Starting phenix.real_space_refine on Thu Jul 2 04:40:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tez_25856/07_2026/7tez_25856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tez_25856/07_2026/7tez_25856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2026/7tez_25856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2026/7tez_25856.map" model { file = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2026/7tez_25856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2026/7tez_25856.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2026/7tez_25856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tez_25856/07_2026/7tez_25856.cif" } resolution = 3.27 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= 0.014 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 4186 2.51 5 N 1082 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6553 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.07, per 1000 atoms: 0.16 Number of scatterers: 6553 At special positions: 0 Unit cell: (81, 84, 121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1248 8.00 N 1082 7.00 C 4186 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=2.02 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: 0.30 Conformation dependent library (CDL) restraints added in 214.6 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: 40 helices and 7 sheets defined 57.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 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 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.713A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.084A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (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: 3.747A 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: 4.084A 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: 3.970A 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: 3.694A 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: 3.745A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.845A 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: 3.766A 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: 3.558A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.667A 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: 4.292A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.901A 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: 3.514A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.312A 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: 3.596A 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: 4.494A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.829A 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: 4.013A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.811A 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: 6.093A 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: 6.377A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2085 1.34 - 1.47: 1765 1.47 - 1.59: 2827 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 8789 2.06 - 4.11: 320 4.11 - 6.17: 32 6.17 - 8.22: 8 8.22 - 10.28: 3 Bond angle restraints: 9152 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 122.36 128.51 -6.15 1.42e+00 4.96e-01 1.87e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 122.85 -8.45 2.30e+00 1.89e-01 1.35e+01 angle pdb=" C HIS E 34 " pdb=" N GLU E 35 " pdb=" CA GLU E 35 " ideal model delta sigma weight residual 122.38 115.83 6.55 1.81e+00 3.05e-01 1.31e+01 angle pdb=" CA LYS E 31 " pdb=" CB LYS E 31 " pdb=" CG LYS E 31 " ideal model delta sigma weight residual 114.10 120.95 -6.85 2.00e+00 2.50e-01 1.17e+01 ... (remaining 9147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 3545 16.72 - 33.43: 302 33.43 - 50.15: 50 50.15 - 66.87: 12 66.87 - 83.58: 12 Dihedral angle restraints: 3921 sinusoidal: 1583 harmonic: 2338 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 -48.44 -37.56 1 1.00e+01 1.00e-02 1.99e+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 16.07 62.93 1 2.00e+01 2.50e-03 1.31e+01 dihedral pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual 122.80 130.82 -8.02 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 3918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 726 0.061 - 0.121: 205 0.121 - 0.182: 38 0.182 - 0.243: 6 0.243 - 0.303: 2 Chirality restraints: 977 Sorted by residual: 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 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 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=" 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 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 974 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.056 5.00e-02 4.00e+02 8.31e-02 1.11e+01 pdb=" N PRO E 590 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.050 5.00e-02 4.00e+02 7.43e-02 8.82e+00 pdb=" N PRO E 500 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 478 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO B 479 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.034 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2097 2.84 - 3.35: 5957 3.35 - 3.87: 11286 3.87 - 4.38: 12699 4.38 - 4.90: 22030 Nonbonded interactions: 54069 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.323 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.344 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.360 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.366 3.120 ... (remaining 54064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.910 Find NCS groups from input model: 0.010 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.006 0.071 6748 Z= 0.256 Angle : 0.922 11.310 9185 Z= 0.516 Chirality : 0.060 0.303 977 Planarity : 0.008 0.083 1178 Dihedral : 13.437 83.585 2403 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.71 % Allowed : 2.57 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 793 helix: 0.58 (0.22), residues: 392 sheet: 1.01 (0.72), residues: 43 loop : -0.62 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 460 TYR 0.041 0.003 TYR B 495 PHE 0.028 0.003 PHE E 369 TRP 0.020 0.002 TRP E 69 HIS 0.013 0.002 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.26 ( 6735) covalent geometry : angle 0.89558 / 0.51 ( 9152) SS BOND : bond 0.00665 / 0.41 ( 6) SS BOND : angle 2.43294 / 1.35 ( 12) hydrogen bonds : bond 0.14602 / 9.89 ( 323) hydrogen bonds : angle 6.06242 / 4.24 ( 912) link_NAG-ASN : bond 0.00838 / 0.46 ( 7) link_NAG-ASN : angle 4.32550 / 3.48 ( 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 153 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.153 Fit side-chains REVERT: B 417 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8826 (mmtm) REVERT: B 470 THR cc_start: 0.8859 (p) cc_final: 0.8567 (t) REVERT: E 291 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8532 (tp) REVERT: E 436 ILE cc_start: 0.9036 (mm) cc_final: 0.8812 (mt) REVERT: E 475 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8003 (tptp) REVERT: E 483 GLU cc_start: 0.8717 (tp30) cc_final: 0.8452 (tp30) outliers start: 5 outliers final: 0 residues processed: 151 average time/residue: 0.0768 time to fit residues: 14.7371 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 345 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.066889 restraints weight = 17126.614| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.35 r_work: 0.2860 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6748 Z= 0.172 Angle : 0.591 7.201 9185 Z= 0.299 Chirality : 0.043 0.175 977 Planarity : 0.004 0.038 1178 Dihedral : 4.295 20.682 868 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.14 % Allowed : 9.14 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.28), residues: 793 helix: 1.42 (0.25), residues: 396 sheet: 0.87 (0.74), residues: 42 loop : 0.01 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 559 TYR 0.014 0.001 TYR E 385 PHE 0.018 0.001 PHE E 428 TRP 0.018 0.001 TRP E 165 HIS 0.008 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 6735) covalent geometry : angle 0.57528 / 0.30 ( 9152) SS BOND : bond 0.00425 / 0.27 ( 6) SS BOND : angle 1.72127 / 0.97 ( 12) hydrogen bonds : bond 0.04297 / 2.83 ( 323) hydrogen bonds : angle 4.58405 / 3.30 ( 912) link_NAG-ASN : bond 0.00542 / 0.33 ( 7) link_NAG-ASN : angle 2.62066 / 2.12 ( 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 87 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.198 Fit side-chains REVERT: B 420 ASP cc_start: 0.8957 (m-30) cc_final: 0.8570 (m-30) REVERT: B 470 THR cc_start: 0.9234 (p) cc_final: 0.8875 (t) REVERT: B 506 GLN cc_start: 0.9267 (mt0) cc_final: 0.8732 (mt0) REVERT: E 483 GLU cc_start: 0.8974 (tp30) cc_final: 0.8673 (tp30) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 0.0558 time to fit residues: 6.6211 Evaluate side-chains 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN E 374 HIS E 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.064119 restraints weight = 17148.776| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.32 r_work: 0.2800 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6748 Z= 0.212 Angle : 0.584 7.519 9185 Z= 0.297 Chirality : 0.043 0.154 977 Planarity : 0.004 0.041 1178 Dihedral : 4.240 15.502 866 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.43 % Allowed : 11.57 % 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: 1.29 (0.29), residues: 793 helix: 1.47 (0.26), residues: 396 sheet: 0.64 (0.71), residues: 42 loop : 0.30 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.018 0.001 TYR E 385 PHE 0.017 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.007 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 6735) covalent geometry : angle 0.57383 / 0.29 ( 9152) SS BOND : bond 0.00440 / 0.28 ( 6) SS BOND : angle 1.44064 / 0.82 ( 12) hydrogen bonds : bond 0.04444 / 2.92 ( 323) hydrogen bonds : angle 4.46140 / 3.21 ( 912) link_NAG-ASN : bond 0.00449 / 0.27 ( 7) link_NAG-ASN : angle 2.15743 / 1.74 ( 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 77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 323 MET cc_start: 0.9189 (mmt) cc_final: 0.8726 (mmt) REVERT: E 376 MET cc_start: 0.9033 (ttm) cc_final: 0.8617 (mmm) REVERT: E 483 GLU cc_start: 0.9017 (tp30) cc_final: 0.8702 (tp30) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.0483 time to fit residues: 5.3147 Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 0.0050 chunk 77 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.066745 restraints weight = 17268.750| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.21 r_work: 0.2865 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6748 Z= 0.132 Angle : 0.531 10.116 9185 Z= 0.265 Chirality : 0.041 0.159 977 Planarity : 0.004 0.040 1178 Dihedral : 4.012 15.836 866 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.14 % Allowed : 11.14 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.29), residues: 793 helix: 1.69 (0.26), residues: 392 sheet: 0.23 (0.69), residues: 44 loop : 0.41 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 559 TYR 0.013 0.001 TYR E 385 PHE 0.014 0.001 PHE E 369 TRP 0.023 0.001 TRP E 610 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6735) covalent geometry : angle 0.52174 / 0.26 ( 9152) SS BOND : bond 0.00378 / 0.23 ( 6) SS BOND : angle 1.33357 / 0.77 ( 12) hydrogen bonds : bond 0.03932 / 2.59 ( 323) hydrogen bonds : angle 4.31519 / 3.10 ( 912) link_NAG-ASN : bond 0.00364 / 0.21 ( 7) link_NAG-ASN : angle 1.95111 / 1.56 ( 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 77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.9281 (mt0) cc_final: 0.8798 (mt0) REVERT: E 323 MET cc_start: 0.9056 (mmt) cc_final: 0.8635 (mmt) REVERT: E 376 MET cc_start: 0.9082 (ttm) cc_final: 0.8724 (mmm) REVERT: E 483 GLU cc_start: 0.8942 (tp30) cc_final: 0.8671 (tp30) outliers start: 8 outliers final: 4 residues processed: 76 average time/residue: 0.0525 time to fit residues: 5.7362 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 0.0570 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.069040 restraints weight = 17329.715| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.28 r_work: 0.2911 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6748 Z= 0.098 Angle : 0.488 7.388 9185 Z= 0.246 Chirality : 0.040 0.152 977 Planarity : 0.003 0.043 1178 Dihedral : 3.731 15.265 866 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.86 % Allowed : 11.71 % Favored : 87.43 % 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: 1.61 (0.29), residues: 793 helix: 1.79 (0.26), residues: 392 sheet: 0.26 (0.69), residues: 44 loop : 0.49 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 559 TYR 0.011 0.001 TYR E 385 PHE 0.010 0.001 PHE E 369 TRP 0.026 0.001 TRP E 610 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 6735) covalent geometry : angle 0.47908 / 0.24 ( 9152) SS BOND : bond 0.00343 / 0.21 ( 6) SS BOND : angle 1.20129 / 0.71 ( 12) hydrogen bonds : bond 0.03543 / 2.33 ( 323) hydrogen bonds : angle 4.17297 / 3.01 ( 912) link_NAG-ASN : bond 0.00332 / 0.18 ( 7) link_NAG-ASN : angle 1.76560 / 1.39 ( 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 82 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.9281 (mt0) cc_final: 0.8827 (mt0) REVERT: E 323 MET cc_start: 0.9020 (mmt) cc_final: 0.8594 (mmt) REVERT: E 376 MET cc_start: 0.9036 (ttm) cc_final: 0.8706 (mmm) REVERT: E 483 GLU cc_start: 0.8960 (tp30) cc_final: 0.8658 (tp30) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.0693 time to fit residues: 7.5872 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 484 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 = 0.3329 r_free = 0.3329 target = 0.083690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.066736 restraints weight = 17455.073| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.28 r_work: 0.2862 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6748 Z= 0.132 Angle : 0.511 8.864 9185 Z= 0.253 Chirality : 0.041 0.154 977 Planarity : 0.003 0.041 1178 Dihedral : 3.769 16.182 866 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.14 % Allowed : 12.14 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.30), residues: 793 helix: 1.84 (0.26), residues: 392 sheet: 0.37 (0.71), residues: 44 loop : 0.63 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 509 TYR 0.013 0.001 TYR E 385 PHE 0.010 0.001 PHE E 369 TRP 0.017 0.001 TRP E 610 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6735) covalent geometry : angle 0.50397 / 0.25 ( 9152) SS BOND : bond 0.00330 / 0.21 ( 6) SS BOND : angle 1.02150 / 0.60 ( 12) hydrogen bonds : bond 0.03756 / 2.48 ( 323) hydrogen bonds : angle 4.13433 / 2.98 ( 912) link_NAG-ASN : bond 0.00302 / 0.19 ( 7) link_NAG-ASN : angle 1.69239 / 1.35 ( 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 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.9297 (mt0) cc_final: 0.8821 (mt0) REVERT: E 376 MET cc_start: 0.9047 (ttm) cc_final: 0.8759 (tpp) REVERT: E 483 GLU cc_start: 0.8976 (tp30) cc_final: 0.8696 (tp30) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.0588 time to fit residues: 6.3216 Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 484 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 = 0.3324 r_free = 0.3324 target = 0.083509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066672 restraints weight = 17367.364| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.23 r_work: 0.2857 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6748 Z= 0.137 Angle : 0.516 8.054 9185 Z= 0.256 Chirality : 0.041 0.164 977 Planarity : 0.003 0.039 1178 Dihedral : 3.773 16.026 866 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.43 % Allowed : 12.29 % Favored : 86.29 % 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: 1.77 (0.30), residues: 793 helix: 1.83 (0.26), residues: 392 sheet: 0.40 (0.71), residues: 44 loop : 0.68 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 219 TYR 0.013 0.001 TYR E 385 PHE 0.011 0.001 PHE E 369 TRP 0.014 0.001 TRP E 610 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6735) covalent geometry : angle 0.50942 / 0.25 ( 9152) SS BOND : bond 0.00321 / 0.21 ( 6) SS BOND : angle 0.99270 / 0.58 ( 12) hydrogen bonds : bond 0.03763 / 2.48 ( 323) hydrogen bonds : angle 4.15003 / 2.99 ( 912) link_NAG-ASN : bond 0.00305 / 0.19 ( 7) link_NAG-ASN : angle 1.65544 / 1.32 ( 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 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.9283 (mt0) cc_final: 0.8792 (mt0) REVERT: E 483 GLU cc_start: 0.8975 (tp30) cc_final: 0.8679 (tp30) REVERT: E 586 ASN cc_start: 0.8936 (t0) cc_final: 0.8602 (t0) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.0549 time to fit residues: 5.6866 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.0040 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.067415 restraints weight = 17286.127| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.26 r_work: 0.2874 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6748 Z= 0.117 Angle : 0.507 7.597 9185 Z= 0.251 Chirality : 0.041 0.150 977 Planarity : 0.003 0.039 1178 Dihedral : 3.730 16.227 866 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.71 % Allowed : 12.57 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.30), residues: 793 helix: 1.83 (0.26), residues: 392 sheet: 0.38 (0.72), residues: 44 loop : 0.68 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 177 TYR 0.012 0.001 TYR E 385 PHE 0.010 0.001 PHE E 369 TRP 0.012 0.001 TRP E 610 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6735) covalent geometry : angle 0.50056 / 0.25 ( 9152) SS BOND : bond 0.00312 / 0.20 ( 6) SS BOND : angle 0.99336 / 0.59 ( 12) hydrogen bonds : bond 0.03662 / 2.41 ( 323) hydrogen bonds : angle 4.13233 / 2.98 ( 912) link_NAG-ASN : bond 0.00295 / 0.18 ( 7) link_NAG-ASN : angle 1.62196 / 1.30 ( 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 81 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 506 GLN cc_start: 0.9285 (mt0) cc_final: 0.8805 (mt0) REVERT: E 483 GLU cc_start: 0.8962 (tp30) cc_final: 0.8681 (tp30) REVERT: E 586 ASN cc_start: 0.8878 (t0) cc_final: 0.8543 (t0) outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 0.0592 time to fit residues: 6.3721 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 484 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 = 0.3325 r_free = 0.3325 target = 0.083487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.066603 restraints weight = 17519.865| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.25 r_work: 0.2857 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6748 Z= 0.136 Angle : 0.542 9.630 9185 Z= 0.265 Chirality : 0.041 0.151 977 Planarity : 0.003 0.037 1178 Dihedral : 3.781 15.960 866 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.29 % Allowed : 13.00 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.30), residues: 793 helix: 1.81 (0.26), residues: 392 sheet: 0.41 (0.72), residues: 44 loop : 0.70 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 454 TYR 0.012 0.001 TYR E 385 PHE 0.012 0.001 PHE E 369 TRP 0.012 0.001 TRP E 610 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6735) covalent geometry : angle 0.53588 / 0.26 ( 9152) SS BOND : bond 0.00308 / 0.20 ( 6) SS BOND : angle 0.93940 / 0.56 ( 12) hydrogen bonds : bond 0.03745 / 2.47 ( 323) hydrogen bonds : angle 4.15120 / 2.99 ( 912) link_NAG-ASN : bond 0.00297 / 0.19 ( 7) link_NAG-ASN : angle 1.63289 / 1.31 ( 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 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8781 (mt-10) cc_final: 0.7965 (tm-30) REVERT: E 483 GLU cc_start: 0.8966 (tp30) cc_final: 0.8667 (tp30) REVERT: E 586 ASN cc_start: 0.8912 (t0) cc_final: 0.8589 (t0) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.0531 time to fit residues: 5.6232 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 ASN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.080964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.064261 restraints weight = 17311.886| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.17 r_work: 0.2813 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6748 Z= 0.222 Angle : 0.604 8.129 9185 Z= 0.300 Chirality : 0.043 0.152 977 Planarity : 0.004 0.039 1178 Dihedral : 4.136 16.101 866 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.57 % Allowed : 13.14 % Favored : 85.29 % 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: 1.57 (0.30), residues: 793 helix: 1.54 (0.26), residues: 401 sheet: 0.43 (0.73), residues: 42 loop : 0.70 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 245 TYR 0.017 0.001 TYR E 385 PHE 0.014 0.001 PHE E 369 TRP 0.036 0.002 TRP E 610 HIS 0.007 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 ( 6735) covalent geometry : angle 0.59814 / 0.30 ( 9152) SS BOND : bond 0.00379 / 0.25 ( 6) SS BOND : angle 0.87624 / 0.51 ( 12) hydrogen bonds : bond 0.04213 / 2.77 ( 323) hydrogen bonds : angle 4.32388 / 3.12 ( 912) link_NAG-ASN : bond 0.00373 / 0.24 ( 7) link_NAG-ASN : angle 1.76351 / 1.40 ( 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 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8806 (mt-10) cc_final: 0.7999 (tm-30) REVERT: E 323 MET cc_start: 0.8556 (mmm) cc_final: 0.8248 (mtm) REVERT: E 483 GLU cc_start: 0.8931 (tp30) cc_final: 0.8667 (tp30) REVERT: E 586 ASN cc_start: 0.9012 (t0) cc_final: 0.8700 (t0) outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 0.0625 time to fit residues: 6.5474 Evaluate side-chains 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.066584 restraints weight = 17279.289| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.21 r_work: 0.2860 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.120 Angle : 0.541 7.335 9185 Z= 0.270 Chirality : 0.041 0.164 977 Planarity : 0.004 0.040 1178 Dihedral : 3.950 16.617 866 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.71 % Allowed : 13.43 % Favored : 85.86 % 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: 1.58 (0.30), residues: 793 helix: 1.55 (0.26), residues: 405 sheet: 0.27 (0.71), residues: 47 loop : 0.72 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 177 TYR 0.013 0.001 TYR E 385 PHE 0.011 0.001 PHE E 369 TRP 0.035 0.001 TRP E 610 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6735) covalent geometry : angle 0.53454 / 0.27 ( 9152) SS BOND : bond 0.00324 / 0.21 ( 6) SS BOND : angle 0.99903 / 0.60 ( 12) hydrogen bonds : bond 0.03785 / 2.50 ( 323) hydrogen bonds : angle 4.21672 / 3.04 ( 912) link_NAG-ASN : bond 0.00321 / 0.20 ( 7) link_NAG-ASN : angle 1.70121 / 1.35 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1242.08 seconds wall clock time: 22 minutes 4.99 seconds (1324.99 seconds total)