loop : 0.55 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.018 0.001 TYR E 50 PHE 0.011 0.001 PHE E 369 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 0.00284 / 0.13 ( 6737) covalent geometry : angle 0.54196 / 0.27 ( 9155) SS BOND : bond 0.00178 / 0.09 ( 6) SS BOND : angle 0.98069 / 0.61 ( 12) hydrogen bonds : bond 0.03747 / 2.44 ( 319) hydrogen bonds : angle 4.25182 / 3.01 ( 906) link_NAG-ASN : bond 0.00230 / 0.13 ( 7) link_NAG-ASN : angle 2.01138 / 1.42 ( 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8776 (mt-10) REVERT: B 442 ASP cc_start: 0.9006 (m-30) cc_final: 0.8787 (m-30) REVERT: B 467 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.7908 (p0) REVERT: B 498 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.8876 (mm-40) REVERT: B 518 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7300 (tt) REVERT: E 23 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9148 (mp0) REVERT: E 37 GLU cc_start: 0.8726 (tt0) cc_final: 0.8524 (tp30) REVERT: E 82 MET cc_start: 0.9301 (mtp) cc_final: 0.8864 (ttm) REVERT: E 86 GLN cc_start: 0.9134 (pm20) cc_final: 0.8798 (pm20) REVERT: E 267 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9299 (mm) REVERT: E 270 MET cc_start: 0.8640 (tpp) cc_final: 0.7954 (tpp) REVERT: E 332 MET cc_start: 0.9086 (ttp) cc_final: 0.8397 (ppp) REVERT: E 360 MET cc_start: 0.7899 (tmm) cc_final: 0.6933 (tmm) REVERT: E 368 ASP cc_start: 0.8859 (m-30) cc_final: 0.8471 (t0) REVERT: E 462 MET cc_start: 0.9586 (mtm) cc_final: 0.9342 (mtm) REVERT: E 480 MET cc_start: 0.9221 (mtp) cc_final: 0.8964 (mtp) REVERT: E 613 TYR cc_start: 0.8619 (t80) cc_final: 0.8189 (t80) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.0500 time to fit residues: 4.4429 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 : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 0.0970 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.061938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.046277 restraints weight = 22686.588| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.85 r_work: 0.2607 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6750 Z= 0.115 Angle : 0.541 15.435 9188 Z= 0.262 Chirality : 0.040 0.135 978 Planarity : 0.003 0.034 1176 Dihedral : 3.857 14.481 866 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.00 % Allowed : 11.71 % Favored : 87.29 % 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: 1.68 (0.30), residues: 793 helix: 1.89 (0.26), residues: 389 sheet: -0.21 (0.69), residues: 45 loop : 0.57 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.019 0.001 TYR E 50 PHE 0.011 0.001 PHE E 369 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 0.00252 / 0.11 ( 6737) covalent geometry : angle 0.53210 / 0.26 ( 9155) SS BOND : bond 0.00155 / 0.08 ( 6) SS BOND : angle 0.93050 / 0.57 ( 12) hydrogen bonds : bond 0.03598 / 2.35 ( 319) hydrogen bonds : angle 4.19613 / 2.97 ( 906) link_NAG-ASN : bond 0.00238 / 0.13 ( 7) link_NAG-ASN : angle 2.03988 / 1.44 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.46 seconds wall clock time: 26 minutes 2.59 seconds (1562.59 seconds total)