Starting phenix.real_space_refine on Thu Jun 5 21:34:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tew_25853/06_2025/7tew_25853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tew_25853/06_2025/7tew_25853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tew_25853/06_2025/7tew_25853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tew_25853/06_2025/7tew_25853.map" model { file = "/net/cci-nas-00/data/ceres_data/7tew_25853/06_2025/7tew_25853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tew_25853/06_2025/7tew_25853.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.013 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 4188 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 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6555 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 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: 5.21, per 1000 atoms: 0.79 Number of scatterers: 6555 At special positions: 0 Unit cell: (80, 86, 122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1248 8.00 N 1082 7.00 C 4188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 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: 1.43 Conformation dependent library (CDL) restraints added in 861.8 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 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 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.752A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.114A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.028A 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: 3.753A 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: 4.041A 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: 4.045A 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: 3.697A 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 220 through 252 removed outlier: 3.928A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.811A 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 319 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.521A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.689A 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: 4.289A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.916A 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: 3.511A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.328A 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: 3.648A 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 513 through 533 removed outlier: 3.614A 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: 3.896A 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: 4.002A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.774A 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: 6.158A 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: 6.347A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.74 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: 2087 1.35 - 1.47: 1795 1.47 - 1.60: 2797 1.60 - 1.73: 0 1.73 - 1.85: 58 Bond restraints: 6737 Sorted by residual: bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.22e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+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 4.15e+00 ... (remaining 6732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8757 1.91 - 3.82: 350 3.82 - 5.73: 34 5.73 - 7.63: 8 7.63 - 9.54: 4 Bond angle restraints: 9153 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 122.36 128.24 -5.88 1.42e+00 4.96e-01 1.71e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 122.95 -8.55 2.30e+00 1.89e-01 1.38e+01 angle pdb=" C HIS E 34 " pdb=" N GLU E 35 " pdb=" CA GLU E 35 " ideal model delta sigma weight residual 122.38 115.72 6.66 1.81e+00 3.05e-01 1.35e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.25 -3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA LYS E 31 " pdb=" CB LYS E 31 " pdb=" CG LYS E 31 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 ... (remaining 9148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 3680 16.87 - 33.74: 316 33.74 - 50.61: 51 50.61 - 67.47: 12 67.47 - 84.34: 12 Dihedral angle restraints: 4071 sinusoidal: 1733 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 -47.25 -38.75 1 1.00e+01 1.00e-02 2.11e+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 14.06 64.94 1 2.00e+01 2.50e-03 1.38e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.88 8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 4068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 729 0.056 - 0.111: 186 0.111 - 0.166: 51 0.166 - 0.222: 8 0.222 - 0.277: 2 Chirality restraints: 976 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 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+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 1.84e+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 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 973 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO E 590 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.048 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO E 500 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.021 2.00e-02 2.50e+03 1.86e-02 6.95e+00 pdb=" CG TYR B 495 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.003 2.00e-02 2.50e+03 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 2224 2.86 - 3.37: 5996 3.37 - 3.88: 11266 3.88 - 4.39: 12492 4.39 - 4.90: 21655 Nonbonded interactions: 53633 Sorted by model distance: nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.344 3.120 nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.346 3.040 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.365 3.040 nonbonded pdb=" O SER E 47 " pdb=" ND2 ASN E 51 " model vdw 2.374 3.120 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.387 3.120 ... (remaining 53628 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 group one per residue 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: 3.750 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.220 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6750 Z= 0.234 Angle : 0.878 11.268 9186 Z= 0.493 Chirality : 0.057 0.277 976 Planarity : 0.008 0.078 1178 Dihedral : 13.336 84.341 2553 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 793 helix: 0.53 (0.22), residues: 392 sheet: 0.98 (0.72), residues: 43 loop : -0.64 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 69 HIS 0.011 0.002 HIS E 34 PHE 0.027 0.003 PHE E 369 TYR 0.045 0.003 TYR B 495 ARG 0.009 0.001 ARG E 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00675 ( 7) link_NAG-ASN : angle 4.09989 ( 21) hydrogen bonds : bond 0.14790 ( 322) hydrogen bonds : angle 6.02989 ( 915) SS BOND : bond 0.00530 ( 6) SS BOND : angle 2.60855 ( 12) covalent geometry : bond 0.00485 ( 6737) covalent geometry : angle 0.85235 ( 9153) *********************** 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 135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8482 (ttpt) REVERT: B 424 LYS cc_start: 0.8692 (tptt) cc_final: 0.8170 (tppt) REVERT: B 448 ASN cc_start: 0.9203 (t0) cc_final: 0.8698 (t0) REVERT: B 458 LYS cc_start: 0.9307 (mtmt) cc_final: 0.9072 (mtmm) REVERT: B 467 ASP cc_start: 0.8432 (t0) cc_final: 0.8085 (t0) REVERT: B 473 TYR cc_start: 0.9316 (t80) cc_final: 0.9062 (t80) REVERT: B 474 GLN cc_start: 0.8885 (tt0) cc_final: 0.8616 (tt0) REVERT: E 108 LEU cc_start: 0.8613 (tp) cc_final: 0.8360 (tp) REVERT: E 249 MET cc_start: 0.8484 (ttm) cc_final: 0.8082 (mtp) REVERT: E 297 MET cc_start: 0.9202 (mtm) cc_final: 0.8996 (mtm) REVERT: E 302 TRP cc_start: 0.8366 (m-10) cc_final: 0.7320 (m100) REVERT: E 498 CYS cc_start: 0.8204 (t) cc_final: 0.7637 (t) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.2545 time to fit residues: 42.9584 Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 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 = 0.3316 r_free = 0.3316 target = 0.066767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053441 restraints weight = 26158.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055538 restraints weight = 12772.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056874 restraints weight = 8036.572| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6750 Z= 0.125 Angle : 0.568 6.634 9186 Z= 0.293 Chirality : 0.040 0.139 976 Planarity : 0.005 0.049 1178 Dihedral : 5.234 52.822 1013 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.86 % Allowed : 8.29 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 793 helix: 1.42 (0.25), residues: 406 sheet: 1.13 (0.75), residues: 42 loop : -0.13 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.015 0.001 PHE E 428 TYR 0.012 0.001 TYR B 453 ARG 0.003 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 7) link_NAG-ASN : angle 2.63294 ( 21) hydrogen bonds : bond 0.04214 ( 322) hydrogen bonds : angle 4.56212 ( 915) SS BOND : bond 0.00367 ( 6) SS BOND : angle 1.83552 ( 12) covalent geometry : bond 0.00272 ( 6737) covalent geometry : angle 0.55090 ( 9153) *********************** 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 86 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9062 (mmmt) REVERT: B 424 LYS cc_start: 0.8704 (tptt) cc_final: 0.8352 (tppt) REVERT: B 448 ASN cc_start: 0.9217 (t0) cc_final: 0.8835 (t0) REVERT: B 458 LYS cc_start: 0.9303 (mtmt) cc_final: 0.9069 (mtmm) REVERT: B 467 ASP cc_start: 0.8276 (t0) cc_final: 0.7928 (t0) REVERT: E 108 LEU cc_start: 0.8542 (tp) cc_final: 0.8166 (tp) REVERT: E 232 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8805 (mp0) REVERT: E 302 TRP cc_start: 0.8473 (m-10) cc_final: 0.7670 (m100) REVERT: E 323 MET cc_start: 0.9516 (mmp) cc_final: 0.9314 (mmm) REVERT: E 366 MET cc_start: 0.8926 (mtp) cc_final: 0.8581 (mtm) REVERT: E 498 CYS cc_start: 0.8441 (t) cc_final: 0.8067 (t) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 0.1987 time to fit residues: 22.1524 Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 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 = 0.3248 r_free = 0.3248 target = 0.064374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.050960 restraints weight = 26499.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052954 restraints weight = 13203.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054276 restraints weight = 8472.640| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6750 Z= 0.142 Angle : 0.533 5.749 9186 Z= 0.273 Chirality : 0.040 0.140 976 Planarity : 0.004 0.046 1178 Dihedral : 4.980 53.699 1013 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.14 % Allowed : 9.14 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.29), residues: 793 helix: 1.68 (0.26), residues: 413 sheet: 0.84 (0.76), residues: 41 loop : 0.10 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.014 0.001 PHE E 369 TYR 0.020 0.001 TYR E 613 ARG 0.003 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 7) link_NAG-ASN : angle 2.05281 ( 21) hydrogen bonds : bond 0.03889 ( 322) hydrogen bonds : angle 4.43598 ( 915) SS BOND : bond 0.00449 ( 6) SS BOND : angle 1.72827 ( 12) covalent geometry : bond 0.00311 ( 6737) covalent geometry : angle 0.52089 ( 9153) *********************** 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 76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7876 (ptmm) REVERT: B 409 GLN cc_start: 0.9287 (mt0) cc_final: 0.9021 (mt0) REVERT: B 448 ASN cc_start: 0.9276 (t0) cc_final: 0.8900 (t0) REVERT: B 458 LYS cc_start: 0.9308 (mtmt) cc_final: 0.9101 (mtmm) REVERT: B 467 ASP cc_start: 0.8290 (t0) cc_final: 0.7960 (t0) REVERT: E 62 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.9138 (mtm) REVERT: E 108 LEU cc_start: 0.8550 (tp) cc_final: 0.8141 (tp) REVERT: E 142 LEU cc_start: 0.8095 (tp) cc_final: 0.7895 (tp) REVERT: E 232 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8845 (mp0) REVERT: E 267 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9284 (mm) REVERT: E 302 TRP cc_start: 0.8467 (m-10) cc_final: 0.7690 (m100) REVERT: E 366 MET cc_start: 0.8990 (mtp) cc_final: 0.8656 (mtm) REVERT: E 435 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8796 (mp0) REVERT: E 498 CYS cc_start: 0.8783 (t) cc_final: 0.8436 (t) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.1845 time to fit residues: 18.4562 Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.049059 restraints weight = 27148.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.051025 restraints weight = 13518.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052301 restraints weight = 8683.290| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6750 Z= 0.170 Angle : 0.531 5.764 9186 Z= 0.273 Chirality : 0.040 0.140 976 Planarity : 0.004 0.043 1178 Dihedral : 5.009 54.635 1013 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.86 % Allowed : 10.29 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 793 helix: 1.71 (0.26), residues: 415 sheet: 0.67 (0.75), residues: 41 loop : 0.22 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.015 0.001 PHE E 369 TYR 0.017 0.001 TYR B 473 ARG 0.003 0.001 ARG E 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 7) link_NAG-ASN : angle 1.85657 ( 21) hydrogen bonds : bond 0.03864 ( 322) hydrogen bonds : angle 4.39906 ( 915) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.59745 ( 12) covalent geometry : bond 0.00374 ( 6737) covalent geometry : angle 0.52170 ( 9153) *********************** 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 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9266 (mt0) cc_final: 0.8979 (mt0) REVERT: B 448 ASN cc_start: 0.9280 (t0) cc_final: 0.8862 (t0) REVERT: B 467 ASP cc_start: 0.8245 (t0) cc_final: 0.7933 (t0) REVERT: E 62 MET cc_start: 0.9433 (mtp) cc_final: 0.8993 (mtm) REVERT: E 108 LEU cc_start: 0.8528 (tp) cc_final: 0.8124 (tp) REVERT: E 208 GLU cc_start: 0.8796 (tt0) cc_final: 0.8489 (tm-30) REVERT: E 232 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8841 (mp0) REVERT: E 277 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8690 (t0) REVERT: E 366 MET cc_start: 0.9020 (mtp) cc_final: 0.8726 (mtp) REVERT: E 435 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8715 (mp0) REVERT: E 498 CYS cc_start: 0.9132 (t) cc_final: 0.8721 (t) outliers start: 13 outliers final: 7 residues processed: 66 average time/residue: 0.2076 time to fit residues: 19.3599 Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.049611 restraints weight = 27022.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.051586 restraints weight = 13650.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052897 restraints weight = 8862.482| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3222 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= 0.123 Angle : 0.510 5.912 9186 Z= 0.260 Chirality : 0.039 0.130 976 Planarity : 0.004 0.043 1178 Dihedral : 4.826 55.344 1013 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.29 % Allowed : 11.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.30), residues: 793 helix: 1.71 (0.26), residues: 415 sheet: 0.39 (0.69), residues: 51 loop : 0.30 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.012 0.001 PHE E 369 TYR 0.011 0.001 TYR B 453 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 7) link_NAG-ASN : angle 1.73489 ( 21) hydrogen bonds : bond 0.03626 ( 322) hydrogen bonds : angle 4.30565 ( 915) SS BOND : bond 0.00385 ( 6) SS BOND : angle 1.58813 ( 12) covalent geometry : bond 0.00273 ( 6737) covalent geometry : angle 0.50099 ( 9153) *********************** 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 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7902 (ptmm) REVERT: B 409 GLN cc_start: 0.9288 (mt0) cc_final: 0.9012 (mt0) REVERT: B 424 LYS cc_start: 0.8823 (tptt) cc_final: 0.8336 (tppt) REVERT: B 448 ASN cc_start: 0.9276 (t0) cc_final: 0.8875 (t0) REVERT: B 467 ASP cc_start: 0.8153 (t0) cc_final: 0.7762 (t0) REVERT: E 62 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9236 (mtp) REVERT: E 108 LEU cc_start: 0.8517 (tp) cc_final: 0.8137 (tp) REVERT: E 208 GLU cc_start: 0.8815 (tt0) cc_final: 0.8489 (tm-30) REVERT: E 232 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8819 (mp0) REVERT: E 277 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8642 (t0) REVERT: E 366 MET cc_start: 0.8992 (mtp) cc_final: 0.8724 (mtp) REVERT: E 435 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: E 498 CYS cc_start: 0.9042 (t) cc_final: 0.8699 (t) outliers start: 16 outliers final: 6 residues processed: 68 average time/residue: 0.2061 time to fit residues: 18.9615 Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049683 restraints weight = 26558.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051640 restraints weight = 13363.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052910 restraints weight = 8614.003| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6750 Z= 0.122 Angle : 0.498 5.527 9186 Z= 0.255 Chirality : 0.039 0.128 976 Planarity : 0.003 0.040 1178 Dihedral : 4.735 55.739 1013 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 11.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.30), residues: 793 helix: 1.79 (0.26), residues: 413 sheet: 0.40 (0.70), residues: 51 loop : 0.41 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.012 0.001 PHE E 369 TYR 0.021 0.001 TYR B 473 ARG 0.002 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 7) link_NAG-ASN : angle 1.67457 ( 21) hydrogen bonds : bond 0.03526 ( 322) hydrogen bonds : angle 4.27270 ( 915) SS BOND : bond 0.00376 ( 6) SS BOND : angle 1.48008 ( 12) covalent geometry : bond 0.00272 ( 6737) covalent geometry : angle 0.48930 ( 9153) *********************** 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 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9304 (mt0) cc_final: 0.9079 (mt0) REVERT: B 424 LYS cc_start: 0.8844 (tptt) cc_final: 0.8397 (tppt) REVERT: B 448 ASN cc_start: 0.9254 (t0) cc_final: 0.8868 (t0) REVERT: B 467 ASP cc_start: 0.8106 (t0) cc_final: 0.7722 (t0) REVERT: E 62 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9184 (mtp) REVERT: E 108 LEU cc_start: 0.8498 (tp) cc_final: 0.8120 (tp) REVERT: E 208 GLU cc_start: 0.8832 (tt0) cc_final: 0.8521 (tm-30) REVERT: E 232 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8817 (mp0) REVERT: E 277 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8718 (t0) REVERT: E 366 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8726 (mtp) REVERT: E 435 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8696 (mp0) REVERT: E 498 CYS cc_start: 0.9138 (t) cc_final: 0.8561 (t) outliers start: 15 outliers final: 8 residues processed: 65 average time/residue: 0.2018 time to fit residues: 18.0281 Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 52 optimal weight: 0.0030 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.049351 restraints weight = 26630.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.051281 restraints weight = 13626.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052567 restraints weight = 8876.023| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6750 Z= 0.123 Angle : 0.507 6.539 9186 Z= 0.257 Chirality : 0.039 0.130 976 Planarity : 0.003 0.039 1178 Dihedral : 4.669 56.012 1013 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.14 % Allowed : 12.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.30), residues: 793 helix: 1.80 (0.26), residues: 413 sheet: 0.42 (0.71), residues: 51 loop : 0.45 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.011 0.001 PHE E 369 TYR 0.017 0.001 TYR B 473 ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 7) link_NAG-ASN : angle 1.63331 ( 21) hydrogen bonds : bond 0.03484 ( 322) hydrogen bonds : angle 4.25374 ( 915) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.39659 ( 12) covalent geometry : bond 0.00277 ( 6737) covalent geometry : angle 0.49962 ( 9153) *********************** 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 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9332 (mt0) cc_final: 0.9096 (mt0) REVERT: B 424 LYS cc_start: 0.8830 (tptt) cc_final: 0.8378 (tppt) REVERT: B 448 ASN cc_start: 0.9254 (t0) cc_final: 0.8865 (t0) REVERT: B 467 ASP cc_start: 0.8108 (t0) cc_final: 0.7780 (t0) REVERT: E 62 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.9239 (mtp) REVERT: E 108 LEU cc_start: 0.8512 (tp) cc_final: 0.8140 (tp) REVERT: E 208 GLU cc_start: 0.8831 (tt0) cc_final: 0.8530 (tm-30) REVERT: E 232 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8811 (mp0) REVERT: E 277 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8806 (t0) REVERT: E 366 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8748 (mtp) REVERT: E 435 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: E 474 MET cc_start: 0.8260 (mmp) cc_final: 0.7987 (mmm) REVERT: E 498 CYS cc_start: 0.9129 (t) cc_final: 0.8724 (t) outliers start: 15 outliers final: 8 residues processed: 67 average time/residue: 0.2124 time to fit residues: 19.2613 Evaluate side-chains 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.063457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.049977 restraints weight = 26671.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.051925 restraints weight = 13355.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053223 restraints weight = 8601.374| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6750 Z= 0.105 Angle : 0.499 6.737 9186 Z= 0.252 Chirality : 0.039 0.129 976 Planarity : 0.003 0.038 1178 Dihedral : 4.548 56.316 1013 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.71 % Allowed : 12.71 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.30), residues: 793 helix: 1.82 (0.26), residues: 413 sheet: 0.41 (0.71), residues: 51 loop : 0.49 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.010 0.001 PHE E 369 TYR 0.017 0.001 TYR B 473 ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 7) link_NAG-ASN : angle 1.59346 ( 21) hydrogen bonds : bond 0.03344 ( 322) hydrogen bonds : angle 4.16802 ( 915) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.35867 ( 12) covalent geometry : bond 0.00237 ( 6737) covalent geometry : angle 0.49125 ( 9153) *********************** 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 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9346 (mt0) cc_final: 0.9118 (mt0) REVERT: B 424 LYS cc_start: 0.8822 (tptt) cc_final: 0.8303 (tppt) REVERT: B 448 ASN cc_start: 0.9252 (t0) cc_final: 0.8873 (t0) REVERT: B 467 ASP cc_start: 0.8036 (t0) cc_final: 0.7743 (t0) REVERT: E 62 MET cc_start: 0.9501 (OUTLIER) cc_final: 0.9191 (mtm) REVERT: E 108 LEU cc_start: 0.8523 (tp) cc_final: 0.8136 (tp) REVERT: E 208 GLU cc_start: 0.8826 (tt0) cc_final: 0.8513 (tm-30) REVERT: E 232 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8806 (mp0) REVERT: E 366 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8738 (mtp) REVERT: E 376 MET cc_start: 0.9044 (ttm) cc_final: 0.8808 (mmm) REVERT: E 435 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8641 (mp0) REVERT: E 474 MET cc_start: 0.8231 (mmp) cc_final: 0.7997 (mmm) REVERT: E 498 CYS cc_start: 0.9112 (t) cc_final: 0.8702 (t) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.1972 time to fit residues: 17.3049 Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN E 277 ASN E 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047277 restraints weight = 27210.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.049186 restraints weight = 13558.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.050451 restraints weight = 8745.734| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6750 Z= 0.203 Angle : 0.566 6.648 9186 Z= 0.289 Chirality : 0.041 0.152 976 Planarity : 0.004 0.040 1178 Dihedral : 4.967 55.463 1013 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.86 % Allowed : 13.14 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.30), residues: 793 helix: 1.73 (0.26), residues: 412 sheet: 0.23 (0.70), residues: 51 loop : 0.50 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.006 0.001 HIS E 34 PHE 0.014 0.002 PHE E 369 TYR 0.023 0.001 TYR E 613 ARG 0.003 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 7) link_NAG-ASN : angle 1.68880 ( 21) hydrogen bonds : bond 0.03861 ( 322) hydrogen bonds : angle 4.35447 ( 915) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.37946 ( 12) covalent geometry : bond 0.00447 ( 6737) covalent geometry : angle 0.55925 ( 9153) *********************** 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 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9315 (mt0) cc_final: 0.9012 (mt0) REVERT: B 424 LYS cc_start: 0.8878 (tptt) cc_final: 0.8484 (tppt) REVERT: B 444 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8915 (ptpp) REVERT: B 467 ASP cc_start: 0.8147 (t0) cc_final: 0.7870 (t0) REVERT: E 62 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.9184 (mtp) REVERT: E 208 GLU cc_start: 0.8839 (tt0) cc_final: 0.8568 (tm-30) REVERT: E 232 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8824 (mp0) REVERT: E 249 MET cc_start: 0.8644 (ttm) cc_final: 0.8235 (mtp) REVERT: E 277 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8923 (t0) REVERT: E 366 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8669 (mtp) REVERT: E 498 CYS cc_start: 0.9218 (t) cc_final: 0.8879 (t) REVERT: E 613 TYR cc_start: 0.8223 (t80) cc_final: 0.7930 (t80) outliers start: 13 outliers final: 7 residues processed: 64 average time/residue: 0.2033 time to fit residues: 17.8979 Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.0070 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.049003 restraints weight = 27221.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050938 restraints weight = 13813.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052211 restraints weight = 8994.428| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6750 Z= 0.112 Angle : 0.538 8.827 9186 Z= 0.269 Chirality : 0.040 0.126 976 Planarity : 0.003 0.041 1178 Dihedral : 4.704 56.057 1013 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.29 % Allowed : 14.14 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.30), residues: 793 helix: 1.73 (0.26), residues: 415 sheet: 0.27 (0.72), residues: 51 loop : 0.49 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.010 0.001 PHE E 369 TYR 0.023 0.001 TYR E 613 ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 7) link_NAG-ASN : angle 1.63551 ( 21) hydrogen bonds : bond 0.03473 ( 322) hydrogen bonds : angle 4.20096 ( 915) SS BOND : bond 0.00309 ( 6) SS BOND : angle 1.33913 ( 12) covalent geometry : bond 0.00253 ( 6737) covalent geometry : angle 0.53118 ( 9153) ********************** 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9326 (mt0) cc_final: 0.9087 (mt0) REVERT: B 424 LYS cc_start: 0.8875 (tptt) cc_final: 0.8408 (tppt) REVERT: B 467 ASP cc_start: 0.8046 (t0) cc_final: 0.7761 (t0) REVERT: E 62 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9079 (mtm) REVERT: E 208 GLU cc_start: 0.8851 (tt0) cc_final: 0.8569 (tm-30) REVERT: E 249 MET cc_start: 0.8602 (ttm) cc_final: 0.8144 (mtp) REVERT: E 277 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8894 (t0) REVERT: E 366 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8672 (mtp) REVERT: E 498 CYS cc_start: 0.9148 (t) cc_final: 0.8612 (t) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.2013 time to fit residues: 17.1483 Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.047161 restraints weight = 27770.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049033 restraints weight = 14030.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050291 restraints weight = 9159.404| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6750 Z= 0.205 Angle : 0.587 8.399 9186 Z= 0.295 Chirality : 0.042 0.142 976 Planarity : 0.004 0.044 1178 Dihedral : 5.011 55.509 1013 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.43 % Allowed : 14.29 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.30), residues: 793 helix: 1.73 (0.26), residues: 415 sheet: 0.12 (0.71), residues: 51 loop : 0.50 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.014 0.001 PHE E 369 TYR 0.015 0.001 TYR B 453 ARG 0.002 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 7) link_NAG-ASN : angle 1.74848 ( 21) hydrogen bonds : bond 0.03802 ( 322) hydrogen bonds : angle 4.37606 ( 915) SS BOND : bond 0.00452 ( 6) SS BOND : angle 1.30814 ( 12) covalent geometry : bond 0.00456 ( 6737) covalent geometry : angle 0.58052 ( 9153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.19 seconds wall clock time: 43 minutes 17.84 seconds (2597.84 seconds total)