Starting phenix.real_space_refine on Tue Feb 3 20:03:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy2_25514/02_2026/7sy2_25514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy2_25514/02_2026/7sy2_25514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy2_25514/02_2026/7sy2_25514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy2_25514/02_2026/7sy2_25514.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy2_25514/02_2026/7sy2_25514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy2_25514/02_2026/7sy2_25514.cif" } resolution = 3.11 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= 0.032 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 4191 2.51 5 N 1077 2.21 5 O 1249 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-2.0-5952/lib/python3.9/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 dihedrals: 3 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.59, per 1000 atoms: 0.24 Number of scatterers: 6554 At special positions: 0 Unit cell: (80, 83, 122, 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 1249 8.00 N 1077 7.00 C 4191 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=2.03 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=2.02 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: 0.59 Conformation dependent library (CDL) restraints added in 167.9 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 57.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 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 removed outlier: 3.502A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.745A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.792A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.751A 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: 3.994A 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: 3.967A 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: 3.710A 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: 3.659A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.754A 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: 3.801A 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: 3.583A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.685A 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: 4.298A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.519A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.358A 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: 3.734A 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: 4.434A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.902A 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: 3.981A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.835A 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: 3.690A 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: 6.005A 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: 6.335A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.76 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: 2083 1.35 - 1.47: 1794 1.47 - 1.60: 2802 1.60 - 1.72: 0 1.72 - 1.85: 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 1.455 -0.049 2.00e-02 2.50e+03 6.07e+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 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 6732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 8815 2.03 - 4.05: 295 4.05 - 6.08: 35 6.08 - 8.10: 7 8.10 - 10.13: 4 Bond angle restraints: 9156 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 122.82 128.95 -6.13 1.42e+00 4.96e-01 1.86e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.57 -9.17 2.30e+00 1.89e-01 1.59e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CB MET E 323 " pdb=" CG MET E 323 " pdb=" SD MET E 323 " ideal model delta sigma weight residual 112.70 122.83 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" C TYR B 495 " ideal model delta sigma weight residual 110.52 105.59 4.93 1.48e+00 4.57e-01 1.11e+01 ... (remaining 9151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3687 17.13 - 34.25: 306 34.25 - 51.38: 48 51.38 - 68.51: 13 68.51 - 85.63: 12 Dihedral angle restraints: 4066 sinusoidal: 1727 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 -43.43 -42.57 1 1.00e+01 1.00e-02 2.53e+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 16.60 62.40 1 2.00e+01 2.50e-03 1.29e+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 -130.73 8.13 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 4063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 713 0.053 - 0.107: 200 0.107 - 0.160: 55 0.160 - 0.213: 8 0.213 - 0.267: 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 2.24 0.27 2.00e-01 2.50e+01 1.78e+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 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN E 437 " pdb=" N ASN E 437 " pdb=" C ASN E 437 " pdb=" CB ASN E 437 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 975 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ARG E 169 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.022 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 168 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C TRP E 168 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP E 168 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG E 169 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 41 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C TYR E 41 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR E 41 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN E 42 " -0.015 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1934 2.83 - 3.34: 5949 3.34 - 3.86: 11371 3.86 - 4.38: 12856 4.38 - 4.90: 22341 Nonbonded interactions: 54451 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.307 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.349 3.120 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.354 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.355 3.120 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.356 3.040 ... (remaining 54446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.280 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.300 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.059 6750 Z= 0.233 Angle : 0.877 12.470 9189 Z= 0.467 Chirality : 0.055 0.267 978 Planarity : 0.007 0.065 1177 Dihedral : 13.461 85.634 2548 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.14 % Allowed : 1.86 % Favored : 98.00 % 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: -0.46 (0.26), residues: 793 helix: -0.05 (0.23), residues: 385 sheet: 0.55 (0.66), residues: 53 loop : -0.59 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 460 TYR 0.029 0.002 TYR E 385 PHE 0.031 0.002 PHE E 369 TRP 0.022 0.002 TRP E 566 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 6737) covalent geometry : angle 0.84419 ( 9156) SS BOND : bond 0.00521 ( 6) SS BOND : angle 2.66283 ( 12) hydrogen bonds : bond 0.13584 ( 321) hydrogen bonds : angle 6.21421 ( 915) link_NAG-ASN : bond 0.00875 ( 7) link_NAG-ASN : angle 4.67517 ( 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 96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8467 (m-30) cc_final: 0.8197 (m-30) REVERT: E 290 ASN cc_start: 0.8480 (t0) cc_final: 0.7702 (t0) REVERT: E 408 MET cc_start: 0.9425 (mmt) cc_final: 0.9219 (mmt) REVERT: E 474 MET cc_start: 0.8855 (mmt) cc_final: 0.8342 (mmm) REVERT: E 498 CYS cc_start: 0.7597 (t) cc_final: 0.6794 (t) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1238 time to fit residues: 14.2797 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 : 0.270 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN E 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.049296 restraints weight = 21581.060| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.57 r_work: 0.2730 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6750 Z= 0.162 Angle : 0.579 9.512 9189 Z= 0.295 Chirality : 0.041 0.148 978 Planarity : 0.004 0.040 1177 Dihedral : 5.667 51.055 1013 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 0.73 (0.28), residues: 793 helix: 1.07 (0.25), residues: 404 sheet: 0.54 (0.68), residues: 51 loop : -0.12 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 306 TYR 0.012 0.001 TYR E 385 PHE 0.018 0.001 PHE E 369 TRP 0.017 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6737) covalent geometry : angle 0.55559 ( 9156) SS BOND : bond 0.00446 ( 6) SS BOND : angle 2.18822 ( 12) hydrogen bonds : bond 0.04454 ( 321) hydrogen bonds : angle 4.66473 ( 915) link_NAG-ASN : bond 0.00515 ( 7) link_NAG-ASN : angle 3.05607 ( 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8964 (m-30) cc_final: 0.8683 (m-30) REVERT: B 406 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8935 (mt-10) REVERT: B 498 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.9053 (mt0) REVERT: E 498 CYS cc_start: 0.8133 (t) cc_final: 0.7526 (t) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.0773 time to fit residues: 5.6525 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.0060 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 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 = 0.063306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.049225 restraints weight = 21152.394| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.41 r_work: 0.2735 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2186 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= 0.139 Angle : 0.531 7.797 9189 Z= 0.268 Chirality : 0.040 0.144 978 Planarity : 0.004 0.033 1177 Dihedral : 5.242 53.233 1013 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.29 % Allowed : 7.43 % Favored : 91.29 % 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: 1.25 (0.29), residues: 793 helix: 1.53 (0.25), residues: 398 sheet: 0.79 (0.75), residues: 42 loop : 0.12 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.013 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6737) covalent geometry : angle 0.51506 ( 9156) SS BOND : bond 0.00243 ( 6) SS BOND : angle 1.29635 ( 12) hydrogen bonds : bond 0.04154 ( 321) hydrogen bonds : angle 4.43984 ( 915) link_NAG-ASN : bond 0.00441 ( 7) link_NAG-ASN : angle 2.58267 ( 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 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8918 (m-30) cc_final: 0.8632 (m-30) REVERT: B 406 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8878 (mt-10) REVERT: E 55 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (p) REVERT: E 270 MET cc_start: 0.8968 (tpp) cc_final: 0.8737 (tpp) REVERT: E 376 MET cc_start: 0.9084 (ttm) cc_final: 0.8876 (tpp) REVERT: E 498 CYS cc_start: 0.8076 (t) cc_final: 0.7347 (t) outliers start: 9 outliers final: 2 residues processed: 60 average time/residue: 0.0900 time to fit residues: 7.3490 Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 0.0670 chunk 51 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.064409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049786 restraints weight = 21454.182| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.56 r_work: 0.2743 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6750 Z= 0.110 Angle : 0.483 5.803 9189 Z= 0.246 Chirality : 0.039 0.134 978 Planarity : 0.003 0.035 1177 Dihedral : 4.851 54.469 1013 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.14 % Allowed : 8.86 % Favored : 90.00 % 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: 1.43 (0.29), residues: 793 helix: 1.66 (0.26), residues: 398 sheet: 0.68 (0.74), residues: 42 loop : 0.27 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.010 0.001 TYR E 385 PHE 0.013 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6737) covalent geometry : angle 0.47080 ( 9156) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.85204 ( 12) hydrogen bonds : bond 0.03833 ( 321) hydrogen bonds : angle 4.35882 ( 915) link_NAG-ASN : bond 0.00363 ( 7) link_NAG-ASN : angle 2.28705 ( 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 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8933 (m-30) cc_final: 0.8632 (m-30) REVERT: B 406 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8876 (mt-10) REVERT: E 55 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8048 (p) REVERT: E 249 MET cc_start: 0.8803 (ttp) cc_final: 0.8506 (ttp) REVERT: E 325 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8262 (tp-100) REVERT: E 498 CYS cc_start: 0.8063 (t) cc_final: 0.7321 (t) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.0688 time to fit residues: 5.4605 Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.0030 chunk 15 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3231 r_free = 0.3231 target = 0.063520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.049478 restraints weight = 21511.777| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.41 r_work: 0.2744 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2575 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= 0.115 Angle : 0.482 6.350 9189 Z= 0.246 Chirality : 0.040 0.145 978 Planarity : 0.003 0.039 1177 Dihedral : 4.676 55.222 1013 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.43 % Allowed : 9.71 % 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: 1.51 (0.29), residues: 793 helix: 1.64 (0.25), residues: 407 sheet: 0.59 (0.74), residues: 42 loop : 0.41 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.010 0.001 TYR E 385 PHE 0.014 0.001 PHE E 523 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6737) covalent geometry : angle 0.47129 ( 9156) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.75575 ( 12) hydrogen bonds : bond 0.03811 ( 321) hydrogen bonds : angle 4.33855 ( 915) link_NAG-ASN : bond 0.00324 ( 7) link_NAG-ASN : angle 2.09803 ( 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: 10 poor density : 48 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8937 (m-30) cc_final: 0.8632 (m-30) REVERT: B 406 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8859 (mt-10) REVERT: E 55 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8065 (p) REVERT: E 131 LYS cc_start: 0.8987 (ptmm) cc_final: 0.8713 (ttpp) REVERT: E 249 MET cc_start: 0.8847 (ttp) cc_final: 0.8474 (ttp) REVERT: E 325 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8247 (tp-100) REVERT: E 498 CYS cc_start: 0.8123 (t) cc_final: 0.7450 (t) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.0872 time to fit residues: 6.8981 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.048650 restraints weight = 21693.033| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.55 r_work: 0.2715 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2749 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= 0.135 Angle : 0.498 7.396 9189 Z= 0.255 Chirality : 0.040 0.133 978 Planarity : 0.003 0.040 1177 Dihedral : 4.643 55.776 1013 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 11.14 % Favored : 88.00 % 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: 1.55 (0.29), residues: 793 helix: 1.67 (0.25), residues: 406 sheet: 0.54 (0.74), residues: 42 loop : 0.46 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.010 0.001 TYR E 385 PHE 0.015 0.001 PHE E 523 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6737) covalent geometry : angle 0.48893 ( 9156) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.77471 ( 12) hydrogen bonds : bond 0.03914 ( 321) hydrogen bonds : angle 4.38902 ( 915) link_NAG-ASN : bond 0.00297 ( 7) link_NAG-ASN : angle 2.00829 ( 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 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8960 (m-30) cc_final: 0.8652 (m-30) REVERT: B 406 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8918 (mt-10) REVERT: E 55 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8041 (p) REVERT: E 325 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8217 (tp-100) REVERT: E 360 MET cc_start: 0.8905 (ttm) cc_final: 0.8663 (ttm) REVERT: E 376 MET cc_start: 0.9127 (tpp) cc_final: 0.8920 (tpp) REVERT: E 474 MET cc_start: 0.8850 (mmt) cc_final: 0.8332 (mmm) REVERT: E 480 MET cc_start: 0.9107 (mtm) cc_final: 0.8841 (ptp) REVERT: E 498 CYS cc_start: 0.7963 (t) cc_final: 0.6753 (t) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.0799 time to fit residues: 5.5208 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE 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: 0.8980 chunk 19 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 0.0370 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 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 = 0.3223 r_free = 0.3223 target = 0.062975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048910 restraints weight = 21180.911| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.39 r_work: 0.2727 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6750 Z= 0.124 Angle : 0.485 6.792 9189 Z= 0.250 Chirality : 0.040 0.130 978 Planarity : 0.003 0.043 1177 Dihedral : 4.549 56.263 1013 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.14 % Allowed : 11.86 % Favored : 87.00 % 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: 1.64 (0.29), residues: 793 helix: 1.71 (0.25), residues: 406 sheet: 0.52 (0.74), residues: 42 loop : 0.54 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.009 0.001 TYR E 516 PHE 0.014 0.001 PHE E 523 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6737) covalent geometry : angle 0.47639 ( 9156) SS BOND : bond 0.00191 ( 6) SS BOND : angle 0.76056 ( 12) hydrogen bonds : bond 0.03806 ( 321) hydrogen bonds : angle 4.37994 ( 915) link_NAG-ASN : bond 0.00281 ( 7) link_NAG-ASN : angle 1.94363 ( 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 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8943 (m-30) cc_final: 0.8633 (m-30) REVERT: B 406 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8909 (mt-10) REVERT: E 55 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.8038 (p) REVERT: E 325 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8203 (tp-100) REVERT: E 360 MET cc_start: 0.8909 (ttm) cc_final: 0.8574 (ttm) REVERT: E 480 MET cc_start: 0.9088 (mtm) cc_final: 0.8790 (ptp) REVERT: E 498 CYS cc_start: 0.7983 (t) cc_final: 0.6975 (t) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.0749 time to fit residues: 5.0973 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET 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: 0.4980 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 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 = 0.3211 r_free = 0.3211 target = 0.062674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.048547 restraints weight = 21334.055| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.38 r_work: 0.2723 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2936 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= 0.125 Angle : 0.484 6.753 9189 Z= 0.249 Chirality : 0.040 0.129 978 Planarity : 0.003 0.043 1177 Dihedral : 4.513 56.451 1013 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.43 % Allowed : 12.14 % Favored : 86.43 % 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: 1.67 (0.30), residues: 793 helix: 1.73 (0.26), residues: 406 sheet: 0.46 (0.75), residues: 42 loop : 0.59 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.010 0.001 TYR E 385 PHE 0.015 0.001 PHE E 523 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6737) covalent geometry : angle 0.47586 ( 9156) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.76717 ( 12) hydrogen bonds : bond 0.03813 ( 321) hydrogen bonds : angle 4.36447 ( 915) link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 1.90928 ( 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8948 (m-30) cc_final: 0.8634 (m-30) REVERT: B 406 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8875 (mt-10) REVERT: B 518 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7569 (tt) REVERT: E 55 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8062 (p) REVERT: E 325 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8178 (tp-100) REVERT: E 360 MET cc_start: 0.8882 (ttm) cc_final: 0.8623 (ttm) REVERT: E 480 MET cc_start: 0.9056 (mtm) cc_final: 0.8848 (ptp) REVERT: E 497 TYR cc_start: 0.8721 (m-80) cc_final: 0.8166 (m-80) REVERT: E 498 CYS cc_start: 0.8028 (t) cc_final: 0.7167 (t) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.0791 time to fit residues: 5.8538 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET 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: 0.9990 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 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 = 0.3213 r_free = 0.3213 target = 0.062787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.048736 restraints weight = 21418.056| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.39 r_work: 0.2728 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2997 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= 0.121 Angle : 0.482 6.523 9189 Z= 0.249 Chirality : 0.040 0.127 978 Planarity : 0.003 0.043 1177 Dihedral : 4.472 56.669 1013 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.14 % Allowed : 12.71 % Favored : 86.14 % 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: 1.71 (0.30), residues: 793 helix: 1.76 (0.26), residues: 406 sheet: 0.45 (0.75), residues: 42 loop : 0.62 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.010 0.001 TYR E 385 PHE 0.014 0.001 PHE E 523 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6737) covalent geometry : angle 0.47329 ( 9156) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.77421 ( 12) hydrogen bonds : bond 0.03780 ( 321) hydrogen bonds : angle 4.35944 ( 915) link_NAG-ASN : bond 0.00267 ( 7) link_NAG-ASN : angle 1.89037 ( 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: 8 poor density : 46 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8937 (m-30) cc_final: 0.8666 (m-30) REVERT: B 406 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8892 (mt-10) REVERT: B 518 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7525 (tt) REVERT: E 55 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.8026 (p) REVERT: E 325 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8174 (tp-100) REVERT: E 497 TYR cc_start: 0.8723 (m-80) cc_final: 0.8164 (m-80) REVERT: E 498 CYS cc_start: 0.8039 (t) cc_final: 0.7193 (t) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.0771 time to fit residues: 5.5683 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.0030 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 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 = 0.3225 r_free = 0.3225 target = 0.063512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.048785 restraints weight = 21186.618| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.54 r_work: 0.2716 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3072 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= 0.126 Angle : 0.498 6.939 9189 Z= 0.258 Chirality : 0.040 0.128 978 Planarity : 0.003 0.042 1177 Dihedral : 4.469 56.687 1013 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.14 % Allowed : 13.43 % Favored : 85.43 % 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: 1.67 (0.30), residues: 793 helix: 1.70 (0.25), residues: 407 sheet: 0.41 (0.75), residues: 42 loop : 0.65 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.010 0.001 TYR E 385 PHE 0.015 0.001 PHE E 523 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6737) covalent geometry : angle 0.48952 ( 9156) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.76480 ( 12) hydrogen bonds : bond 0.03792 ( 321) hydrogen bonds : angle 4.38680 ( 915) link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 1.89185 ( 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 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8952 (m-30) cc_final: 0.8687 (m-30) REVERT: B 406 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8904 (mt-10) REVERT: B 518 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7470 (tt) REVERT: E 55 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8010 (p) REVERT: E 325 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8170 (tp-100) REVERT: E 360 MET cc_start: 0.8859 (ttm) cc_final: 0.8590 (ttm) REVERT: E 497 TYR cc_start: 0.8726 (m-80) cc_final: 0.8171 (m-80) REVERT: E 498 CYS cc_start: 0.8013 (t) cc_final: 0.7162 (t) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.0671 time to fit residues: 4.5082 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 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 = 0.3198 r_free = 0.3198 target = 0.062283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.048120 restraints weight = 21256.421| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.40 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: 0.8630 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6750 Z= 0.141 Angle : 0.508 6.612 9189 Z= 0.262 Chirality : 0.040 0.130 978 Planarity : 0.003 0.044 1177 Dihedral : 4.504 56.623 1013 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.00 % Allowed : 13.57 % Favored : 85.43 % 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: 1.67 (0.30), residues: 793 helix: 1.67 (0.25), residues: 407 sheet: 0.39 (0.75), residues: 42 loop : 0.67 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.012 0.001 TYR E 385 PHE 0.015 0.001 PHE E 523 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6737) covalent geometry : angle 0.50018 ( 9156) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.76970 ( 12) hydrogen bonds : bond 0.03872 ( 321) hydrogen bonds : angle 4.41543 ( 915) link_NAG-ASN : bond 0.00272 ( 7) link_NAG-ASN : angle 1.90803 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1476.34 seconds wall clock time: 26 minutes 4.16 seconds (1564.16 seconds total)