Starting phenix.real_space_refine on Thu Jul 2 03:28:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ddo_30655/07_2026/7ddo_30655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ddo_30655/07_2026/7ddo_30655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ddo_30655/07_2026/7ddo_30655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ddo_30655/07_2026/7ddo_30655.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ddo_30655/07_2026/7ddo_30655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ddo_30655/07_2026/7ddo_30655.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ddo_30655/07_2026/7ddo_30655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ddo_30655/07_2026/7ddo_30655.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4133 2.51 5 N 1067 2.21 5 O 1230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6468 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "C" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1534 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 Time building chain proxies: 2.54, per 1000 atoms: 0.39 Number of scatterers: 6468 At special positions: 0 Unit cell: (101.362, 96.3937, 106.331, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1230 8.00 N 1067 7.00 C 4133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 53 " " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 600.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 55.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.599A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.737A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.621A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.564A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 143 through 155 removed outlier: 4.233A pdb=" N ASN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.192A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.720A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.643A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.591A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.565A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.666A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.619A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.780A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.929A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.715A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.815A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.174A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.774A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.815A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 875 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: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2077 1.34 - 1.46: 1660 1.46 - 1.58: 2854 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6649 Sorted by residual: bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" CA VAL C 524 " pdb=" CB VAL C 524 " ideal model delta sigma weight residual 1.531 1.545 -0.014 1.11e-02 8.12e+03 1.61e+00 ... (remaining 6644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 8752 1.37 - 2.74: 223 2.74 - 4.11: 55 4.11 - 5.48: 9 5.48 - 6.85: 3 Bond angle restraints: 9042 Sorted by residual: angle pdb=" N VAL C 524 " pdb=" CA VAL C 524 " pdb=" C VAL C 524 " ideal model delta sigma weight residual 106.53 110.71 -4.18 1.41e+00 5.03e-01 8.81e+00 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.22 109.75 3.47 1.23e+00 6.61e-01 7.95e+00 angle pdb=" N GLU A 589 " pdb=" CA GLU A 589 " pdb=" C GLU A 589 " ideal model delta sigma weight residual 109.81 115.20 -5.39 2.21e+00 2.05e-01 5.95e+00 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 120.97 124.12 -3.15 1.48e+00 4.57e-01 4.53e+00 angle pdb=" N VAL A 506 " pdb=" CA VAL A 506 " pdb=" C VAL A 506 " ideal model delta sigma weight residual 111.45 109.52 1.93 9.30e-01 1.16e+00 4.30e+00 ... (remaining 9037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3486 17.31 - 34.63: 314 34.63 - 51.94: 61 51.94 - 69.25: 15 69.25 - 86.56: 12 Dihedral angle restraints: 3888 sinusoidal: 1564 harmonic: 2324 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 6.44 86.56 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 25.85 67.15 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -22.59 -63.41 1 1.00e+01 1.00e-02 5.30e+01 ... (remaining 3885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 571 0.028 - 0.056: 251 0.056 - 0.084: 80 0.084 - 0.111: 51 0.111 - 0.139: 6 Chirality restraints: 959 Sorted by residual: chirality pdb=" CA GLU A 589 " pdb=" N GLU A 589 " pdb=" C GLU A 589 " pdb=" CB GLU A 589 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA THR C 372 " pdb=" N THR C 372 " pdb=" C THR C 372 " pdb=" CB THR C 372 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 956 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 583 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 235 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 463 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.018 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 79 2.63 - 3.20: 5772 3.20 - 3.76: 10356 3.76 - 4.33: 14430 4.33 - 4.90: 23518 Nonbonded interactions: 54155 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.062 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD2 ASP A 509 " model vdw 2.226 3.040 nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.260 3.040 ... (remaining 54150 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: 0.360 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.830 Find NCS groups from input model: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.004 0.162 6662 Z= 0.159 Angle : 0.557 6.846 9068 Z= 0.314 Chirality : 0.039 0.139 959 Planarity : 0.003 0.038 1169 Dihedral : 14.153 86.321 2377 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -1.39 (0.27), residues: 788 helix: -0.30 (0.23), residues: 403 sheet: -1.61 (0.64), residues: 57 loop : -1.49 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.014 0.001 TYR A 381 PHE 0.014 0.001 PHE C 490 TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 6649) covalent geometry : angle 0.54891 / 0.31 ( 9042) SS BOND : bond 0.00150 / 0.09 ( 7) SS BOND : angle 2.10156 / 1.23 ( 14) hydrogen bonds : bond 0.14490 / 9.26 ( 304) hydrogen bonds : angle 5.67191 / 4.01 ( 875) metal coordination : bond 0.13450 / 6.60 ( 2) link_NAG-ASN : bond 0.00152 / 0.07 ( 4) link_NAG-ASN : angle 1.45957 / 0.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.183 Fit side-chains REVERT: A 190 MET cc_start: 0.8484 (tmm) cc_final: 0.8223 (tmm) REVERT: A 382 ASP cc_start: 0.8527 (m-30) cc_final: 0.8105 (m-30) REVERT: C 396 TYR cc_start: 0.6757 (m-80) cc_final: 0.6205 (m-80) REVERT: C 408 ARG cc_start: 0.8277 (ptp90) cc_final: 0.7999 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0673 time to fit residues: 13.1120 Evaluate side-chains 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 210 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN A 338 ASN A 340 GLN C 460 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116023 restraints weight = 9717.829| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.40 r_work: 0.3152 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6662 Z= 0.124 Angle : 0.539 6.935 9068 Z= 0.271 Chirality : 0.042 0.144 959 Planarity : 0.004 0.032 1169 Dihedral : 3.710 16.504 861 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.15 % Allowed : 8.76 % Favored : 90.09 % 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: -0.19 (0.29), residues: 788 helix: 0.72 (0.25), residues: 402 sheet: -1.21 (0.65), residues: 57 loop : -0.91 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 219 TYR 0.018 0.001 TYR A 381 PHE 0.015 0.001 PHE C 490 TRP 0.015 0.001 TRP A 594 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6649) covalent geometry : angle 0.52897 / 0.27 ( 9042) SS BOND : bond 0.00268 / 0.16 ( 7) SS BOND : angle 1.99745 / 1.16 ( 14) hydrogen bonds : bond 0.04164 / 2.77 ( 304) hydrogen bonds : angle 4.56953 / 3.22 ( 875) metal coordination : bond 0.00405 / 0.20 ( 2) link_NAG-ASN : bond 0.00334 / 0.17 ( 4) link_NAG-ASN : angle 1.98574 / 1.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.176 Fit side-chains REVERT: A 376 MET cc_start: 0.8611 (mmm) cc_final: 0.8401 (mtp) REVERT: A 382 ASP cc_start: 0.8587 (m-30) cc_final: 0.8201 (m-30) REVERT: A 455 MET cc_start: 0.8853 (tmm) cc_final: 0.8188 (tmm) REVERT: A 489 GLU cc_start: 0.8754 (pm20) cc_final: 0.8138 (pm20) REVERT: C 356 LYS cc_start: 0.8091 (mppt) cc_final: 0.7801 (mmtt) outliers start: 8 outliers final: 6 residues processed: 120 average time/residue: 0.0616 time to fit residues: 10.5574 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN A 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119064 restraints weight = 18670.226| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.51 r_work: 0.3080 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6662 Z= 0.105 Angle : 0.511 6.974 9068 Z= 0.257 Chirality : 0.041 0.142 959 Planarity : 0.004 0.032 1169 Dihedral : 3.623 16.510 861 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.29 % Allowed : 10.49 % Favored : 88.22 % 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: 0.27 (0.29), residues: 788 helix: 1.03 (0.25), residues: 411 sheet: -1.03 (0.64), residues: 55 loop : -0.63 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.013 0.001 TYR A 381 PHE 0.011 0.001 PHE C 490 TRP 0.021 0.001 TRP A 594 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 6649) covalent geometry : angle 0.49939 / 0.25 ( 9042) SS BOND : bond 0.00249 / 0.15 ( 7) SS BOND : angle 1.80050 / 1.06 ( 14) hydrogen bonds : bond 0.03847 / 2.58 ( 304) hydrogen bonds : angle 4.36683 / 3.09 ( 875) metal coordination : bond 0.00070 / 0.04 ( 2) link_NAG-ASN : bond 0.00197 / 0.10 ( 4) link_NAG-ASN : angle 2.30346 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.237 Fit side-chains REVERT: A 267 LEU cc_start: 0.8530 (mt) cc_final: 0.8302 (mt) REVERT: A 382 ASP cc_start: 0.8502 (m-30) cc_final: 0.8092 (m-30) REVERT: A 455 MET cc_start: 0.8776 (tmm) cc_final: 0.8116 (tmm) REVERT: A 474 MET cc_start: 0.8529 (mmp) cc_final: 0.8173 (mmp) REVERT: A 489 GLU cc_start: 0.8701 (pm20) cc_final: 0.8082 (pm20) REVERT: C 343 ASN cc_start: 0.7073 (m-40) cc_final: 0.6657 (p0) REVERT: C 356 LYS cc_start: 0.8058 (mppt) cc_final: 0.7785 (mmtt) REVERT: C 442 ASP cc_start: 0.8603 (m-30) cc_final: 0.8286 (m-30) outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 0.0609 time to fit residues: 10.8158 Evaluate side-chains 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 52 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114468 restraints weight = 11926.715| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.67 r_work: 0.3149 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6662 Z= 0.122 Angle : 0.534 6.971 9068 Z= 0.267 Chirality : 0.041 0.148 959 Planarity : 0.004 0.031 1169 Dihedral : 3.691 16.478 861 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.29 % Allowed : 11.93 % Favored : 86.78 % 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: 0.46 (0.30), residues: 788 helix: 1.20 (0.25), residues: 405 sheet: -0.96 (0.64), residues: 56 loop : -0.52 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.019 0.001 TYR A 183 PHE 0.011 0.001 PHE C 490 TRP 0.021 0.001 TRP A 594 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6649) covalent geometry : angle 0.52425 / 0.26 ( 9042) SS BOND : bond 0.00272 / 0.17 ( 7) SS BOND : angle 1.92666 / 1.12 ( 14) hydrogen bonds : bond 0.03946 / 2.63 ( 304) hydrogen bonds : angle 4.32725 / 3.06 ( 875) metal coordination : bond 0.00171 / 0.08 ( 2) link_NAG-ASN : bond 0.00171 / 0.08 ( 4) link_NAG-ASN : angle 1.98745 / 1.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.214 Fit side-chains REVERT: A 267 LEU cc_start: 0.8405 (mt) cc_final: 0.8114 (mt) REVERT: A 474 MET cc_start: 0.8480 (mmp) cc_final: 0.8081 (mmp) REVERT: A 489 GLU cc_start: 0.8666 (pm20) cc_final: 0.8245 (pm20) REVERT: C 356 LYS cc_start: 0.8049 (mppt) cc_final: 0.7739 (mmtp) REVERT: C 396 TYR cc_start: 0.6983 (m-80) cc_final: 0.6392 (m-80) outliers start: 9 outliers final: 7 residues processed: 113 average time/residue: 0.0670 time to fit residues: 10.6344 Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113915 restraints weight = 12329.514| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.68 r_work: 0.3148 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6662 Z= 0.136 Angle : 0.534 6.741 9068 Z= 0.270 Chirality : 0.041 0.143 959 Planarity : 0.004 0.032 1169 Dihedral : 3.770 16.814 861 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.44 % Allowed : 11.78 % Favored : 86.78 % 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: 0.59 (0.30), residues: 788 helix: 1.29 (0.25), residues: 405 sheet: -0.74 (0.65), residues: 56 loop : -0.47 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.017 0.001 TYR A 183 PHE 0.017 0.001 PHE C 490 TRP 0.016 0.001 TRP A 594 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 6649) covalent geometry : angle 0.52153 / 0.27 ( 9042) SS BOND : bond 0.00293 / 0.18 ( 7) SS BOND : angle 2.08775 / 1.22 ( 14) hydrogen bonds : bond 0.04040 / 2.70 ( 304) hydrogen bonds : angle 4.33332 / 3.07 ( 875) metal coordination : bond 0.00207 / 0.10 ( 2) link_NAG-ASN : bond 0.00166 / 0.08 ( 4) link_NAG-ASN : angle 2.25548 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.242 Fit side-chains REVERT: A 267 LEU cc_start: 0.8457 (mt) cc_final: 0.8148 (mt) REVERT: A 474 MET cc_start: 0.8507 (mmp) cc_final: 0.8116 (mmp) REVERT: A 489 GLU cc_start: 0.8664 (pm20) cc_final: 0.8012 (pm20) REVERT: C 356 LYS cc_start: 0.8053 (mppt) cc_final: 0.7795 (mmtp) REVERT: C 396 TYR cc_start: 0.6968 (m-80) cc_final: 0.6321 (m-80) REVERT: C 489 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.5750 (p90) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.0641 time to fit residues: 10.0599 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119081 restraints weight = 18949.437| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.55 r_work: 0.3116 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6662 Z= 0.100 Angle : 0.513 7.004 9068 Z= 0.259 Chirality : 0.040 0.136 959 Planarity : 0.004 0.032 1169 Dihedral : 3.630 16.544 861 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.72 % Allowed : 12.07 % Favored : 86.21 % 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: 0.82 (0.30), residues: 788 helix: 1.45 (0.26), residues: 405 sheet: -0.57 (0.66), residues: 55 loop : -0.32 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.018 0.001 TYR A 183 PHE 0.008 0.001 PHE A 230 TRP 0.013 0.001 TRP A 594 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6649) covalent geometry : angle 0.50399 / 0.26 ( 9042) SS BOND : bond 0.00292 / 0.20 ( 7) SS BOND : angle 1.79679 / 1.09 ( 14) hydrogen bonds : bond 0.03673 / 2.47 ( 304) hydrogen bonds : angle 4.24057 / 3.01 ( 875) metal coordination : bond 0.00091 / 0.04 ( 2) link_NAG-ASN : bond 0.00195 / 0.10 ( 4) link_NAG-ASN : angle 1.95809 / 1.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.238 Fit side-chains REVERT: A 249 MET cc_start: 0.8392 (ptp) cc_final: 0.7987 (ttp) REVERT: A 267 LEU cc_start: 0.8504 (mt) cc_final: 0.8232 (mt) REVERT: A 350 ASP cc_start: 0.8050 (t0) cc_final: 0.7336 (p0) REVERT: A 474 MET cc_start: 0.8550 (mmp) cc_final: 0.8187 (mmp) REVERT: A 489 GLU cc_start: 0.8674 (pm20) cc_final: 0.8251 (pm20) REVERT: A 589 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8177 (tm-30) REVERT: C 343 ASN cc_start: 0.7234 (m-40) cc_final: 0.6726 (p0) REVERT: C 396 TYR cc_start: 0.6975 (m-80) cc_final: 0.6168 (m-80) REVERT: C 489 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.5911 (p90) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.0599 time to fit residues: 9.7198 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116942 restraints weight = 11779.901| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.62 r_work: 0.3196 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6662 Z= 0.105 Angle : 0.514 7.578 9068 Z= 0.258 Chirality : 0.041 0.165 959 Planarity : 0.004 0.031 1169 Dihedral : 3.594 16.291 861 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.72 % Allowed : 12.64 % Favored : 85.63 % 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: 0.97 (0.30), residues: 788 helix: 1.51 (0.26), residues: 403 sheet: -0.57 (0.68), residues: 56 loop : -0.13 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.011 0.001 TYR A 381 PHE 0.011 0.001 PHE C 490 TRP 0.012 0.001 TRP A 594 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 6649) covalent geometry : angle 0.50615 / 0.26 ( 9042) SS BOND : bond 0.00262 / 0.17 ( 7) SS BOND : angle 1.76710 / 1.05 ( 14) hydrogen bonds : bond 0.03704 / 2.49 ( 304) hydrogen bonds : angle 4.21770 / 2.99 ( 875) metal coordination : bond 0.00129 / 0.06 ( 2) link_NAG-ASN : bond 0.00199 / 0.10 ( 4) link_NAG-ASN : angle 1.76374 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.314 Fit side-chains REVERT: A 82 MET cc_start: 0.7726 (mtp) cc_final: 0.7461 (mpp) REVERT: A 249 MET cc_start: 0.8352 (ptp) cc_final: 0.7938 (ttp) REVERT: A 267 LEU cc_start: 0.8492 (mt) cc_final: 0.8157 (mt) REVERT: A 270 MET cc_start: 0.8377 (tpt) cc_final: 0.7742 (tpt) REVERT: A 350 ASP cc_start: 0.7990 (t0) cc_final: 0.7237 (p0) REVERT: A 474 MET cc_start: 0.8480 (mmp) cc_final: 0.8083 (mmp) REVERT: A 489 GLU cc_start: 0.8630 (pm20) cc_final: 0.8224 (pm20) REVERT: A 589 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 343 ASN cc_start: 0.6967 (m-40) cc_final: 0.6456 (p0) REVERT: C 396 TYR cc_start: 0.6956 (m-80) cc_final: 0.6262 (m-80) REVERT: C 489 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.5736 (p90) outliers start: 12 outliers final: 7 residues processed: 109 average time/residue: 0.0554 time to fit residues: 8.6211 Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116445 restraints weight = 12219.488| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.70 r_work: 0.3172 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6662 Z= 0.107 Angle : 0.517 7.382 9068 Z= 0.260 Chirality : 0.041 0.153 959 Planarity : 0.004 0.032 1169 Dihedral : 3.634 16.386 861 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.58 % Allowed : 13.36 % Favored : 85.06 % 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: 1.00 (0.30), residues: 788 helix: 1.52 (0.26), residues: 403 sheet: -0.11 (0.71), residues: 50 loop : -0.19 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.012 0.001 TYR A 381 PHE 0.019 0.001 PHE C 490 TRP 0.011 0.001 TRP A 594 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6649) covalent geometry : angle 0.50754 / 0.26 ( 9042) SS BOND : bond 0.00232 / 0.14 ( 7) SS BOND : angle 2.12261 / 1.30 ( 14) hydrogen bonds : bond 0.03701 / 2.49 ( 304) hydrogen bonds : angle 4.20184 / 2.98 ( 875) metal coordination : bond 0.00136 / 0.07 ( 2) link_NAG-ASN : bond 0.00194 / 0.10 ( 4) link_NAG-ASN : angle 1.68625 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.222 Fit side-chains REVERT: A 82 MET cc_start: 0.7746 (mtp) cc_final: 0.7503 (mpp) REVERT: A 249 MET cc_start: 0.8358 (ptp) cc_final: 0.7957 (ttp) REVERT: A 267 LEU cc_start: 0.8512 (mt) cc_final: 0.8190 (mt) REVERT: A 270 MET cc_start: 0.8384 (tpt) cc_final: 0.7739 (tpt) REVERT: A 350 ASP cc_start: 0.8000 (t0) cc_final: 0.7249 (p0) REVERT: A 376 MET cc_start: 0.8584 (mmm) cc_final: 0.8366 (mmm) REVERT: A 489 GLU cc_start: 0.8638 (pm20) cc_final: 0.8012 (pm20) REVERT: A 589 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 396 TYR cc_start: 0.6944 (m-80) cc_final: 0.6268 (m-80) REVERT: C 489 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.5827 (p90) REVERT: C 493 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6441 (tm-30) outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.0571 time to fit residues: 8.5190 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116462 restraints weight = 12370.102| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.71 r_work: 0.3191 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6662 Z= 0.107 Angle : 0.515 7.501 9068 Z= 0.259 Chirality : 0.041 0.149 959 Planarity : 0.004 0.031 1169 Dihedral : 3.628 16.335 861 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.29 % Allowed : 13.51 % Favored : 85.20 % 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: 1.13 (0.30), residues: 788 helix: 1.61 (0.26), residues: 397 sheet: -0.21 (0.69), residues: 50 loop : -0.04 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.012 0.001 TYR A 381 PHE 0.014 0.001 PHE C 490 TRP 0.010 0.001 TRP A 594 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 6649) covalent geometry : angle 0.50633 / 0.26 ( 9042) SS BOND : bond 0.00236 / 0.14 ( 7) SS BOND : angle 2.01806 / 1.20 ( 14) hydrogen bonds : bond 0.03695 / 2.48 ( 304) hydrogen bonds : angle 4.18559 / 2.97 ( 875) metal coordination : bond 0.00139 / 0.07 ( 2) link_NAG-ASN : bond 0.00194 / 0.10 ( 4) link_NAG-ASN : angle 1.64087 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.184 Fit side-chains REVERT: A 82 MET cc_start: 0.7754 (mtp) cc_final: 0.7496 (mpp) REVERT: A 249 MET cc_start: 0.8375 (ptp) cc_final: 0.7983 (ttp) REVERT: A 267 LEU cc_start: 0.8510 (mt) cc_final: 0.8199 (mt) REVERT: A 270 MET cc_start: 0.8411 (tpt) cc_final: 0.7760 (tpt) REVERT: A 350 ASP cc_start: 0.8010 (t0) cc_final: 0.7256 (p0) REVERT: A 474 MET cc_start: 0.8428 (mmp) cc_final: 0.8123 (mmp) REVERT: A 489 GLU cc_start: 0.8634 (pm20) cc_final: 0.7997 (pm20) REVERT: C 396 TYR cc_start: 0.6942 (m-80) cc_final: 0.6304 (m-80) REVERT: C 489 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.5705 (p90) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.0514 time to fit residues: 7.9830 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 25 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 345 HIS C 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116966 restraints weight = 11711.221| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.63 r_work: 0.3196 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6662 Z= 0.104 Angle : 0.515 7.603 9068 Z= 0.258 Chirality : 0.041 0.144 959 Planarity : 0.004 0.031 1169 Dihedral : 3.641 16.442 861 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.29 % Allowed : 13.65 % Favored : 85.06 % 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: 1.10 (0.30), residues: 788 helix: 1.59 (0.26), residues: 399 sheet: -0.19 (0.68), residues: 50 loop : -0.08 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.011 0.001 TYR A 381 PHE 0.009 0.001 PHE C 490 TRP 0.010 0.001 TRP A 594 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 6649) covalent geometry : angle 0.50623 / 0.26 ( 9042) SS BOND : bond 0.00188 / 0.09 ( 7) SS BOND : angle 2.05886 / 1.23 ( 14) hydrogen bonds : bond 0.03640 / 2.45 ( 304) hydrogen bonds : angle 4.18545 / 2.97 ( 875) metal coordination : bond 0.00113 / 0.05 ( 2) link_NAG-ASN : bond 0.00181 / 0.09 ( 4) link_NAG-ASN : angle 1.62195 / 0.87 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.228 Fit side-chains REVERT: A 82 MET cc_start: 0.7742 (mtp) cc_final: 0.7480 (mpp) REVERT: A 249 MET cc_start: 0.8372 (ptp) cc_final: 0.7988 (ttp) REVERT: A 267 LEU cc_start: 0.8463 (mt) cc_final: 0.8150 (mt) REVERT: A 270 MET cc_start: 0.8423 (tpt) cc_final: 0.7767 (tpt) REVERT: A 350 ASP cc_start: 0.8002 (t0) cc_final: 0.7254 (p0) REVERT: A 474 MET cc_start: 0.8429 (mmp) cc_final: 0.8108 (mmp) REVERT: A 489 GLU cc_start: 0.8629 (pm20) cc_final: 0.8007 (pm20) REVERT: C 396 TYR cc_start: 0.6955 (m-80) cc_final: 0.6269 (m-80) REVERT: C 489 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.5815 (p90) outliers start: 9 outliers final: 6 residues processed: 104 average time/residue: 0.0563 time to fit residues: 8.3437 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.0070 chunk 36 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 0.0370 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119977 restraints weight = 17384.046| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.02 r_work: 0.3163 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6662 Z= 0.099 Angle : 0.517 7.639 9068 Z= 0.261 Chirality : 0.041 0.140 959 Planarity : 0.003 0.031 1169 Dihedral : 3.581 16.377 861 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.15 % Allowed : 14.22 % Favored : 84.63 % 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: 1.15 (0.30), residues: 788 helix: 1.60 (0.26), residues: 399 sheet: -0.20 (0.68), residues: 50 loop : -0.00 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.009 0.001 TYR A 381 PHE 0.016 0.001 PHE C 490 TRP 0.010 0.001 TRP A 594 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6649) covalent geometry : angle 0.50860 / 0.26 ( 9042) SS BOND : bond 0.00231 / 0.14 ( 7) SS BOND : angle 1.95693 / 1.16 ( 14) hydrogen bonds : bond 0.03554 / 2.39 ( 304) hydrogen bonds : angle 4.14217 / 2.94 ( 875) metal coordination : bond 0.00076 / 0.04 ( 2) link_NAG-ASN : bond 0.00189 / 0.09 ( 4) link_NAG-ASN : angle 1.56373 / 0.84 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.82 seconds wall clock time: 27 minutes 33.75 seconds (1653.75 seconds total)