Starting phenix.real_space_refine on Tue Mar 3 15:45:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy4_25516/03_2026/7sy4_25516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy4_25516/03_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_25516/03_2026/7sy4_25516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy4_25516/03_2026/7sy4_25516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sy4_25516/03_2026/7sy4_25516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy4_25516/03_2026/7sy4_25516.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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: 1.54, per 1000 atoms: 0.23 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: 0.67 Conformation dependent library (CDL) restraints added in 168.7 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: 0.17 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: 1.01 Time building geometry restraints manager: 0.81 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: 3689 17.13 - 34.26: 312 34.26 - 51.39: 45 51.39 - 68.52: 9 68.52 - 85.65: 12 Dihedral angle restraints: 4067 sinusoidal: 1728 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 4064 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: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.650 Find NCS groups from input model: 0.040 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- 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 0.055 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 : 13.360 85.655 2549 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 covalent geometry : bond 0.00480 ( 6737) covalent geometry : angle 0.84592 ( 9155) SS BOND : bond 0.00517 ( 6) SS BOND : angle 2.62702 ( 12) hydrogen bonds : bond 0.13994 ( 319) hydrogen bonds : angle 6.06874 ( 906) link_NAG-ASN : bond 0.00762 ( 7) link_NAG-ASN : angle 4.81526 ( 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 : 0.328 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: 0.1136 time to fit residues: 15.1855 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 : 0.144 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.046175 restraints weight = 22686.069| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.88 r_work: 0.2569 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2024 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= 0.207 Angle : 0.616 6.921 9188 Z= 0.316 Chirality : 0.043 0.188 978 Planarity : 0.005 0.037 1176 Dihedral : 5.380 50.789 1013 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.86 % Allowed : 8.14 % 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: 0.77 (0.28), residues: 793 helix: 1.15 (0.25), residues: 386 sheet: 0.79 (0.74), residues: 43 loop : -0.12 (0.32), residues: 364 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 0.015 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 covalent geometry : bond 0.00454 ( 6737) covalent geometry : angle 0.59292 ( 9155) SS BOND : bond 0.00376 ( 6) SS BOND : angle 2.25428 ( 12) hydrogen bonds : bond 0.04468 ( 319) hydrogen bonds : angle 4.58228 ( 906) link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 3.12377 ( 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8637 (mt-10) REVERT: B 467 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8084 (p0) REVERT: B 498 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8757 (mm-40) REVERT: E 37 GLU cc_start: 0.8664 (tt0) cc_final: 0.8455 (tp30) REVERT: E 270 MET cc_start: 0.9216 (tpp) cc_final: 0.8816 (tpp) REVERT: E 323 MET cc_start: 0.9418 (mmp) cc_final: 0.9089 (mmm) REVERT: E 332 MET cc_start: 0.8938 (ptm) cc_final: 0.8688 (ttp) REVERT: E 429 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8028 (tm-30) REVERT: E 462 MET cc_start: 0.9594 (mtm) cc_final: 0.9224 (mtm) REVERT: E 471 ASP cc_start: 0.9053 (p0) cc_final: 0.8772 (t0) outliers start: 6 outliers final: 1 residues processed: 61 average time/residue: 0.0456 time to fit residues: 4.2435 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 : 0.186 ------------------------------------------------------------------------------- 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: 0.7980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046223 restraints weight = 22543.563| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.85 r_work: 0.2581 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2381 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 : 0.530 5.893 9188 Z= 0.271 Chirality : 0.041 0.155 978 Planarity : 0.004 0.037 1176 Dihedral : 4.988 52.671 1013 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 9.00 % Favored : 90.14 % 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: 1.23 (0.29), residues: 793 helix: 1.59 (0.26), residues: 388 sheet: 0.45 (0.71), residues: 43 loop : 0.10 (0.32), residues: 362 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 0.013 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 covalent geometry : bond 0.00324 ( 6737) covalent geometry : angle 0.51084 ( 9155) SS BOND : bond 0.00423 ( 6) SS BOND : angle 2.12600 ( 12) hydrogen bonds : bond 0.04036 ( 319) hydrogen bonds : angle 4.33463 ( 906) link_NAG-ASN : bond 0.00322 ( 7) link_NAG-ASN : angle 2.59029 ( 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 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8799 (mt-10) REVERT: B 467 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8028 (p0) REVERT: B 498 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8848 (mm-40) REVERT: E 37 GLU cc_start: 0.8707 (tt0) cc_final: 0.8457 (tp30) REVERT: E 270 MET cc_start: 0.9079 (tpp) cc_final: 0.8523 (tpp) REVERT: E 323 MET cc_start: 0.9541 (mmp) cc_final: 0.9073 (mmm) REVERT: E 360 MET cc_start: 0.8124 (tmm) cc_final: 0.7683 (tmm) REVERT: E 368 ASP cc_start: 0.9076 (m-30) cc_final: 0.8548 (t0) REVERT: E 462 MET cc_start: 0.9627 (mtm) cc_final: 0.9195 (mtt) outliers start: 6 outliers final: 1 residues processed: 58 average time/residue: 0.0503 time to fit residues: 4.7361 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 : 0.234 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 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: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.062383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.046693 restraints weight = 22690.855| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.86 r_work: 0.2623 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2619 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= 0.119 Angle : 0.486 5.403 9188 Z= 0.250 Chirality : 0.040 0.140 978 Planarity : 0.003 0.037 1176 Dihedral : 4.766 54.218 1013 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.29 % Allowed : 10.57 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.29), residues: 793 helix: 1.86 (0.26), residues: 380 sheet: 0.35 (0.72), residues: 43 loop : 0.25 (0.32), 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 covalent geometry : bond 0.00259 ( 6737) covalent geometry : angle 0.47157 ( 9155) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.46614 ( 12) hydrogen bonds : bond 0.03713 ( 319) hydrogen bonds : angle 4.17996 ( 906) link_NAG-ASN : bond 0.00278 ( 7) link_NAG-ASN : angle 2.25407 ( 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 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8796 (mt-10) REVERT: B 467 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.7987 (p0) REVERT: E 270 MET cc_start: 0.8982 (tpp) cc_final: 0.8394 (tpp) REVERT: E 332 MET cc_start: 0.8968 (ttp) cc_final: 0.8382 (ppp) REVERT: E 360 MET cc_start: 0.7919 (tmm) cc_final: 0.6762 (tmm) REVERT: E 368 ASP cc_start: 0.9084 (m-30) cc_final: 0.8471 (t0) REVERT: E 462 MET cc_start: 0.9631 (mtm) cc_final: 0.9161 (mtt) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.0516 time to fit residues: 4.1673 Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain E residue 447 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.0030 chunk 15 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 overall best weight: 0.5528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.046818 restraints weight = 22844.804| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.88 r_work: 0.2628 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6750 Z= 0.110 Angle : 0.475 5.365 9188 Z= 0.243 Chirality : 0.040 0.141 978 Planarity : 0.003 0.035 1176 Dihedral : 4.599 55.119 1013 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.71 % Allowed : 10.00 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.30), residues: 793 helix: 1.96 (0.26), residues: 386 sheet: 0.31 (0.71), residues: 43 loop : 0.37 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.015 0.001 TYR E 50 PHE 0.012 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 covalent geometry : bond 0.00240 ( 6737) covalent geometry : angle 0.46378 ( 9155) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.10461 ( 12) hydrogen bonds : bond 0.03589 ( 319) hydrogen bonds : angle 4.11481 ( 906) link_NAG-ASN : bond 0.00258 ( 7) link_NAG-ASN : angle 2.10700 ( 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 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.9179 (m-30) cc_final: 0.8972 (p0) REVERT: B 406 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8718 (mt-10) REVERT: B 467 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7976 (p0) REVERT: B 498 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8893 (mm-40) REVERT: E 267 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9252 (mm) REVERT: E 270 MET cc_start: 0.8897 (tpp) cc_final: 0.8299 (tpp) REVERT: E 332 MET cc_start: 0.8991 (ttp) cc_final: 0.8425 (ppp) REVERT: E 360 MET cc_start: 0.7890 (tmm) cc_final: 0.6784 (tmm) REVERT: E 368 ASP cc_start: 0.9035 (m-30) cc_final: 0.8448 (t0) REVERT: E 462 MET cc_start: 0.9621 (mtm) cc_final: 0.9403 (mtm) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 0.0526 time to fit residues: 4.2217 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 506 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046148 restraints weight = 22840.785| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.88 r_work: 0.2611 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2909 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= 0.128 Angle : 0.477 5.360 9188 Z= 0.244 Chirality : 0.040 0.147 978 Planarity : 0.003 0.035 1176 Dihedral : 4.541 55.322 1013 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.29 % Allowed : 9.57 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.30), residues: 793 helix: 2.01 (0.26), residues: 386 sheet: 0.44 (0.72), residues: 43 loop : 0.45 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.015 0.001 TYR E 50 PHE 0.012 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 covalent geometry : bond 0.00283 ( 6737) covalent geometry : angle 0.46731 ( 9155) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.99135 ( 12) hydrogen bonds : bond 0.03641 ( 319) hydrogen bonds : angle 4.08843 ( 906) link_NAG-ASN : bond 0.00226 ( 7) link_NAG-ASN : angle 1.99467 ( 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8714 (mt-10) REVERT: B 467 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.7927 (p0) REVERT: B 498 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8904 (mm-40) REVERT: B 518 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7166 (tt) REVERT: E 82 MET cc_start: 0.9276 (mtp) cc_final: 0.8794 (ttp) REVERT: E 86 GLN cc_start: 0.9114 (pm20) cc_final: 0.8778 (pm20) REVERT: E 267 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9267 (mm) REVERT: E 270 MET cc_start: 0.8851 (tpp) cc_final: 0.8228 (tpp) REVERT: E 323 MET cc_start: 0.9190 (mmm) cc_final: 0.8744 (mmm) REVERT: E 332 MET cc_start: 0.9039 (ttp) cc_final: 0.8346 (ppp) REVERT: E 360 MET cc_start: 0.7866 (tmm) cc_final: 0.6603 (tmm) REVERT: E 368 ASP cc_start: 0.9060 (m-30) cc_final: 0.8477 (t0) REVERT: E 462 MET cc_start: 0.9631 (mtm) cc_final: 0.9147 (mtt) outliers start: 9 outliers final: 3 residues processed: 57 average time/residue: 0.0511 time to fit residues: 4.5944 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 447 VAL 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: 0.1980 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.046377 restraints weight = 22497.763| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.85 r_work: 0.2616 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3034 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= 0.125 Angle : 0.489 6.594 9188 Z= 0.248 Chirality : 0.040 0.143 978 Planarity : 0.003 0.035 1176 Dihedral : 4.490 55.851 1013 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 1.79 (0.30), residues: 793 helix: 2.03 (0.26), residues: 385 sheet: 0.41 (0.72), residues: 43 loop : 0.48 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 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 covalent geometry : bond 0.00275 ( 6737) covalent geometry : angle 0.47988 ( 9155) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.97531 ( 12) hydrogen bonds : bond 0.03613 ( 319) hydrogen bonds : angle 4.07231 ( 906) link_NAG-ASN : bond 0.00207 ( 7) link_NAG-ASN : angle 1.95528 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8851 (mt-10) REVERT: B 467 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.7900 (p0) REVERT: B 498 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8900 (mm-40) REVERT: B 518 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7192 (tt) REVERT: E 82 MET cc_start: 0.9300 (mtp) cc_final: 0.8810 (ttp) REVERT: E 86 GLN cc_start: 0.9110 (pm20) cc_final: 0.8776 (pm20) REVERT: E 267 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9266 (mm) REVERT: E 270 MET cc_start: 0.8748 (tpp) cc_final: 0.8068 (tpp) REVERT: E 332 MET cc_start: 0.9036 (ttp) cc_final: 0.8350 (ppp) REVERT: E 360 MET cc_start: 0.7777 (tmm) cc_final: 0.6477 (tmm) REVERT: E 368 ASP cc_start: 0.8993 (m-30) cc_final: 0.8413 (t0) REVERT: E 462 MET cc_start: 0.9623 (mtm) cc_final: 0.9332 (mtm) REVERT: E 474 MET cc_start: 0.8836 (mmp) cc_final: 0.8609 (mmp) outliers start: 10 outliers final: 3 residues processed: 55 average time/residue: 0.0502 time to fit residues: 4.4336 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 447 VAL 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: 4.9990 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.044040 restraints weight = 22976.093| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.83 r_work: 0.2534 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6750 Z= 0.252 Angle : 0.593 6.165 9188 Z= 0.303 Chirality : 0.043 0.172 978 Planarity : 0.004 0.058 1176 Dihedral : 4.887 54.608 1013 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.29 % Allowed : 10.43 % 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: 1.70 (0.30), residues: 793 helix: 1.87 (0.26), residues: 391 sheet: -0.01 (0.70), residues: 45 loop : 0.59 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 403 TYR 0.018 0.001 TYR B 453 PHE 0.014 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 covalent geometry : bond 0.00554 ( 6737) covalent geometry : angle 0.58346 ( 9155) SS BOND : bond 0.00202 ( 6) SS BOND : angle 1.12234 ( 12) hydrogen bonds : bond 0.04315 ( 319) hydrogen bonds : angle 4.34905 ( 906) link_NAG-ASN : bond 0.00166 ( 7) link_NAG-ASN : angle 2.15098 ( 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8873 (mt-10) REVERT: B 442 ASP cc_start: 0.9023 (m-30) cc_final: 0.8726 (m-30) REVERT: B 467 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.7825 (p0) REVERT: B 518 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7290 (tt) REVERT: E 82 MET cc_start: 0.9280 (mtp) cc_final: 0.8867 (ttm) REVERT: E 270 MET cc_start: 0.8746 (tpp) cc_final: 0.8031 (tpp) REVERT: E 323 MET cc_start: 0.9360 (mmm) cc_final: 0.8980 (mmm) REVERT: E 332 MET cc_start: 0.9167 (ttp) cc_final: 0.8524 (ppp) REVERT: E 360 MET cc_start: 0.7913 (tmm) cc_final: 0.7004 (tmm) REVERT: E 368 ASP cc_start: 0.9037 (m-30) cc_final: 0.8690 (t0) REVERT: E 474 MET cc_start: 0.9109 (mmp) cc_final: 0.8909 (mmm) REVERT: E 613 TYR cc_start: 0.8629 (t80) cc_final: 0.8317 (t80) outliers start: 9 outliers final: 1 residues processed: 54 average time/residue: 0.0464 time to fit residues: 3.9117 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 : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 318 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: 2.9990 chunk 46 optimal weight: 0.0010 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.061835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.045988 restraints weight = 22846.204| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.91 r_work: 0.2599 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6750 Z= 0.118 Angle : 0.513 7.185 9188 Z= 0.259 Chirality : 0.040 0.143 978 Planarity : 0.003 0.034 1176 Dihedral : 4.624 56.533 1013 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.57 % Allowed : 11.14 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.30), residues: 793 helix: 1.90 (0.26), residues: 391 sheet: -0.08 (0.71), residues: 45 loop : 0.48 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.018 0.001 TYR E 50 PHE 0.011 0.001 PHE E 369 TRP 0.010 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6737) covalent geometry : angle 0.50321 ( 9155) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.97100 ( 12) hydrogen bonds : bond 0.03703 ( 319) hydrogen bonds : angle 4.17165 ( 906) link_NAG-ASN : bond 0.00222 ( 7) link_NAG-ASN : angle 2.06432 ( 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 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8864 (mt-10) REVERT: B 442 ASP cc_start: 0.8963 (m-30) cc_final: 0.8714 (m-30) REVERT: B 467 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.7900 (p0) REVERT: B 518 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7226 (tt) REVERT: E 82 MET cc_start: 0.9284 (mtp) cc_final: 0.8836 (ttm) REVERT: E 86 GLN cc_start: 0.9144 (pm20) cc_final: 0.8800 (pm20) REVERT: E 270 MET cc_start: 0.8680 (tpp) cc_final: 0.8012 (tpp) REVERT: E 332 MET cc_start: 0.9076 (ttp) cc_final: 0.8431 (ppp) REVERT: E 360 MET cc_start: 0.7609 (tmm) cc_final: 0.6660 (tmm) REVERT: E 368 ASP cc_start: 0.8955 (m-30) cc_final: 0.8624 (t0) REVERT: E 462 MET cc_start: 0.9649 (mtm) cc_final: 0.9268 (mtt) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.0496 time to fit residues: 4.0971 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 233 ILE 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: 0.8980 chunk 66 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 0.0040 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.046854 restraints weight = 22374.802| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.88 r_work: 0.2592 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6750 Z= 0.110 Angle : 0.524 9.142 9188 Z= 0.262 Chirality : 0.041 0.204 978 Planarity : 0.003 0.034 1176 Dihedral : 4.529 56.534 1013 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.71 % Allowed : 10.71 % Favored : 88.57 % 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: 1.90 (0.26), residues: 388 sheet: -0.08 (0.70), residues: 45 loop : 0.53 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 covalent geometry : bond 0.00242 ( 6737) covalent geometry : angle 0.51447 ( 9155) SS BOND : bond 0.00162 ( 6) SS BOND : angle 0.91467 ( 12) hydrogen bonds : bond 0.03585 ( 319) hydrogen bonds : angle 4.12080 ( 906) link_NAG-ASN : bond 0.00236 ( 7) link_NAG-ASN : angle 2.03611 ( 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8714 (mt-10) REVERT: B 409 GLN cc_start: 0.9625 (mt0) cc_final: 0.9383 (mt0) REVERT: B 442 ASP cc_start: 0.8952 (m-30) cc_final: 0.8698 (m-30) REVERT: B 467 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.7840 (p0) REVERT: B 518 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7189 (tt) REVERT: E 82 MET cc_start: 0.9303 (mtp) cc_final: 0.8844 (ttm) REVERT: E 86 GLN cc_start: 0.9123 (pm20) cc_final: 0.8778 (pm20) REVERT: E 267 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9210 (mm) REVERT: E 270 MET cc_start: 0.8635 (tpp) cc_final: 0.7966 (tpp) REVERT: E 332 MET cc_start: 0.8979 (ttp) cc_final: 0.8383 (ppp) REVERT: E 360 MET cc_start: 0.7589 (tmm) cc_final: 0.6693 (tmm) REVERT: E 368 ASP cc_start: 0.8898 (m-30) cc_final: 0.8553 (t0) REVERT: E 613 TYR cc_start: 0.8608 (t80) cc_final: 0.8207 (t80) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.0556 time to fit residues: 4.8720 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ASP 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: 0.5980 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.045043 restraints weight = 22724.510| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.87 r_work: 0.2571 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6750 Z= 0.187 Angle : 0.600 16.309 9188 Z= 0.293 Chirality : 0.042 0.153 978 Planarity : 0.004 0.035 1176 Dihedral : 4.688 55.445 1013 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.71 % Allowed : 10.86 % 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: 1.70 (0.30), residues: 793 helix: 1.85 (0.26), residues: 391 sheet: -0.12 (0.70), residues: 45 loop : 0.63 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.019 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 covalent geometry : bond 0.00415 ( 6737) covalent geometry : angle 0.59069 ( 9155) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.99658 ( 12) hydrogen bonds : bond 0.03961 ( 319) hydrogen bonds : angle 4.28946 ( 906) link_NAG-ASN : bond 0.00203 ( 7) link_NAG-ASN : angle 2.14017 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1500.59 seconds wall clock time: 26 minutes 29.38 seconds (1589.38 seconds total)