Starting phenix.real_space_refine on Thu Jul 2 04:36:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sxy_25510/07_2026/7sxy_25510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxy_25510/07_2026/7sxy_25510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxy_25510/07_2026/7sxy_25510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxy_25510/07_2026/7sxy_25510.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sxy_25510/07_2026/7sxy_25510.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sxy_25510/07_2026/7sxy_25510.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sxy_25510/07_2026/7sxy_25510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxy_25510/07_2026/7sxy_25510.cif" } resolution = 2.79 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= -0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4191 2.51 5 N 1080 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6557 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 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: 1.65, per 1000 atoms: 0.25 Number of scatterers: 6557 At special positions: 0 Unit cell: (80, 83, 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 1249 8.00 N 1080 7.00 C 4191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 515.8 milliseconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 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: 0.14 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: 3.674A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.832A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.742A 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: 4.034A 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: 3.942A 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: 3.707A 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: 3.682A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.762A 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: 3.765A 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: 3.545A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.658A 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: 4.219A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.344A 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: 3.706A 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: 4.397A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.905A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.860A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.657A 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: 6.069A 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: 6.304A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 917 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: 0.77 Time building geometry restraints manager: 0.57 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: 1785 1.47 - 1.60: 2811 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6741 Sorted by residual: 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 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.75e+00 ... (remaining 6736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8820 2.02 - 4.05: 297 4.05 - 6.07: 35 6.07 - 8.09: 7 8.09 - 10.12: 4 Bond angle restraints: 9163 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 128.94 -6.12 1.42e+00 4.96e-01 1.86e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.47 -9.07 2.30e+00 1.89e-01 1.55e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CB MET E 323 " pdb=" CG MET E 323 " pdb=" SD MET E 323 " ideal model delta sigma weight residual 112.70 122.82 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 117.77 -4.61 1.42e+00 4.96e-01 1.05e+01 ... (remaining 9158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3565 17.13 - 34.25: 297 34.25 - 51.37: 42 51.37 - 68.50: 8 68.50 - 85.62: 12 Dihedral angle restraints: 3924 sinusoidal: 1582 harmonic: 2342 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -43.13 -42.87 1 1.00e+01 1.00e-02 2.56e+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 16.37 62.63 1 2.00e+01 2.50e-03 1.30e+01 dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 698 0.051 - 0.102: 202 0.102 - 0.153: 63 0.153 - 0.203: 13 0.203 - 0.254: 3 Chirality restraints: 979 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASN E 437 " pdb=" N ASN E 437 " pdb=" C ASN E 437 " pdb=" CB ASN E 437 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 976 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ARG E 169 " -0.059 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.022 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 168 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C TRP E 168 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP E 168 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG E 169 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO E 590 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.037 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1911 2.82 - 3.34: 6008 3.34 - 3.86: 11540 3.86 - 4.38: 13065 4.38 - 4.90: 22546 Nonbonded interactions: 55070 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR E 41 " model vdw 2.317 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.333 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.343 3.040 nonbonded pdb=" OH TYR E 237 " pdb=" O VAL E 485 " model vdw 2.353 3.040 ... (remaining 55065 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=0.50 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: 3.960 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.620 Find NCS groups from input model: 0.030 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:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 0.057 6754 Z= 0.242 Angle : 0.871 11.463 9196 Z= 0.462 Chirality : 0.056 0.254 979 Planarity : 0.007 0.065 1179 Dihedral : 13.351 85.622 2404 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.48 (0.26), residues: 794 helix: -0.05 (0.23), residues: 396 sheet: 0.71 (0.65), residues: 52 loop : -0.67 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 460 TYR 0.033 0.002 TYR E 385 PHE 0.029 0.003 PHE E 369 TRP 0.020 0.002 TRP E 473 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 ( 6741) covalent geometry : angle 0.83966 / 0.46 ( 9163) SS BOND : bond 0.00630 / 0.39 ( 6) SS BOND : angle 2.76808 / 1.60 ( 12) hydrogen bonds : bond 0.14004 / 9.59 ( 325) hydrogen bonds : angle 6.29074 / 4.40 ( 917) link_NAG-ASN : bond 0.00779 / 0.40 ( 7) link_NAG-ASN : angle 4.47900 / 3.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: E 156 LEU cc_start: 0.9544 (mm) cc_final: 0.8932 (tm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.5428 time to fit residues: 40.9371 Evaluate side-chains 50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.053062 restraints weight = 17489.786| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.12 r_work: 0.2734 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6754 Z= 0.164 Angle : 0.604 7.269 9196 Z= 0.304 Chirality : 0.042 0.155 979 Planarity : 0.005 0.047 1179 Dihedral : 4.427 17.243 867 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.86 % Allowed : 7.85 % Favored : 91.30 % 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: 0.65 (0.28), residues: 794 helix: 1.01 (0.25), residues: 398 sheet: 0.70 (0.66), residues: 53 loop : -0.19 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 219 TYR 0.015 0.001 TYR E 385 PHE 0.017 0.001 PHE E 369 TRP 0.020 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 6741) covalent geometry : angle 0.58174 / 0.30 ( 9163) SS BOND : bond 0.00488 / 0.30 ( 6) SS BOND : angle 2.26941 / 1.24 ( 12) hydrogen bonds : bond 0.04822 / 3.09 ( 325) hydrogen bonds : angle 4.71386 / 3.32 ( 917) link_NAG-ASN : bond 0.00431 / 0.22 ( 7) link_NAG-ASN : angle 3.04910 / 2.23 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8949 (ptpp) cc_final: 0.8748 (ptpp) REVERT: B 471 GLU cc_start: 0.8848 (tp30) cc_final: 0.8620 (tp30) REVERT: E 91 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8761 (tm) REVERT: E 249 MET cc_start: 0.8880 (ttm) cc_final: 0.8639 (mtt) REVERT: E 360 MET cc_start: 0.9260 (ttm) cc_final: 0.9040 (ttm) REVERT: E 480 MET cc_start: 0.9180 (mtp) cc_final: 0.8949 (mtm) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 0.5196 time to fit residues: 28.4121 Evaluate side-chains 51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 354 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.050689 restraints weight = 21308.436| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.35 r_work: 0.2667 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6754 Z= 0.209 Angle : 0.594 7.755 9196 Z= 0.302 Chirality : 0.042 0.156 979 Planarity : 0.004 0.042 1179 Dihedral : 4.399 17.606 867 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.00 % Allowed : 9.13 % Favored : 89.87 % 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: 1.04 (0.29), residues: 794 helix: 1.27 (0.25), residues: 397 sheet: 0.65 (0.67), residues: 53 loop : 0.12 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.018 0.001 TYR E 385 PHE 0.019 0.002 PHE E 523 TRP 0.018 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 ( 6741) covalent geometry : angle 0.57713 / 0.30 ( 9163) SS BOND : bond 0.00531 / 0.31 ( 6) SS BOND : angle 2.08737 / 1.12 ( 12) hydrogen bonds : bond 0.04966 / 3.20 ( 325) hydrogen bonds : angle 4.57188 / 3.23 ( 917) link_NAG-ASN : bond 0.00324 / 0.17 ( 7) link_NAG-ASN : angle 2.60879 / 1.89 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.8989 (tp30) cc_final: 0.8773 (tp30) REVERT: E 91 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8844 (tm) REVERT: E 249 MET cc_start: 0.8904 (ttm) cc_final: 0.8672 (mtt) REVERT: E 332 MET cc_start: 0.9113 (ttp) cc_final: 0.8874 (ttm) REVERT: E 360 MET cc_start: 0.9257 (ttm) cc_final: 0.9038 (ttm) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.5004 time to fit residues: 25.8534 Evaluate side-chains 49 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.069648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.051116 restraints weight = 30482.293| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.00 r_work: 0.2663 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6754 Z= 0.143 Angle : 0.537 6.791 9196 Z= 0.270 Chirality : 0.040 0.139 979 Planarity : 0.004 0.042 1179 Dihedral : 4.171 15.479 867 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.00 % Allowed : 8.99 % Favored : 90.01 % 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: 1.17 (0.29), residues: 794 helix: 1.37 (0.26), residues: 399 sheet: 0.71 (0.68), residues: 53 loop : 0.20 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.014 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.015 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6741) covalent geometry : angle 0.52334 / 0.27 ( 9163) SS BOND : bond 0.00380 / 0.23 ( 6) SS BOND : angle 1.61073 / 0.87 ( 12) hydrogen bonds : bond 0.04473 / 2.86 ( 325) hydrogen bonds : angle 4.44930 / 3.14 ( 917) link_NAG-ASN : bond 0.00313 / 0.16 ( 7) link_NAG-ASN : angle 2.30166 / 1.64 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.253 Fit side-chains REVERT: E 91 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8784 (tm) REVERT: E 249 MET cc_start: 0.8901 (ttm) cc_final: 0.8676 (mtt) REVERT: E 332 MET cc_start: 0.9107 (ttp) cc_final: 0.8853 (ttm) REVERT: E 360 MET cc_start: 0.9269 (ttm) cc_final: 0.9023 (ttm) REVERT: E 366 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8426 (ttp) outliers start: 7 outliers final: 0 residues processed: 48 average time/residue: 0.5156 time to fit residues: 26.0524 Evaluate side-chains 46 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.049091 restraints weight = 20521.267| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.35 r_work: 0.2619 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 6754 Z= 0.246 Angle : 0.600 7.834 9196 Z= 0.304 Chirality : 0.043 0.155 979 Planarity : 0.004 0.042 1179 Dihedral : 4.358 15.907 867 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.57 % Allowed : 8.56 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 794 helix: 1.39 (0.26), residues: 397 sheet: 0.65 (0.69), residues: 53 loop : 0.33 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.018 0.001 TYR E 385 PHE 0.018 0.002 PHE E 523 TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.25 ( 6741) covalent geometry : angle 0.58997 / 0.30 ( 9163) SS BOND : bond 0.00369 / 0.25 ( 6) SS BOND : angle 1.21666 / 0.65 ( 12) hydrogen bonds : bond 0.05002 / 3.23 ( 325) hydrogen bonds : angle 4.53676 / 3.21 ( 917) link_NAG-ASN : bond 0.00236 / 0.14 ( 7) link_NAG-ASN : angle 2.23919 / 1.57 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.248 Fit side-chains REVERT: B 356 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8999 (ttmt) REVERT: B 471 GLU cc_start: 0.9026 (tp30) cc_final: 0.8793 (tp30) REVERT: E 55 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8083 (p) REVERT: E 91 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8822 (tm) REVERT: E 156 LEU cc_start: 0.9495 (mm) cc_final: 0.9093 (tm) REVERT: E 249 MET cc_start: 0.8888 (ttm) cc_final: 0.8617 (mtt) REVERT: E 332 MET cc_start: 0.9031 (ttp) cc_final: 0.8804 (ttm) REVERT: E 360 MET cc_start: 0.9270 (ttm) cc_final: 0.9025 (ttm) REVERT: E 366 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8485 (ttp) outliers start: 11 outliers final: 1 residues processed: 52 average time/residue: 0.4739 time to fit residues: 25.9668 Evaluate side-chains 49 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** E 34 HIS A ** 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 = 0.3225 r_free = 0.3225 target = 0.068454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.049943 restraints weight = 30987.392| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 4.07 r_work: 0.2624 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6754 Z= 0.145 Angle : 0.539 7.145 9196 Z= 0.270 Chirality : 0.040 0.135 979 Planarity : 0.004 0.042 1179 Dihedral : 4.190 14.936 867 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.71 % Allowed : 9.42 % Favored : 89.87 % 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: 1.32 (0.29), residues: 794 helix: 1.54 (0.26), residues: 390 sheet: 0.56 (0.69), residues: 53 loop : 0.28 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.014 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6741) covalent geometry : angle 0.52885 / 0.27 ( 9163) SS BOND : bond 0.00313 / 0.21 ( 6) SS BOND : angle 0.92675 / 0.52 ( 12) hydrogen bonds : bond 0.04483 / 2.87 ( 325) hydrogen bonds : angle 4.42348 / 3.12 ( 917) link_NAG-ASN : bond 0.00270 / 0.13 ( 7) link_NAG-ASN : angle 2.13591 / 1.48 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.190 Fit side-chains REVERT: B 471 GLU cc_start: 0.9078 (tp30) cc_final: 0.8829 (tp30) REVERT: E 55 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8164 (p) REVERT: E 156 LEU cc_start: 0.9490 (mm) cc_final: 0.9085 (tm) REVERT: E 249 MET cc_start: 0.8860 (ttm) cc_final: 0.8624 (mtt) REVERT: E 332 MET cc_start: 0.9064 (ttp) cc_final: 0.8842 (ttm) REVERT: E 360 MET cc_start: 0.9263 (ttm) cc_final: 0.8996 (ttm) REVERT: E 366 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8437 (ttp) REVERT: E 480 MET cc_start: 0.9066 (mtp) cc_final: 0.8785 (mtm) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.4883 time to fit residues: 25.7052 Evaluate side-chains 50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS A ** 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 = 0.3229 r_free = 0.3229 target = 0.068633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.050091 restraints weight = 31357.527| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 4.08 r_work: 0.2630 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6754 Z= 0.144 Angle : 0.530 6.844 9196 Z= 0.266 Chirality : 0.040 0.137 979 Planarity : 0.004 0.042 1179 Dihedral : 4.123 14.944 867 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.00 % Allowed : 9.42 % Favored : 89.59 % 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: 1.34 (0.29), residues: 794 helix: 1.56 (0.26), residues: 392 sheet: 0.54 (0.70), residues: 53 loop : 0.30 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.014 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6741) covalent geometry : angle 0.52047 / 0.26 ( 9163) SS BOND : bond 0.00285 / 0.19 ( 6) SS BOND : angle 0.83043 / 0.47 ( 12) hydrogen bonds : bond 0.04428 / 2.83 ( 325) hydrogen bonds : angle 4.37982 / 3.09 ( 917) link_NAG-ASN : bond 0.00250 / 0.12 ( 7) link_NAG-ASN : angle 2.05828 / 1.42 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.155 Fit side-chains REVERT: B 471 GLU cc_start: 0.9079 (tp30) cc_final: 0.8828 (tp30) REVERT: E 55 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8181 (p) REVERT: E 91 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8798 (tm) REVERT: E 156 LEU cc_start: 0.9493 (mm) cc_final: 0.9099 (tm) REVERT: E 249 MET cc_start: 0.8868 (ttm) cc_final: 0.8625 (mtt) REVERT: E 332 MET cc_start: 0.9017 (ttp) cc_final: 0.8790 (ttm) REVERT: E 360 MET cc_start: 0.9260 (ttm) cc_final: 0.8989 (ttm) REVERT: E 366 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8404 (ttp) REVERT: E 480 MET cc_start: 0.9108 (mtp) cc_final: 0.8834 (mtm) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.5387 time to fit residues: 29.4978 Evaluate side-chains 53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS A ** 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 = 0.3221 r_free = 0.3221 target = 0.068205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.050757 restraints weight = 17940.725| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.17 r_work: 0.2670 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6754 Z= 0.168 Angle : 0.543 7.405 9196 Z= 0.272 Chirality : 0.041 0.141 979 Planarity : 0.004 0.042 1179 Dihedral : 4.130 15.194 867 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.86 % Allowed : 9.99 % Favored : 89.16 % 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: 1.38 (0.29), residues: 794 helix: 1.56 (0.26), residues: 393 sheet: 0.52 (0.70), residues: 53 loop : 0.37 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.015 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 6741) covalent geometry : angle 0.53409 / 0.27 ( 9163) SS BOND : bond 0.00313 / 0.21 ( 6) SS BOND : angle 0.85564 / 0.50 ( 12) hydrogen bonds : bond 0.04497 / 2.89 ( 325) hydrogen bonds : angle 4.38523 / 3.10 ( 917) link_NAG-ASN : bond 0.00224 / 0.12 ( 7) link_NAG-ASN : angle 2.02950 / 1.41 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.170 Fit side-chains REVERT: E 55 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8178 (p) REVERT: E 91 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8799 (tm) REVERT: E 152 MET cc_start: 0.8849 (mmm) cc_final: 0.8601 (tpt) REVERT: E 156 LEU cc_start: 0.9498 (mm) cc_final: 0.9102 (tm) REVERT: E 249 MET cc_start: 0.8834 (ttm) cc_final: 0.8586 (mtt) REVERT: E 366 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8404 (ttp) REVERT: E 480 MET cc_start: 0.9094 (mtp) cc_final: 0.8811 (mtm) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.5184 time to fit residues: 26.6871 Evaluate side-chains 52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 0.0670 chunk 32 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS A ** 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 = 0.3222 r_free = 0.3222 target = 0.068283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.049743 restraints weight = 32310.022| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 4.13 r_work: 0.2618 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6754 Z= 0.161 Angle : 0.544 8.399 9196 Z= 0.272 Chirality : 0.041 0.139 979 Planarity : 0.004 0.042 1179 Dihedral : 4.117 15.116 867 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.86 % Allowed : 10.27 % Favored : 88.87 % 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: 1.41 (0.29), residues: 794 helix: 1.57 (0.26), residues: 393 sheet: 0.51 (0.71), residues: 53 loop : 0.41 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.015 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6741) covalent geometry : angle 0.53545 / 0.27 ( 9163) SS BOND : bond 0.00311 / 0.21 ( 6) SS BOND : angle 0.84902 / 0.50 ( 12) hydrogen bonds : bond 0.04476 / 2.87 ( 325) hydrogen bonds : angle 4.37618 / 3.10 ( 917) link_NAG-ASN : bond 0.00230 / 0.12 ( 7) link_NAG-ASN : angle 2.02085 / 1.39 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.8972 (tp30) cc_final: 0.8762 (tp30) REVERT: E 55 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8202 (p) REVERT: E 91 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8806 (tm) REVERT: E 152 MET cc_start: 0.8835 (mmm) cc_final: 0.8579 (tpt) REVERT: E 156 LEU cc_start: 0.9486 (mm) cc_final: 0.9080 (tm) REVERT: E 249 MET cc_start: 0.8834 (ttm) cc_final: 0.8573 (mtt) REVERT: E 332 MET cc_start: 0.9023 (ttp) cc_final: 0.8666 (ttm) REVERT: E 360 MET cc_start: 0.9263 (ttm) cc_final: 0.9023 (ttm) REVERT: E 366 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8422 (ttp) REVERT: E 480 MET cc_start: 0.9107 (mtp) cc_final: 0.8834 (mtm) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.5185 time to fit residues: 28.2626 Evaluate side-chains 54 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 19 optimal weight: 0.0170 chunk 73 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** E 34 HIS A ** 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 = 0.3246 r_free = 0.3246 target = 0.069476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.051013 restraints weight = 29089.355| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.97 r_work: 0.2660 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6754 Z= 0.116 Angle : 0.528 9.294 9196 Z= 0.263 Chirality : 0.040 0.131 979 Planarity : 0.004 0.042 1179 Dihedral : 4.030 14.958 867 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.71 % Allowed : 10.70 % Favored : 88.59 % 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: 1.44 (0.29), residues: 794 helix: 1.59 (0.26), residues: 394 sheet: 0.44 (0.71), residues: 53 loop : 0.45 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.013 0.001 TYR E 385 PHE 0.015 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6741) covalent geometry : angle 0.51969 / 0.26 ( 9163) SS BOND : bond 0.00274 / 0.18 ( 6) SS BOND : angle 0.77514 / 0.46 ( 12) hydrogen bonds : bond 0.04259 / 2.73 ( 325) hydrogen bonds : angle 4.33140 / 3.06 ( 917) link_NAG-ASN : bond 0.00287 / 0.14 ( 7) link_NAG-ASN : angle 1.99238 / 1.37 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: B 458 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9082 (mmpt) REVERT: B 471 GLU cc_start: 0.8966 (tp30) cc_final: 0.8736 (tp30) REVERT: E 55 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8208 (p) REVERT: E 91 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8784 (tm) REVERT: E 156 LEU cc_start: 0.9485 (mm) cc_final: 0.9087 (tm) REVERT: E 249 MET cc_start: 0.8829 (ttm) cc_final: 0.8569 (mtt) REVERT: E 325 GLN cc_start: 0.8763 (tt0) cc_final: 0.8528 (tt0) REVERT: E 332 MET cc_start: 0.8999 (ttp) cc_final: 0.8650 (ttm) REVERT: E 360 MET cc_start: 0.9267 (ttm) cc_final: 0.8985 (ttm) REVERT: E 366 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8351 (ttp) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 0.5255 time to fit residues: 28.2538 Evaluate side-chains 50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS A ** 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 = 0.3238 r_free = 0.3238 target = 0.069079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.051136 restraints weight = 22057.629| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.49 r_work: 0.2665 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6754 Z= 0.139 Angle : 0.535 9.206 9196 Z= 0.267 Chirality : 0.040 0.136 979 Planarity : 0.004 0.042 1179 Dihedral : 4.009 14.905 867 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.71 % Allowed : 11.13 % Favored : 88.16 % 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: 794 helix: 1.60 (0.26), residues: 395 sheet: 0.41 (0.71), residues: 53 loop : 0.49 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.014 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6741) covalent geometry : angle 0.52712 / 0.27 ( 9163) SS BOND : bond 0.00279 / 0.19 ( 6) SS BOND : angle 0.78985 / 0.46 ( 12) hydrogen bonds : bond 0.04314 / 2.76 ( 325) hydrogen bonds : angle 4.33150 / 3.05 ( 917) link_NAG-ASN : bond 0.00238 / 0.12 ( 7) link_NAG-ASN : angle 1.98759 / 1.37 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.30 seconds wall clock time: 32 minutes 14.94 seconds (1934.94 seconds total)