Starting phenix.real_space_refine on Thu Jul 2 03:51:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dqa_30816/07_2026/7dqa_30816.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dqa_30816/07_2026/7dqa_30816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2026/7dqa_30816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2026/7dqa_30816.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2026/7dqa_30816.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2026/7dqa_30816.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2026/7dqa_30816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2026/7dqa_30816.cif" } resolution = 2.8 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= 0.008 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4151 2.51 5 N 1070 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 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: 6576 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "C" Number of atoms: 1547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1577 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 2.40, per 1000 atoms: 0.36 Number of scatterers: 6576 At special positions: 0 Unit cell: (101.362, 96.3937, 102.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1316 8.00 N 1070 7.00 C 4151 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=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 460.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.9% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.847A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 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: 3.749A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.612A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (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 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.601A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.703A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.722A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.772A 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: 3.595A 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 447 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 484 removed outlier: 3.725A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.870A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.131A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.757A pdb=" N SER A 563 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.034A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.153A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AA6, first strand: chain 'C' and resid 473 through 474 319 hydrogen bonds defined for protein. 905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.60 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: 2085 1.35 - 1.47: 1808 1.47 - 1.60: 2726 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6677 Sorted by residual: bond pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta sigma weight residual 1.460 1.428 0.031 1.50e-02 4.44e+03 4.37e+00 bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" CB VAL A 581 " pdb=" CG1 VAL A 581 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.01e+00 bond pdb=" C1 NAG A 906 " pdb=" O5 NAG A 906 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CB TRP A 566 " pdb=" CG TRP A 566 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.27e+00 ... (remaining 6672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 8944 2.78 - 5.57: 120 5.57 - 8.35: 12 8.35 - 11.13: 2 11.13 - 13.91: 1 Bond angle restraints: 9079 Sorted by residual: angle pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " ideal model delta sigma weight residual 114.40 123.74 -9.34 2.30e+00 1.89e-01 1.65e+01 angle pdb=" C VAL A 581 " pdb=" CA VAL A 581 " pdb=" CB VAL A 581 " ideal model delta sigma weight residual 111.85 106.72 5.13 1.27e+00 6.20e-01 1.63e+01 angle pdb=" CA LEU A 73 " pdb=" CB LEU A 73 " pdb=" CG LEU A 73 " ideal model delta sigma weight residual 116.30 130.21 -13.91 3.50e+00 8.16e-02 1.58e+01 angle pdb=" N CYS A 498 " pdb=" CA CYS A 498 " pdb=" C CYS A 498 " ideal model delta sigma weight residual 110.06 104.49 5.57 1.43e+00 4.89e-01 1.52e+01 angle pdb=" C PHE C 497 " pdb=" N GLN C 498 " pdb=" CA GLN C 498 " ideal model delta sigma weight residual 122.48 116.77 5.71 1.62e+00 3.81e-01 1.24e+01 ... (remaining 9074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3367 17.91 - 35.83: 395 35.83 - 53.74: 105 53.74 - 71.65: 26 71.65 - 89.56: 11 Dihedral angle restraints: 3904 sinusoidal: 1574 harmonic: 2330 Sorted by residual: dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU C 390 " pdb=" C LEU C 390 " pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA VAL C 524 " pdb=" C VAL C 524 " pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 3901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 679 0.052 - 0.104: 244 0.104 - 0.156: 38 0.156 - 0.209: 1 0.209 - 0.261: 2 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1 NAG A 906 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 906 " pdb=" O5 NAG A 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA CYS C 432 " pdb=" N CYS C 432 " pdb=" C CYS C 432 " pdb=" CB CYS C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 961 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 498 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO C 499 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 235 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 498 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C CYS A 498 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS A 498 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 499 " -0.010 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 102 2.51 - 3.11: 5149 3.11 - 3.71: 10900 3.71 - 4.30: 15977 4.30 - 4.90: 25314 Nonbonded interactions: 57442 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 1.918 2.230 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.007 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.043 3.040 nonbonded pdb=" O HOH A1022 " pdb=" O HOH A1034 " model vdw 2.069 3.040 nonbonded pdb=" O HOH A1011 " pdb=" O HOH A1052 " model vdw 2.100 3.040 ... (remaining 57437 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.330 Find NCS groups from input model: 0.020 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:7.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 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 : 0.011 0.660 6691 Z= 0.438 Angle : 0.892 13.914 9108 Z= 0.498 Chirality : 0.051 0.261 964 Planarity : 0.005 0.065 1173 Dihedral : 17.467 89.563 2389 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.03 % Allowed : 19.80 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -3.29 (0.24), residues: 789 helix: -2.34 (0.19), residues: 393 sheet: -1.53 (0.62), residues: 58 loop : -1.91 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.021 0.002 TYR C 495 PHE 0.016 0.003 PHE A 285 TRP 0.012 0.002 TRP A 48 HIS 0.006 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.34 ( 6677) covalent geometry : angle 0.86337 / 0.49 ( 9079) SS BOND : bond 0.00712 / 0.44 ( 7) SS BOND : angle 2.50332 / 1.47 ( 14) hydrogen bonds : bond 0.15756 / 10.15 ( 319) hydrogen bonds : angle 6.98489 / 5.10 ( 905) metal coordination : bond 0.48187 / 23.10 ( 2) link_NAG-ASN : bond 0.00165 / 0.08 ( 5) link_NAG-ASN : angle 5.09070 / 2.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.240 Fit side-chains REVERT: A 23 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6902 (mm-30) REVERT: A 30 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6469 (t0) REVERT: A 62 MET cc_start: 0.7554 (ttt) cc_final: 0.7204 (ttp) REVERT: A 68 LYS cc_start: 0.6424 (mtpp) cc_final: 0.6189 (tttm) REVERT: A 73 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.4740 (mt) REVERT: A 131 LYS cc_start: 0.7440 (ptpp) cc_final: 0.7196 (ptmm) REVERT: A 136 ASP cc_start: 0.3336 (OUTLIER) cc_final: 0.2870 (p0) REVERT: A 146 PRO cc_start: 0.6097 (Cg_endo) cc_final: 0.5814 (Cg_exo) REVERT: A 151 ILE cc_start: 0.6579 (mt) cc_final: 0.5640 (mp) REVERT: A 159 ASN cc_start: 0.6007 (m-40) cc_final: 0.5716 (m110) REVERT: A 249 MET cc_start: 0.5732 (ptt) cc_final: 0.5487 (ttp) REVERT: A 313 LYS cc_start: 0.6775 (ttmt) cc_final: 0.6533 (mtpp) REVERT: A 314 PHE cc_start: 0.7063 (t80) cc_final: 0.6496 (t80) REVERT: A 341 LYS cc_start: 0.6040 (tptt) cc_final: 0.5729 (tttm) REVERT: A 368 ASP cc_start: 0.7211 (t0) cc_final: 0.6560 (m-30) REVERT: A 401 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8186 (m-70) REVERT: A 429 GLN cc_start: 0.5970 (OUTLIER) cc_final: 0.5184 (tm-30) REVERT: A 540 HIS cc_start: 0.7053 (p-80) cc_final: 0.6777 (p90) REVERT: A 600 LYS cc_start: 0.6515 (mtmt) cc_final: 0.6286 (mtmm) REVERT: C 356 LYS cc_start: 0.6965 (mptt) cc_final: 0.6707 (mtpp) REVERT: C 459 SER cc_start: 0.6597 (OUTLIER) cc_final: 0.6086 (p) REVERT: C 467 ASP cc_start: 0.5688 (t0) cc_final: 0.5427 (t0) REVERT: C 516 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4878 (pp20) outliers start: 40 outliers final: 6 residues processed: 183 average time/residue: 0.4295 time to fit residues: 83.1392 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 516 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.0000 chunk 74 optimal weight: 0.0030 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 117 ASN A 194 ASN A 239 HIS A 325 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 535 HIS A 580 ASN C 388 ASN C 450 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153239 restraints weight = 16227.715| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.70 r_work: 0.3513 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6691 Z= 0.151 Angle : 0.667 8.481 9108 Z= 0.345 Chirality : 0.044 0.173 964 Planarity : 0.005 0.039 1173 Dihedral : 6.978 64.580 884 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.44 % Allowed : 25.11 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.27), residues: 789 helix: -0.34 (0.24), residues: 399 sheet: -1.36 (0.69), residues: 47 loop : -0.79 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 219 TYR 0.016 0.002 TYR A 385 PHE 0.019 0.002 PHE A 588 TRP 0.011 0.001 TRP C 353 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6677) covalent geometry : angle 0.64965 / 0.34 ( 9079) SS BOND : bond 0.00890 / 0.59 ( 7) SS BOND : angle 2.43191 / 1.43 ( 14) hydrogen bonds : bond 0.05454 / 3.74 ( 319) hydrogen bonds : angle 5.22279 / 3.83 ( 905) metal coordination : bond 0.00804 / 0.41 ( 2) link_NAG-ASN : bond 0.00327 / 0.18 ( 5) link_NAG-ASN : angle 3.09243 / 1.70 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.168 Fit side-chains REVERT: A 23 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 151 ILE cc_start: 0.6546 (mt) cc_final: 0.6263 (mp) REVERT: A 249 MET cc_start: 0.5484 (ptt) cc_final: 0.5237 (ttp) REVERT: A 341 LYS cc_start: 0.6345 (tptt) cc_final: 0.6035 (tttm) REVERT: A 476 LYS cc_start: 0.7940 (tppt) cc_final: 0.7105 (tptm) REVERT: A 597 ASP cc_start: 0.6318 (t0) cc_final: 0.6051 (t70) REVERT: A 607 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7232 (m) REVERT: C 356 LYS cc_start: 0.7354 (mptt) cc_final: 0.7016 (mtpp) REVERT: C 467 ASP cc_start: 0.5954 (t0) cc_final: 0.5653 (t0) outliers start: 22 outliers final: 4 residues processed: 128 average time/residue: 0.4043 time to fit residues: 54.7664 Evaluate side-chains 93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 607 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 194 ASN A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.179866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149689 restraints weight = 17563.736| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.21 r_work: 0.3453 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6691 Z= 0.148 Angle : 0.639 10.016 9108 Z= 0.329 Chirality : 0.045 0.218 964 Planarity : 0.004 0.036 1173 Dihedral : 4.841 23.849 863 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.73 % Allowed : 25.82 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.17 (0.29), residues: 789 helix: 0.35 (0.25), residues: 400 sheet: -1.13 (0.66), residues: 48 loop : -0.36 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.018 0.002 TYR A 521 PHE 0.028 0.002 PHE A 285 TRP 0.010 0.002 TRP A 594 HIS 0.008 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6677) covalent geometry : angle 0.62314 / 0.32 ( 9079) SS BOND : bond 0.01283 / 0.94 ( 7) SS BOND : angle 2.32558 / 1.36 ( 14) hydrogen bonds : bond 0.05365 / 3.64 ( 319) hydrogen bonds : angle 4.93608 / 3.63 ( 905) metal coordination : bond 0.00105 / 0.05 ( 2) link_NAG-ASN : bond 0.00231 / 0.13 ( 5) link_NAG-ASN : angle 2.83015 / 1.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.228 Fit side-chains REVERT: A 151 ILE cc_start: 0.6716 (mt) cc_final: 0.6426 (mp) REVERT: A 171 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: A 194 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7528 (t0) REVERT: A 249 MET cc_start: 0.5529 (ptt) cc_final: 0.5272 (ttp) REVERT: A 270 MET cc_start: 0.7451 (tpt) cc_final: 0.7191 (tpp) REVERT: A 341 LYS cc_start: 0.6456 (tptt) cc_final: 0.6093 (tttm) REVERT: A 408 MET cc_start: 0.8021 (mmt) cc_final: 0.7634 (mpm) REVERT: C 406 GLU cc_start: 0.8084 (mp0) cc_final: 0.7820 (mt-10) REVERT: C 467 ASP cc_start: 0.5891 (t0) cc_final: 0.5478 (t0) REVERT: C 468 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6759 (mm) outliers start: 17 outliers final: 5 residues processed: 96 average time/residue: 0.4782 time to fit residues: 48.6257 Evaluate side-chains 84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.0070 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 194 ASN A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.182089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153077 restraints weight = 9675.952| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.62 r_work: 0.3594 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6691 Z= 0.126 Angle : 0.594 11.348 9108 Z= 0.306 Chirality : 0.043 0.229 964 Planarity : 0.004 0.035 1173 Dihedral : 4.577 24.086 863 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.44 % Allowed : 26.40 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.26 (0.29), residues: 789 helix: 0.75 (0.25), residues: 399 sheet: -0.77 (0.69), residues: 46 loop : -0.25 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 192 TYR 0.021 0.001 TYR C 351 PHE 0.011 0.001 PHE A 315 TRP 0.011 0.001 TRP A 165 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 6677) covalent geometry : angle 0.58025 / 0.30 ( 9079) SS BOND : bond 0.00854 / 0.58 ( 7) SS BOND : angle 2.11500 / 1.18 ( 14) hydrogen bonds : bond 0.04881 / 3.31 ( 319) hydrogen bonds : angle 4.82928 / 3.55 ( 905) metal coordination : bond 0.00101 / 0.05 ( 2) link_NAG-ASN : bond 0.00200 / 0.11 ( 5) link_NAG-ASN : angle 2.50105 / 1.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.6289 (mp10) cc_final: 0.5956 (mp10) REVERT: A 114 LYS cc_start: 0.7726 (ptmm) cc_final: 0.7018 (pttp) REVERT: A 171 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: A 194 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7435 (t0) REVERT: A 249 MET cc_start: 0.5503 (ptt) cc_final: 0.5253 (ttp) REVERT: A 297 MET cc_start: 0.6773 (mtm) cc_final: 0.6004 (mtt) REVERT: A 341 LYS cc_start: 0.6477 (tptt) cc_final: 0.6097 (tttm) REVERT: A 408 MET cc_start: 0.8009 (mmt) cc_final: 0.7603 (mpm) REVERT: A 470 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7263 (tptt) REVERT: C 406 GLU cc_start: 0.8108 (mp0) cc_final: 0.7864 (mt-10) REVERT: C 467 ASP cc_start: 0.5944 (t0) cc_final: 0.5421 (t0) REVERT: C 468 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6713 (mm) outliers start: 15 outliers final: 6 residues processed: 98 average time/residue: 0.4337 time to fit residues: 45.0364 Evaluate side-chains 82 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 6 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 535 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145062 restraints weight = 16938.000| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.17 r_work: 0.3425 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6691 Z= 0.185 Angle : 0.677 10.815 9108 Z= 0.345 Chirality : 0.046 0.201 964 Planarity : 0.004 0.030 1173 Dihedral : 4.891 28.309 863 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.58 % Allowed : 26.83 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.15 (0.29), residues: 789 helix: 0.62 (0.25), residues: 401 sheet: -0.26 (0.77), residues: 47 loop : -0.34 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 192 TYR 0.021 0.002 TYR C 351 PHE 0.019 0.002 PHE A 285 TRP 0.014 0.002 TRP A 594 HIS 0.006 0.002 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 6677) covalent geometry : angle 0.65837 / 0.34 ( 9079) SS BOND : bond 0.01178 / 0.84 ( 7) SS BOND : angle 2.98402 / 1.67 ( 14) hydrogen bonds : bond 0.05694 / 3.88 ( 319) hydrogen bonds : angle 4.97965 / 3.63 ( 905) metal coordination : bond 0.00414 / 0.21 ( 2) link_NAG-ASN : bond 0.00330 / 0.18 ( 5) link_NAG-ASN : angle 2.80679 / 1.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.231 Fit side-chains REVERT: A 146 PRO cc_start: 0.7459 (Cg_endo) cc_final: 0.6957 (Cg_exo) REVERT: A 148 LEU cc_start: 0.6980 (mt) cc_final: 0.6713 (mt) REVERT: A 171 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: A 341 LYS cc_start: 0.6562 (tptt) cc_final: 0.6188 (tttm) outliers start: 16 outliers final: 7 residues processed: 95 average time/residue: 0.4287 time to fit residues: 43.1799 Evaluate side-chains 84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 443 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 535 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147331 restraints weight = 12021.990| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.16 r_work: 0.3528 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6691 Z= 0.166 Angle : 0.645 9.446 9108 Z= 0.327 Chirality : 0.045 0.181 964 Planarity : 0.004 0.032 1173 Dihedral : 4.773 23.783 863 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.15 % Allowed : 26.69 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.15 (0.29), residues: 789 helix: 0.63 (0.25), residues: 403 sheet: -0.32 (0.78), residues: 46 loop : -0.36 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 509 TYR 0.022 0.002 TYR C 351 PHE 0.021 0.002 PHE C 486 TRP 0.020 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 6677) covalent geometry : angle 0.62703 / 0.32 ( 9079) SS BOND : bond 0.00925 / 0.63 ( 7) SS BOND : angle 2.84092 / 1.57 ( 14) hydrogen bonds : bond 0.05361 / 3.66 ( 319) hydrogen bonds : angle 5.01149 / 3.64 ( 905) metal coordination : bond 0.00362 / 0.19 ( 2) link_NAG-ASN : bond 0.00359 / 0.19 ( 5) link_NAG-ASN : angle 2.69919 / 1.50 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.211 Fit side-chains REVERT: A 37 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: A 82 MET cc_start: 0.6145 (mmt) cc_final: 0.5744 (mmp) REVERT: A 146 PRO cc_start: 0.7660 (Cg_endo) cc_final: 0.7144 (Cg_exo) REVERT: A 159 ASN cc_start: 0.7364 (m-40) cc_final: 0.6916 (t0) REVERT: A 163 TRP cc_start: 0.7593 (t60) cc_final: 0.7315 (t60) REVERT: A 171 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: A 341 LYS cc_start: 0.6604 (tptt) cc_final: 0.6256 (tttm) REVERT: A 531 GLN cc_start: 0.7762 (mt0) cc_final: 0.7536 (mp10) REVERT: C 467 ASP cc_start: 0.6470 (t0) cc_final: 0.6073 (t0) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.4671 time to fit residues: 47.2878 Evaluate side-chains 90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 55 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS C 474 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150298 restraints weight = 12661.302| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.52 r_work: 0.3560 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6691 Z= 0.133 Angle : 0.607 8.047 9108 Z= 0.308 Chirality : 0.043 0.131 964 Planarity : 0.004 0.031 1173 Dihedral : 4.596 24.204 863 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.58 % Allowed : 26.83 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.40 (0.30), residues: 789 helix: 0.86 (0.25), residues: 400 sheet: -0.12 (0.82), residues: 45 loop : -0.27 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.024 0.002 TYR C 351 PHE 0.016 0.002 PHE C 486 TRP 0.024 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6677) covalent geometry : angle 0.59206 / 0.30 ( 9079) SS BOND : bond 0.00846 / 0.58 ( 7) SS BOND : angle 2.47951 / 1.35 ( 14) hydrogen bonds : bond 0.04898 / 3.34 ( 319) hydrogen bonds : angle 4.97223 / 3.61 ( 905) metal coordination : bond 0.00167 / 0.09 ( 2) link_NAG-ASN : bond 0.00244 / 0.13 ( 5) link_NAG-ASN : angle 2.44090 / 1.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.194 Fit side-chains REVERT: A 82 MET cc_start: 0.5854 (mmt) cc_final: 0.5556 (mmt) REVERT: A 121 ASN cc_start: 0.7838 (m-40) cc_final: 0.7127 (t0) REVERT: A 146 PRO cc_start: 0.7540 (Cg_endo) cc_final: 0.7050 (Cg_exo) REVERT: A 152 MET cc_start: 0.7239 (mmp) cc_final: 0.6608 (mmt) REVERT: A 159 ASN cc_start: 0.7357 (m-40) cc_final: 0.6831 (t0) REVERT: A 171 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: A 249 MET cc_start: 0.5635 (mtp) cc_final: 0.5311 (ttp) REVERT: A 341 LYS cc_start: 0.6521 (tptt) cc_final: 0.6207 (tttm) REVERT: A 408 MET cc_start: 0.8032 (mmt) cc_final: 0.7651 (mpm) REVERT: A 474 MET cc_start: 0.7943 (mmp) cc_final: 0.7257 (mmp) outliers start: 9 outliers final: 6 residues processed: 97 average time/residue: 0.4611 time to fit residues: 47.2740 Evaluate side-chains 87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 443 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.179770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149293 restraints weight = 18084.080| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.48 r_work: 0.3452 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6691 Z= 0.134 Angle : 0.601 7.953 9108 Z= 0.305 Chirality : 0.042 0.132 964 Planarity : 0.004 0.030 1173 Dihedral : 4.543 24.085 863 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.72 % Allowed : 26.97 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.44 (0.30), residues: 789 helix: 0.89 (0.25), residues: 403 sheet: 0.04 (0.84), residues: 45 loop : -0.28 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.027 0.002 TYR C 351 PHE 0.015 0.002 PHE A 588 TRP 0.023 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6677) covalent geometry : angle 0.58692 / 0.30 ( 9079) SS BOND : bond 0.00818 / 0.56 ( 7) SS BOND : angle 2.42425 / 1.31 ( 14) hydrogen bonds : bond 0.04906 / 3.33 ( 319) hydrogen bonds : angle 4.96673 / 3.59 ( 905) metal coordination : bond 0.00245 / 0.12 ( 2) link_NAG-ASN : bond 0.00243 / 0.14 ( 5) link_NAG-ASN : angle 2.31865 / 1.29 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.204 Fit side-chains REVERT: A 37 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6547 (tp30) REVERT: A 82 MET cc_start: 0.5895 (mmt) cc_final: 0.5511 (mmm) REVERT: A 114 LYS cc_start: 0.7664 (ptmm) cc_final: 0.6872 (pttp) REVERT: A 121 ASN cc_start: 0.7963 (m-40) cc_final: 0.7284 (t0) REVERT: A 146 PRO cc_start: 0.7606 (Cg_endo) cc_final: 0.7104 (Cg_exo) REVERT: A 152 MET cc_start: 0.7157 (mmp) cc_final: 0.6585 (mmt) REVERT: A 159 ASN cc_start: 0.7538 (m-40) cc_final: 0.7103 (t0) REVERT: A 171 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: A 249 MET cc_start: 0.5747 (mtp) cc_final: 0.5247 (ttp) REVERT: A 341 LYS cc_start: 0.6588 (tptt) cc_final: 0.6190 (tttm) REVERT: A 408 MET cc_start: 0.8075 (mmt) cc_final: 0.7692 (mpm) REVERT: A 474 MET cc_start: 0.7995 (mmp) cc_final: 0.7482 (mmp) REVERT: A 479 GLU cc_start: 0.6557 (mt-10) cc_final: 0.5963 (tp30) REVERT: C 351 TYR cc_start: 0.7650 (p90) cc_final: 0.7414 (p90) REVERT: C 467 ASP cc_start: 0.6254 (t0) cc_final: 0.5900 (t0) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.5093 time to fit residues: 50.5695 Evaluate side-chains 90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 443 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.184545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152406 restraints weight = 9956.466| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.90 r_work: 0.3628 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6691 Z= 0.117 Angle : 0.575 8.042 9108 Z= 0.293 Chirality : 0.042 0.131 964 Planarity : 0.004 0.030 1173 Dihedral : 4.353 24.588 863 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.58 % Allowed : 27.55 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.66 (0.30), residues: 789 helix: 1.05 (0.26), residues: 406 sheet: 0.03 (0.85), residues: 45 loop : -0.14 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.026 0.001 TYR C 351 PHE 0.013 0.001 PHE C 486 TRP 0.025 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 6677) covalent geometry : angle 0.56297 / 0.29 ( 9079) SS BOND : bond 0.00706 / 0.49 ( 7) SS BOND : angle 2.28443 / 1.23 ( 14) hydrogen bonds : bond 0.04415 / 2.98 ( 319) hydrogen bonds : angle 4.89124 / 3.54 ( 905) metal coordination : bond 0.00072 / 0.04 ( 2) link_NAG-ASN : bond 0.00202 / 0.12 ( 5) link_NAG-ASN : angle 2.03457 / 1.13 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7722 (ptmm) cc_final: 0.6954 (pttp) REVERT: A 121 ASN cc_start: 0.7846 (m-40) cc_final: 0.7183 (t0) REVERT: A 146 PRO cc_start: 0.7303 (Cg_endo) cc_final: 0.6856 (Cg_exo) REVERT: A 152 MET cc_start: 0.7134 (mmp) cc_final: 0.6802 (mmt) REVERT: A 159 ASN cc_start: 0.7600 (m-40) cc_final: 0.7179 (t0) REVERT: A 171 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: A 249 MET cc_start: 0.5493 (mtp) cc_final: 0.5117 (ttp) REVERT: A 288 LYS cc_start: 0.7222 (mmmm) cc_final: 0.6582 (ttmm) REVERT: A 341 LYS cc_start: 0.6593 (tptt) cc_final: 0.6194 (tttm) REVERT: A 408 MET cc_start: 0.8013 (mmt) cc_final: 0.7639 (mpm) REVERT: A 470 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7823 (mtpt) REVERT: A 474 MET cc_start: 0.7893 (mmp) cc_final: 0.7410 (mmp) REVERT: A 479 GLU cc_start: 0.6508 (mt-10) cc_final: 0.6016 (tp30) REVERT: C 424 LYS cc_start: 0.7649 (tppt) cc_final: 0.7439 (tptp) REVERT: C 467 ASP cc_start: 0.6109 (t0) cc_final: 0.5825 (t0) outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 0.4884 time to fit residues: 51.5620 Evaluate side-chains 86 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 443 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 55 optimal weight: 0.0050 chunk 64 optimal weight: 0.8980 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN C 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.185373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155839 restraints weight = 12449.503| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.67 r_work: 0.3607 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6691 Z= 0.116 Angle : 0.578 8.916 9108 Z= 0.293 Chirality : 0.041 0.130 964 Planarity : 0.004 0.034 1173 Dihedral : 4.282 24.620 863 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.43 % Allowed : 27.55 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.69 (0.30), residues: 789 helix: 1.08 (0.26), residues: 408 sheet: -0.15 (0.81), residues: 46 loop : -0.11 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 482 TYR 0.025 0.001 TYR C 351 PHE 0.011 0.001 PHE C 486 TRP 0.025 0.001 TRP A 594 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 6677) covalent geometry : angle 0.56538 / 0.29 ( 9079) SS BOND : bond 0.00691 / 0.47 ( 7) SS BOND : angle 2.53032 / 1.34 ( 14) hydrogen bonds : bond 0.04400 / 2.97 ( 319) hydrogen bonds : angle 4.84344 / 3.50 ( 905) metal coordination : bond 0.00169 / 0.08 ( 2) link_NAG-ASN : bond 0.00192 / 0.11 ( 5) link_NAG-ASN : angle 1.93615 / 1.08 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.235 Fit side-chains REVERT: A 114 LYS cc_start: 0.7670 (ptmm) cc_final: 0.6908 (pttp) REVERT: A 121 ASN cc_start: 0.7734 (m-40) cc_final: 0.7047 (t0) REVERT: A 146 PRO cc_start: 0.7280 (Cg_endo) cc_final: 0.6828 (Cg_exo) REVERT: A 152 MET cc_start: 0.7105 (mmp) cc_final: 0.6710 (mmt) REVERT: A 159 ASN cc_start: 0.7467 (m-40) cc_final: 0.7005 (t0) REVERT: A 171 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: A 249 MET cc_start: 0.5333 (mtp) cc_final: 0.5059 (ttp) REVERT: A 288 LYS cc_start: 0.7087 (mmmm) cc_final: 0.6459 (ttmm) REVERT: A 341 LYS cc_start: 0.6512 (tptt) cc_final: 0.6172 (tttm) REVERT: A 383 MET cc_start: 0.7775 (mtt) cc_final: 0.7547 (mtm) REVERT: A 408 MET cc_start: 0.7981 (mmt) cc_final: 0.7612 (mpm) REVERT: A 474 MET cc_start: 0.7879 (mmp) cc_final: 0.7398 (mmp) REVERT: A 479 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5858 (tp30) REVERT: C 406 GLU cc_start: 0.8107 (mp0) cc_final: 0.7817 (mt-10) REVERT: C 424 LYS cc_start: 0.7683 (tppt) cc_final: 0.7427 (tptp) REVERT: C 467 ASP cc_start: 0.5817 (t0) cc_final: 0.5492 (t0) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.4861 time to fit residues: 47.1315 Evaluate side-chains 84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS C 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152284 restraints weight = 10565.657| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.08 r_work: 0.3581 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6691 Z= 0.131 Angle : 0.601 8.581 9108 Z= 0.304 Chirality : 0.042 0.135 964 Planarity : 0.004 0.032 1173 Dihedral : 4.414 24.094 863 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.15 % Allowed : 27.83 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.63 (0.30), residues: 789 helix: 1.00 (0.26), residues: 408 sheet: -0.11 (0.83), residues: 46 loop : -0.10 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 482 TYR 0.029 0.002 TYR A 521 PHE 0.019 0.002 PHE C 486 TRP 0.032 0.002 TRP A 594 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6677) covalent geometry : angle 0.58747 / 0.30 ( 9079) SS BOND : bond 0.00743 / 0.51 ( 7) SS BOND : angle 2.72317 / 1.47 ( 14) hydrogen bonds : bond 0.04678 / 3.17 ( 319) hydrogen bonds : angle 4.86002 / 3.51 ( 905) metal coordination : bond 0.00199 / 0.10 ( 2) link_NAG-ASN : bond 0.00225 / 0.13 ( 5) link_NAG-ASN : angle 1.96572 / 1.10 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.37 seconds wall clock time: 40 minutes 7.60 seconds (2407.60 seconds total)