Starting phenix.real_space_refine on Thu Jul 2 04:34:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dlq_27510/07_2026/8dlq_27510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlq_27510/07_2026/8dlq_27510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2026/8dlq_27510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2026/8dlq_27510.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2026/8dlq_27510.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2026/8dlq_27510.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2026/8dlq_27510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2026/8dlq_27510.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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 4190 2.51 5 N 1077 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 6552 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 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: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.56, per 1000 atoms: 0.24 Number of scatterers: 6552 At special positions: 0 Unit cell: (80, 83, 122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1248 8.00 N 1077 7.00 C 4190 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: 0.52 Conformation dependent library (CDL) restraints added in 385.0 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 57.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 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 405 through 410 removed outlier: 4.013A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.568A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.645A 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: 3.692A 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: 4.030A 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 147 through 155 Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.693A 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: 3.742A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.707A 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: 3.793A 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 Processing helix chain 'E' and resid 365 through 385 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: 4.296A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.509A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.315A 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: 3.654A 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: 4.420A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.851A 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: 3.864A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.578A 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: 6.123A 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: 6.521A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 924 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: 1.05 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2079 1.35 - 1.47: 1810 1.47 - 1.60: 2788 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.52e+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 5.58e+00 bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.31e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 8629 1.80 - 3.61: 455 3.61 - 5.41: 49 5.41 - 7.21: 15 7.21 - 9.01: 6 Bond angle restraints: 9154 Sorted by residual: angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 122.91 -9.01 1.80e+00 3.09e-01 2.51e+01 angle pdb=" CA TYR E 385 " pdb=" CB TYR E 385 " pdb=" CG TYR E 385 " ideal model delta sigma weight residual 113.90 122.12 -8.22 1.80e+00 3.09e-01 2.08e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.19 -5.83 1.42e+00 4.96e-01 1.69e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 112.60 115.96 -3.36 1.00e+00 1.00e+00 1.13e+01 ... (remaining 9149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 3553 16.95 - 33.90: 301 33.90 - 50.85: 38 50.85 - 67.80: 15 67.80 - 84.75: 10 Dihedral angle restraints: 3917 sinusoidal: 1578 harmonic: 2339 Sorted by residual: 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 15.31 63.69 1 2.00e+01 2.50e-03 1.34e+01 dihedral pdb=" SG CYS E 133 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " pdb=" CA CYS E 141 " ideal model delta sinusoidal sigma weight residual 79.00 16.53 62.47 1 2.00e+01 2.50e-03 1.29e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.95 8.35 0 2.50e+00 1.60e-01 1.12e+01 ... (remaining 3914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 687 0.053 - 0.106: 213 0.106 - 0.159: 63 0.159 - 0.212: 14 0.212 - 0.265: 2 Chirality restraints: 979 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 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+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 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASN E 437 " pdb=" N ASN E 437 " pdb=" C ASN E 437 " pdb=" CB ASN E 437 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 976 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C ARG E 169 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.019 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.030 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR B 495 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.62e+00 pdb=" N PRO E 590 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.039 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1891 2.82 - 3.34: 6027 3.34 - 3.86: 11482 3.86 - 4.38: 13057 4.38 - 4.90: 22523 Nonbonded interactions: 54980 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.296 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.353 3.120 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.354 3.120 nonbonded pdb=" OH TYR E 237 " pdb=" O VAL E 485 " model vdw 2.370 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.384 3.040 ... (remaining 54975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 6748 Z= 0.272 Angle : 0.939 11.763 9187 Z= 0.527 Chirality : 0.059 0.265 979 Planarity : 0.007 0.069 1176 Dihedral : 13.328 84.755 2399 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.43 % Allowed : 4.29 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.27), residues: 793 helix: 0.75 (0.24), residues: 391 sheet: 1.02 (0.65), residues: 42 loop : -0.35 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 460 TYR 0.046 0.002 TYR B 495 PHE 0.029 0.003 PHE E 369 TRP 0.021 0.002 TRP E 566 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.27 ( 6735) covalent geometry : angle 0.90869 / 0.52 ( 9154) SS BOND : bond 0.00637 / 0.39 ( 6) SS BOND : angle 2.29191 / 1.37 ( 12) hydrogen bonds : bond 0.14365 / 10.05 ( 326) hydrogen bonds : angle 6.28092 / 4.46 ( 924) link_NAG-ASN : bond 0.00918 / 0.48 ( 7) link_NAG-ASN : angle 4.79484 / 3.53 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.255 Fit side-chains REVERT: B 386 LYS cc_start: 0.8764 (pttm) cc_final: 0.8134 (pttm) REVERT: B 390 LEU cc_start: 0.8852 (mt) cc_final: 0.8415 (mt) REVERT: E 117 ASN cc_start: 0.8976 (t0) cc_final: 0.8354 (p0) REVERT: E 121 ASN cc_start: 0.8679 (m-40) cc_final: 0.8440 (m110) outliers start: 3 outliers final: 0 residues processed: 93 average time/residue: 0.6820 time to fit residues: 66.2395 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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: 0.0870 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN E 42 GLN E 374 HIS E 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.067132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.050555 restraints weight = 17537.715| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.09 r_work: 0.2671 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6748 Z= 0.146 Angle : 0.582 9.292 9187 Z= 0.294 Chirality : 0.041 0.146 979 Planarity : 0.004 0.041 1176 Dihedral : 4.273 16.075 866 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.43 % Allowed : 10.71 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.28), residues: 793 helix: 1.48 (0.25), residues: 398 sheet: 0.99 (0.73), residues: 42 loop : -0.13 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.024 0.001 TYR B 495 PHE 0.017 0.001 PHE E 369 TRP 0.015 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6735) covalent geometry : angle 0.55995 / 0.29 ( 9154) SS BOND : bond 0.00512 / 0.30 ( 6) SS BOND : angle 1.37125 / 0.72 ( 12) hydrogen bonds : bond 0.04698 / 3.11 ( 326) hydrogen bonds : angle 4.84294 / 3.42 ( 924) link_NAG-ASN : bond 0.00481 / 0.24 ( 7) link_NAG-ASN : angle 3.25643 / 2.41 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: B 528 LYS cc_start: 0.3636 (OUTLIER) cc_final: 0.3143 (pttp) REVERT: E 117 ASN cc_start: 0.9122 (t0) cc_final: 0.8434 (p0) REVERT: E 121 ASN cc_start: 0.8977 (m-40) cc_final: 0.8643 (m-40) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 0.6130 time to fit residues: 43.6639 Evaluate side-chains 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3210 r_free = 0.3210 target = 0.067270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.050569 restraints weight = 17490.858| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.04 r_work: 0.2675 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6748 Z= 0.136 Angle : 0.535 9.226 9187 Z= 0.269 Chirality : 0.040 0.128 979 Planarity : 0.004 0.042 1176 Dihedral : 4.114 15.889 866 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.00 % Allowed : 11.57 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.29), residues: 793 helix: 1.71 (0.26), residues: 398 sheet: 1.01 (0.76), residues: 42 loop : 0.14 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.021 0.001 TYR B 495 PHE 0.017 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 6735) covalent geometry : angle 0.51859 / 0.26 ( 9154) SS BOND : bond 0.00315 / 0.20 ( 6) SS BOND : angle 1.18638 / 0.65 ( 12) hydrogen bonds : bond 0.04377 / 2.90 ( 326) hydrogen bonds : angle 4.50289 / 3.19 ( 924) link_NAG-ASN : bond 0.00407 / 0.22 ( 7) link_NAG-ASN : angle 2.69459 / 2.02 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: B 528 LYS cc_start: 0.3520 (OUTLIER) cc_final: 0.3182 (pttp) REVERT: E 117 ASN cc_start: 0.9137 (t0) cc_final: 0.8425 (p0) REVERT: E 121 ASN cc_start: 0.8988 (m-40) cc_final: 0.8632 (m110) REVERT: E 123 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7721 (mtt) REVERT: E 480 MET cc_start: 0.9087 (mtp) cc_final: 0.8864 (mtm) REVERT: E 483 GLU cc_start: 0.8985 (tp30) cc_final: 0.8526 (tm-30) outliers start: 14 outliers final: 4 residues processed: 68 average time/residue: 0.6469 time to fit residues: 46.2616 Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3158 r_free = 0.3158 target = 0.064939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.048012 restraints weight = 17755.034| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.08 r_work: 0.2621 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6748 Z= 0.191 Angle : 0.556 7.548 9187 Z= 0.280 Chirality : 0.042 0.131 979 Planarity : 0.004 0.042 1176 Dihedral : 4.159 16.829 866 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.71 % Allowed : 12.29 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.29), residues: 793 helix: 1.82 (0.26), residues: 392 sheet: 0.84 (0.78), residues: 43 loop : 0.26 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.022 0.001 TYR B 495 PHE 0.018 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 6735) covalent geometry : angle 0.54204 / 0.28 ( 9154) SS BOND : bond 0.00293 / 0.20 ( 6) SS BOND : angle 1.16174 / 0.64 ( 12) hydrogen bonds : bond 0.04683 / 3.09 ( 326) hydrogen bonds : angle 4.49569 / 3.19 ( 924) link_NAG-ASN : bond 0.00334 / 0.19 ( 7) link_NAG-ASN : angle 2.54119 / 1.89 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: B 528 LYS cc_start: 0.3787 (OUTLIER) cc_final: 0.3443 (pttp) REVERT: E 291 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8005 (pp) REVERT: E 483 GLU cc_start: 0.8953 (tp30) cc_final: 0.8503 (tm-30) REVERT: E 534 LYS cc_start: 0.9511 (OUTLIER) cc_final: 0.9065 (mtpp) outliers start: 19 outliers final: 3 residues processed: 66 average time/residue: 0.6200 time to fit residues: 42.8397 Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 534 LYS Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3182 r_free = 0.3182 target = 0.065941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.049311 restraints weight = 17812.339| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.07 r_work: 0.2653 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6748 Z= 0.137 Angle : 0.527 6.647 9187 Z= 0.263 Chirality : 0.040 0.126 979 Planarity : 0.003 0.041 1176 Dihedral : 4.023 16.381 866 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.86 % Allowed : 13.86 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.30), residues: 793 helix: 1.73 (0.26), residues: 406 sheet: 0.76 (0.78), residues: 43 loop : 0.25 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.017 0.001 TYR B 495 PHE 0.016 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 0.00310 / 0.14 ( 6735) covalent geometry : angle 0.51440 / 0.26 ( 9154) SS BOND : bond 0.00287 / 0.19 ( 6) SS BOND : angle 1.10830 / 0.63 ( 12) hydrogen bonds : bond 0.04256 / 2.81 ( 326) hydrogen bonds : angle 4.37431 / 3.10 ( 924) link_NAG-ASN : bond 0.00324 / 0.18 ( 7) link_NAG-ASN : angle 2.31978 / 1.72 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 458 LYS cc_start: 0.9090 (mmpt) cc_final: 0.8886 (mmpt) REVERT: B 518 LEU cc_start: 0.8856 (mt) cc_final: 0.8422 (tt) REVERT: B 528 LYS cc_start: 0.3743 (OUTLIER) cc_final: 0.3211 (pttp) REVERT: E 483 GLU cc_start: 0.8931 (tp30) cc_final: 0.8479 (tm-30) outliers start: 13 outliers final: 3 residues processed: 63 average time/residue: 0.6170 time to fit residues: 40.7997 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3171 r_free = 0.3171 target = 0.065411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.048696 restraints weight = 17851.344| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.05 r_work: 0.2637 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6748 Z= 0.152 Angle : 0.532 6.800 9187 Z= 0.266 Chirality : 0.040 0.126 979 Planarity : 0.004 0.041 1176 Dihedral : 4.017 16.350 866 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.00 % Allowed : 14.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.30), residues: 793 helix: 1.70 (0.25), residues: 412 sheet: 0.87 (0.80), residues: 42 loop : 0.36 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.018 0.001 TYR B 495 PHE 0.016 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 0.00348 / 0.15 ( 6735) covalent geometry : angle 0.52102 / 0.26 ( 9154) SS BOND : bond 0.00302 / 0.20 ( 6) SS BOND : angle 1.09285 / 0.62 ( 12) hydrogen bonds : bond 0.04322 / 2.86 ( 326) hydrogen bonds : angle 4.37538 / 3.10 ( 924) link_NAG-ASN : bond 0.00301 / 0.17 ( 7) link_NAG-ASN : angle 2.21802 / 1.63 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: B 518 LEU cc_start: 0.8863 (mt) cc_final: 0.8434 (tt) REVERT: E 483 GLU cc_start: 0.8955 (tp30) cc_final: 0.8511 (tm-30) outliers start: 14 outliers final: 4 residues processed: 59 average time/residue: 0.6420 time to fit residues: 39.7944 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.0060 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3188 r_free = 0.3188 target = 0.066345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049767 restraints weight = 17506.156| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.02 r_work: 0.2666 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6748 Z= 0.121 Angle : 0.521 7.188 9187 Z= 0.260 Chirality : 0.040 0.124 979 Planarity : 0.003 0.041 1176 Dihedral : 3.923 15.567 866 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.29 % Allowed : 15.29 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.30), residues: 793 helix: 1.80 (0.26), residues: 406 sheet: 0.94 (0.81), residues: 42 loop : 0.36 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.016 0.001 TYR B 495 PHE 0.015 0.001 PHE E 369 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6735) covalent geometry : angle 0.51080 / 0.26 ( 9154) SS BOND : bond 0.00301 / 0.19 ( 6) SS BOND : angle 1.10940 / 0.64 ( 12) hydrogen bonds : bond 0.04046 / 2.67 ( 326) hydrogen bonds : angle 4.30359 / 3.05 ( 924) link_NAG-ASN : bond 0.00300 / 0.17 ( 7) link_NAG-ASN : angle 2.10548 / 1.54 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9209 (pt0) cc_final: 0.8778 (pm20) REVERT: B 518 LEU cc_start: 0.8882 (mt) cc_final: 0.8449 (tt) REVERT: E 291 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7729 (mm) REVERT: E 483 GLU cc_start: 0.8943 (tp30) cc_final: 0.8505 (tm-30) outliers start: 9 outliers final: 4 residues processed: 59 average time/residue: 0.6633 time to fit residues: 41.0595 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3183 r_free = 0.3183 target = 0.065913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.049426 restraints weight = 17668.759| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.03 r_work: 0.2657 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6748 Z= 0.136 Angle : 0.535 7.646 9187 Z= 0.266 Chirality : 0.040 0.125 979 Planarity : 0.003 0.040 1176 Dihedral : 3.932 15.724 866 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.29 % Allowed : 15.71 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.30), residues: 793 helix: 1.82 (0.26), residues: 406 sheet: 1.08 (0.81), residues: 42 loop : 0.41 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.017 0.001 TYR B 495 PHE 0.016 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 0.00312 / 0.14 ( 6735) covalent geometry : angle 0.52551 / 0.26 ( 9154) SS BOND : bond 0.00315 / 0.21 ( 6) SS BOND : angle 1.10824 / 0.64 ( 12) hydrogen bonds : bond 0.04109 / 2.72 ( 326) hydrogen bonds : angle 4.28706 / 3.04 ( 924) link_NAG-ASN : bond 0.00283 / 0.16 ( 7) link_NAG-ASN : angle 2.05851 / 1.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9217 (pt0) cc_final: 0.8794 (pm20) REVERT: B 458 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8717 (mmtt) REVERT: B 462 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8577 (mmmm) REVERT: B 518 LEU cc_start: 0.8920 (mt) cc_final: 0.8498 (tt) REVERT: B 528 LYS cc_start: 0.3927 (OUTLIER) cc_final: 0.3551 (pttp) REVERT: E 483 GLU cc_start: 0.8944 (tp30) cc_final: 0.8511 (tm-30) outliers start: 9 outliers final: 5 residues processed: 58 average time/residue: 0.6326 time to fit residues: 38.4465 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048671 restraints weight = 17887.105| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.04 r_work: 0.2638 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6748 Z= 0.153 Angle : 0.538 6.962 9187 Z= 0.270 Chirality : 0.040 0.127 979 Planarity : 0.003 0.040 1176 Dihedral : 3.982 16.011 866 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.86 % Allowed : 16.43 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.30), residues: 793 helix: 1.82 (0.26), residues: 406 sheet: 0.94 (0.81), residues: 42 loop : 0.44 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.018 0.001 TYR B 495 PHE 0.016 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6735) covalent geometry : angle 0.52837 / 0.27 ( 9154) SS BOND : bond 0.00300 / 0.20 ( 6) SS BOND : angle 1.12026 / 0.65 ( 12) hydrogen bonds : bond 0.04253 / 2.82 ( 326) hydrogen bonds : angle 4.32682 / 3.06 ( 924) link_NAG-ASN : bond 0.00282 / 0.16 ( 7) link_NAG-ASN : angle 2.08702 / 1.52 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9235 (pt0) cc_final: 0.8785 (pm20) REVERT: B 458 LYS cc_start: 0.9142 (mmmt) cc_final: 0.8808 (mmtt) REVERT: B 462 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8574 (mmmm) REVERT: B 518 LEU cc_start: 0.8945 (mt) cc_final: 0.8521 (tt) REVERT: B 528 LYS cc_start: 0.3935 (OUTLIER) cc_final: 0.3583 (pttp) REVERT: E 483 GLU cc_start: 0.8946 (tp30) cc_final: 0.8496 (tm-30) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.5713 time to fit residues: 32.4320 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL 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 46 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.0170 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3195 r_free = 0.3195 target = 0.066687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.049886 restraints weight = 17608.381| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.06 r_work: 0.2678 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6748 Z= 0.116 Angle : 0.523 7.514 9187 Z= 0.262 Chirality : 0.039 0.124 979 Planarity : 0.003 0.040 1176 Dihedral : 3.851 14.704 866 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.57 % Allowed : 16.86 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.30), residues: 793 helix: 1.80 (0.26), residues: 412 sheet: 1.07 (0.82), residues: 42 loop : 0.50 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.015 0.001 TYR B 495 PHE 0.015 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6735) covalent geometry : angle 0.51330 / 0.26 ( 9154) SS BOND : bond 0.00298 / 0.19 ( 6) SS BOND : angle 1.07146 / 0.63 ( 12) hydrogen bonds : bond 0.03921 / 2.59 ( 326) hydrogen bonds : angle 4.26401 / 3.01 ( 924) link_NAG-ASN : bond 0.00299 / 0.16 ( 7) link_NAG-ASN : angle 2.02298 / 1.47 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9232 (pt0) cc_final: 0.8790 (pm20) REVERT: B 462 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8564 (mmmm) REVERT: B 528 LYS cc_start: 0.4022 (OUTLIER) cc_final: 0.3567 (pttp) REVERT: E 483 GLU cc_start: 0.8934 (tp30) cc_final: 0.8472 (tm-30) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.5365 time to fit residues: 31.5608 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL 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 72 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3196 r_free = 0.3196 target = 0.066409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.049802 restraints weight = 17622.638| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.05 r_work: 0.2667 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6748 Z= 0.129 Angle : 0.530 7.497 9187 Z= 0.267 Chirality : 0.040 0.125 979 Planarity : 0.004 0.042 1176 Dihedral : 3.851 15.079 866 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 17.00 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.30), residues: 793 helix: 1.83 (0.26), residues: 411 sheet: 1.07 (0.81), residues: 42 loop : 0.49 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.016 0.001 TYR B 495 PHE 0.015 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6735) covalent geometry : angle 0.52049 / 0.26 ( 9154) SS BOND : bond 0.00293 / 0.19 ( 6) SS BOND : angle 1.06660 / 0.62 ( 12) hydrogen bonds : bond 0.03993 / 2.64 ( 326) hydrogen bonds : angle 4.27152 / 3.02 ( 924) link_NAG-ASN : bond 0.00281 / 0.16 ( 7) link_NAG-ASN : angle 1.99981 / 1.45 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.20 seconds wall clock time: 35 minutes 16.58 seconds (2116.58 seconds total)