Starting phenix.real_space_refine on Tue Mar 3 15:07:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dqa_30816/03_2026/7dqa_30816.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dqa_30816/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7dqa_30816/03_2026/7dqa_30816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dqa_30816/03_2026/7dqa_30816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dqa_30816/03_2026/7dqa_30816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dqa_30816/03_2026/7dqa_30816.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 12 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 dihedrals: 3 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: 2.61, per 1000 atoms: 0.40 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: 0.71 Conformation dependent library (CDL) restraints added in 404.0 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: 0.20 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: 1.08 Time building geometry restraints manager: 0.90 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: 3452 17.91 - 35.83: 402 35.83 - 53.74: 116 53.74 - 71.65: 28 71.65 - 89.56: 11 Dihedral angle restraints: 4009 sinusoidal: 1679 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 4006 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: 0.240 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.180 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 : 17.506 89.563 2494 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 covalent geometry : bond 0.00743 ( 6677) covalent geometry : angle 0.86337 ( 9079) SS BOND : bond 0.00712 ( 7) SS BOND : angle 2.50332 ( 14) hydrogen bonds : bond 0.15756 ( 319) hydrogen bonds : angle 6.98489 ( 905) metal coordination : bond 0.48187 ( 2) link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 5.09070 ( 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 : 0.235 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: 0.4971 time to fit residues: 95.9450 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 : 0.240 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4081 r_free = 0.4081 target = 0.182136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151890 restraints weight = 16169.050| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.13 r_work: 0.3497 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6691 Z= 0.159 Angle : 0.671 8.697 9108 Z= 0.348 Chirality : 0.044 0.183 964 Planarity : 0.005 0.040 1173 Dihedral : 7.942 61.693 989 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.44 % Allowed : 24.96 % 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: -1.13 (0.27), residues: 789 helix: -0.43 (0.23), residues: 398 sheet: -1.38 (0.69), residues: 47 loop : -0.88 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 219 TYR 0.015 0.002 TYR A 385 PHE 0.018 0.002 PHE A 588 TRP 0.010 0.001 TRP C 353 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6677) covalent geometry : angle 0.65172 ( 9079) SS BOND : bond 0.00760 ( 7) SS BOND : angle 2.63395 ( 14) hydrogen bonds : bond 0.05667 ( 319) hydrogen bonds : angle 5.25020 ( 905) metal coordination : bond 0.03666 ( 2) link_NAG-ASN : bond 0.00318 ( 5) link_NAG-ASN : angle 3.15267 ( 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 133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.316 Fit side-chains REVERT: A 23 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 151 ILE cc_start: 0.6611 (mt) cc_final: 0.6244 (mp) REVERT: A 249 MET cc_start: 0.5551 (ptt) cc_final: 0.5278 (ttp) REVERT: A 341 LYS cc_start: 0.6360 (tptt) cc_final: 0.6048 (tttm) REVERT: A 408 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7300 (mmt) REVERT: A 511 SER cc_start: 0.7296 (p) cc_final: 0.7083 (t) REVERT: C 356 LYS cc_start: 0.7199 (mptt) cc_final: 0.6881 (mtpp) REVERT: C 467 ASP cc_start: 0.5842 (t0) cc_final: 0.5535 (t0) outliers start: 22 outliers final: 4 residues processed: 125 average time/residue: 0.5023 time to fit residues: 66.3272 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 : 0.228 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 68 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.2298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.185949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155984 restraints weight = 16768.864| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.90 r_work: 0.3546 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3249 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= 0.125 Angle : 0.598 10.560 9108 Z= 0.310 Chirality : 0.043 0.227 964 Planarity : 0.004 0.041 1173 Dihedral : 5.366 36.610 968 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.87 % Allowed : 26.40 % Favored : 71.74 % 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: -0.06 (0.29), residues: 789 helix: 0.50 (0.25), residues: 400 sheet: -1.20 (0.67), residues: 48 loop : -0.36 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 192 TYR 0.020 0.001 TYR C 351 PHE 0.012 0.001 PHE A 315 TRP 0.013 0.001 TRP A 594 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6677) covalent geometry : angle 0.58276 ( 9079) SS BOND : bond 0.00867 ( 7) SS BOND : angle 2.32084 ( 14) hydrogen bonds : bond 0.04804 ( 319) hydrogen bonds : angle 4.85608 ( 905) metal coordination : bond 0.00384 ( 2) link_NAG-ASN : bond 0.00231 ( 5) link_NAG-ASN : angle 2.56122 ( 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 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.179 Fit side-chains REVERT: A 151 ILE cc_start: 0.6629 (mt) cc_final: 0.6284 (mp) REVERT: A 171 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: A 249 MET cc_start: 0.5369 (ptt) cc_final: 0.5096 (ttp) REVERT: A 297 MET cc_start: 0.6863 (mtm) cc_final: 0.6172 (mtp) REVERT: A 300 GLN cc_start: 0.6266 (mt0) cc_final: 0.5817 (tt0) REVERT: A 341 LYS cc_start: 0.6265 (tptt) cc_final: 0.5972 (tttm) REVERT: C 356 LYS cc_start: 0.7290 (mptt) cc_final: 0.7075 (tttp) REVERT: C 446 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5225 (mm-30) REVERT: C 467 ASP cc_start: 0.5779 (t0) cc_final: 0.5496 (t0) outliers start: 11 outliers final: 1 residues processed: 105 average time/residue: 0.4945 time to fit residues: 55.0611 Evaluate side-chains 86 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148277 restraints weight = 9993.266| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.82 r_work: 0.3563 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6691 Z= 0.149 Angle : 0.633 11.603 9108 Z= 0.323 Chirality : 0.044 0.182 964 Planarity : 0.004 0.032 1173 Dihedral : 5.067 36.157 968 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.16 % Allowed : 24.96 % Favored : 71.88 % 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: 0.17 (0.29), residues: 789 helix: 0.62 (0.25), residues: 400 sheet: -0.58 (0.71), residues: 46 loop : -0.25 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 482 TYR 0.022 0.002 TYR A 521 PHE 0.014 0.002 PHE C 515 TRP 0.012 0.002 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6677) covalent geometry : angle 0.61816 ( 9079) SS BOND : bond 0.01021 ( 7) SS BOND : angle 2.29348 ( 14) hydrogen bonds : bond 0.05255 ( 319) hydrogen bonds : angle 4.84928 ( 905) metal coordination : bond 0.00219 ( 2) link_NAG-ASN : bond 0.00244 ( 5) link_NAG-ASN : angle 2.69992 ( 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 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.158 Fit side-chains REVERT: A 89 GLN cc_start: 0.6312 (mp10) cc_final: 0.5969 (mp10) REVERT: A 114 LYS cc_start: 0.7811 (ptmm) cc_final: 0.7070 (pttp) REVERT: A 151 ILE cc_start: 0.6865 (mt) cc_final: 0.6558 (mp) REVERT: A 171 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: A 249 MET cc_start: 0.5540 (ptt) cc_final: 0.5311 (ttp) REVERT: A 300 GLN cc_start: 0.6390 (mt0) cc_final: 0.5935 (tt0) REVERT: A 341 LYS cc_start: 0.6410 (tptt) cc_final: 0.6050 (tttm) REVERT: C 356 LYS cc_start: 0.7346 (mptt) cc_final: 0.7115 (tttp) REVERT: C 467 ASP cc_start: 0.5940 (t0) cc_final: 0.5682 (t0) outliers start: 20 outliers final: 9 residues processed: 107 average time/residue: 0.4898 time to fit residues: 55.2172 Evaluate side-chains 91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 142 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 194 ASN A 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.175960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145354 restraints weight = 16605.572| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.04 r_work: 0.3426 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6691 Z= 0.182 Angle : 0.682 10.647 9108 Z= 0.347 Chirality : 0.046 0.193 964 Planarity : 0.004 0.032 1173 Dihedral : 5.243 35.533 968 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.01 % Allowed : 25.54 % 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: 0.04 (0.29), residues: 789 helix: 0.50 (0.25), residues: 402 sheet: -0.28 (0.77), residues: 47 loop : -0.36 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.022 0.002 TYR A 521 PHE 0.014 0.002 PHE A 308 TRP 0.013 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6677) covalent geometry : angle 0.66367 ( 9079) SS BOND : bond 0.00944 ( 7) SS BOND : angle 2.75070 ( 14) hydrogen bonds : bond 0.05668 ( 319) hydrogen bonds : angle 5.00015 ( 905) metal coordination : bond 0.00417 ( 2) link_NAG-ASN : bond 0.00343 ( 5) link_NAG-ASN : angle 2.91412 ( 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 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 146 PRO cc_start: 0.7530 (Cg_endo) cc_final: 0.7056 (Cg_exo) REVERT: A 148 LEU cc_start: 0.7011 (mt) cc_final: 0.6797 (mt) REVERT: A 151 ILE cc_start: 0.7370 (mt) cc_final: 0.7106 (tt) REVERT: A 152 MET cc_start: 0.7373 (mmp) cc_final: 0.6833 (mmt) REVERT: A 171 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: A 300 GLN cc_start: 0.6469 (mt0) cc_final: 0.6007 (tt0) REVERT: A 341 LYS cc_start: 0.6557 (tptt) cc_final: 0.6169 (tttm) REVERT: A 383 MET cc_start: 0.8220 (mtt) cc_final: 0.7975 (mtm) REVERT: C 356 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7197 (tttp) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 0.4605 time to fit residues: 52.8016 Evaluate side-chains 93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 142 LEU 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 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 356 LYS 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: 8.9990 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 194 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 522 GLN A 535 HIS C 474 GLN 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 = 0.179241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149406 restraints weight = 11742.429| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.28 r_work: 0.3533 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6691 Z= 0.137 Angle : 0.622 8.224 9108 Z= 0.316 Chirality : 0.043 0.149 964 Planarity : 0.004 0.032 1173 Dihedral : 4.916 35.881 968 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.30 % Allowed : 25.68 % Favored : 72.02 % 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: 0.26 (0.29), residues: 789 helix: 0.69 (0.25), residues: 400 sheet: -0.10 (0.81), residues: 44 loop : -0.28 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 192 TYR 0.026 0.002 TYR C 351 PHE 0.025 0.002 PHE C 486 TRP 0.019 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6677) covalent geometry : angle 0.60470 ( 9079) SS BOND : bond 0.00931 ( 7) SS BOND : angle 2.62921 ( 14) hydrogen bonds : bond 0.04995 ( 319) hydrogen bonds : angle 4.90967 ( 905) metal coordination : bond 0.00195 ( 2) link_NAG-ASN : bond 0.00267 ( 5) link_NAG-ASN : angle 2.63843 ( 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 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.6250 (mmt) cc_final: 0.5825 (mmp) REVERT: A 121 ASN cc_start: 0.7971 (m-40) cc_final: 0.7319 (t0) REVERT: A 146 PRO cc_start: 0.7657 (Cg_endo) cc_final: 0.7129 (Cg_exo) REVERT: A 151 ILE cc_start: 0.7510 (mt) cc_final: 0.7153 (tt) REVERT: A 163 TRP cc_start: 0.7375 (t60) cc_final: 0.7154 (t60) REVERT: A 171 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: A 300 GLN cc_start: 0.6515 (mt0) cc_final: 0.5987 (tt0) REVERT: A 341 LYS cc_start: 0.6543 (tptt) cc_final: 0.6154 (tttm) REVERT: A 383 MET cc_start: 0.8108 (mtt) cc_final: 0.7893 (mtm) REVERT: A 470 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7657 (ttmm) REVERT: C 356 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7067 (tttp) REVERT: C 467 ASP cc_start: 0.6321 (t0) cc_final: 0.6038 (t0) outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 0.5480 time to fit residues: 55.8734 Evaluate side-chains 90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 418 ILE 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: 0.2980 chunk 61 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 55 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.177806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148645 restraints weight = 12908.782| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.34 r_work: 0.3514 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6691 Z= 0.156 Angle : 0.635 8.306 9108 Z= 0.323 Chirality : 0.043 0.131 964 Planarity : 0.004 0.031 1173 Dihedral : 4.926 36.053 968 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.30 % Allowed : 25.97 % Favored : 71.74 % 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: 0.24 (0.29), residues: 789 helix: 0.69 (0.25), residues: 403 sheet: 0.06 (0.85), residues: 44 loop : -0.34 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.026 0.002 TYR C 351 PHE 0.017 0.002 PHE C 486 TRP 0.026 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6677) covalent geometry : angle 0.61978 ( 9079) SS BOND : bond 0.00906 ( 7) SS BOND : angle 2.51341 ( 14) hydrogen bonds : bond 0.05205 ( 319) hydrogen bonds : angle 4.97686 ( 905) metal coordination : bond 0.00312 ( 2) link_NAG-ASN : bond 0.00305 ( 5) link_NAG-ASN : angle 2.59085 ( 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 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.5957 (mmt) cc_final: 0.5640 (mmp) REVERT: A 146 PRO cc_start: 0.7750 (Cg_endo) cc_final: 0.7173 (Cg_exo) REVERT: A 151 ILE cc_start: 0.7488 (mt) cc_final: 0.7256 (tt) REVERT: A 163 TRP cc_start: 0.7365 (t60) cc_final: 0.7158 (t60) REVERT: A 171 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: A 249 MET cc_start: 0.5610 (mtp) cc_final: 0.5277 (ttp) REVERT: A 300 GLN cc_start: 0.6516 (mt0) cc_final: 0.5985 (tt0) REVERT: A 341 LYS cc_start: 0.6553 (tptt) cc_final: 0.6234 (tttm) REVERT: A 470 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7633 (ttmm) REVERT: A 474 MET cc_start: 0.8033 (mmp) cc_final: 0.7481 (mmp) REVERT: C 351 TYR cc_start: 0.7626 (p90) cc_final: 0.7420 (p90) outliers start: 14 outliers final: 7 residues processed: 96 average time/residue: 0.5814 time to fit residues: 58.7183 Evaluate side-chains 90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 491 VAL Chi-restraints excluded: chain C residue 418 ILE 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: 5.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** 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 A 535 HIS C 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.181046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151345 restraints weight = 18978.884| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.55 r_work: 0.3449 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6691 Z= 0.131 Angle : 0.606 7.412 9108 Z= 0.309 Chirality : 0.042 0.131 964 Planarity : 0.004 0.031 1173 Dihedral : 4.718 35.309 968 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.15 % Allowed : 26.11 % Favored : 71.74 % 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: 0.39 (0.30), residues: 789 helix: 0.83 (0.25), residues: 406 sheet: -0.13 (0.81), residues: 45 loop : -0.26 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.025 0.002 TYR C 351 PHE 0.016 0.001 PHE C 486 TRP 0.030 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6677) covalent geometry : angle 0.59204 ( 9079) SS BOND : bond 0.00802 ( 7) SS BOND : angle 2.38496 ( 14) hydrogen bonds : bond 0.04844 ( 319) hydrogen bonds : angle 4.96665 ( 905) metal coordination : bond 0.00169 ( 2) link_NAG-ASN : bond 0.00215 ( 5) link_NAG-ASN : angle 2.35883 ( 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 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.5958 (mmt) cc_final: 0.5509 (mmm) REVERT: A 114 LYS cc_start: 0.7656 (ptmm) cc_final: 0.6853 (pttp) REVERT: A 121 ASN cc_start: 0.8001 (m-40) cc_final: 0.7327 (t0) REVERT: A 146 PRO cc_start: 0.7792 (Cg_endo) cc_final: 0.7227 (Cg_exo) REVERT: A 151 ILE cc_start: 0.7522 (mt) cc_final: 0.7184 (tt) REVERT: A 159 ASN cc_start: 0.7109 (t0) cc_final: 0.6729 (t0) REVERT: A 171 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: A 249 MET cc_start: 0.5784 (mtp) cc_final: 0.5294 (ttp) REVERT: A 300 GLN cc_start: 0.6491 (mt0) cc_final: 0.5921 (tt0) REVERT: A 341 LYS cc_start: 0.6553 (tptt) cc_final: 0.6128 (tttm) REVERT: A 408 MET cc_start: 0.8079 (mmt) cc_final: 0.7702 (mpm) REVERT: A 470 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7590 (ttmm) REVERT: A 474 MET cc_start: 0.7937 (mmp) cc_final: 0.7324 (mmp) REVERT: C 467 ASP cc_start: 0.6289 (t0) cc_final: 0.5946 (t0) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.5690 time to fit residues: 57.4027 Evaluate side-chains 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 418 ILE 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: 7.9990 chunk 31 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150366 restraints weight = 11116.699| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.01 r_work: 0.3572 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- 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 = 0.42 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6691 Z= 0.135 Angle : 0.608 8.627 9108 Z= 0.310 Chirality : 0.042 0.132 964 Planarity : 0.004 0.033 1173 Dihedral : 4.724 34.942 968 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.58 % Allowed : 25.25 % Favored : 72.17 % 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: 0.36 (0.30), residues: 789 helix: 0.81 (0.25), residues: 409 sheet: -0.08 (0.82), residues: 45 loop : -0.31 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 482 TYR 0.029 0.002 TYR C 351 PHE 0.021 0.002 PHE C 486 TRP 0.035 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6677) covalent geometry : angle 0.59334 ( 9079) SS BOND : bond 0.00800 ( 7) SS BOND : angle 2.54970 ( 14) hydrogen bonds : bond 0.04876 ( 319) hydrogen bonds : angle 4.99745 ( 905) metal coordination : bond 0.00204 ( 2) link_NAG-ASN : bond 0.00240 ( 5) link_NAG-ASN : angle 2.27206 ( 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 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.215 Fit side-chains REVERT: A 37 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6614 (tp30) REVERT: A 114 LYS cc_start: 0.7726 (ptmm) cc_final: 0.6938 (pttp) REVERT: A 121 ASN cc_start: 0.8017 (m-40) cc_final: 0.7358 (t0) REVERT: A 146 PRO cc_start: 0.7826 (Cg_endo) cc_final: 0.7298 (Cg_exo) REVERT: A 151 ILE cc_start: 0.7548 (mt) cc_final: 0.7210 (tt) REVERT: A 159 ASN cc_start: 0.7198 (t0) cc_final: 0.6852 (t0) REVERT: A 171 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: A 249 MET cc_start: 0.5499 (mtp) cc_final: 0.5105 (ttp) REVERT: A 300 GLN cc_start: 0.6581 (mt0) cc_final: 0.6042 (tt0) REVERT: A 341 LYS cc_start: 0.6587 (tptt) cc_final: 0.6186 (tttm) REVERT: A 408 MET cc_start: 0.8079 (mmt) cc_final: 0.7708 (mpm) REVERT: A 470 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7565 (ttmm) REVERT: A 474 MET cc_start: 0.7972 (mmp) cc_final: 0.7365 (mmp) REVERT: A 475 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7103 (tmmt) REVERT: C 351 TYR cc_start: 0.7565 (p90) cc_final: 0.7126 (p90) REVERT: C 467 ASP cc_start: 0.6266 (t0) cc_final: 0.5961 (t0) REVERT: C 474 GLN cc_start: 0.5684 (tt0) cc_final: 0.4885 (tp-100) outliers start: 16 outliers final: 7 residues processed: 94 average time/residue: 0.5700 time to fit residues: 56.2407 Evaluate side-chains 93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 475 LYS 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: 6.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 72 optimal weight: 0.0040 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153173 restraints weight = 12577.286| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.33 r_work: 0.3583 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6691 Z= 0.127 Angle : 0.598 8.616 9108 Z= 0.305 Chirality : 0.042 0.129 964 Planarity : 0.004 0.032 1173 Dihedral : 4.596 34.593 968 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.43 % Allowed : 26.26 % Favored : 72.31 % 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: 0.45 (0.30), residues: 789 helix: 0.87 (0.26), residues: 406 sheet: -0.08 (0.84), residues: 45 loop : -0.24 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 482 TYR 0.027 0.002 TYR C 351 PHE 0.012 0.001 PHE A 588 TRP 0.032 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6677) covalent geometry : angle 0.58445 ( 9079) SS BOND : bond 0.00745 ( 7) SS BOND : angle 2.50442 ( 14) hydrogen bonds : bond 0.04673 ( 319) hydrogen bonds : angle 4.98431 ( 905) metal coordination : bond 0.00128 ( 2) link_NAG-ASN : bond 0.00207 ( 5) link_NAG-ASN : angle 2.13284 ( 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 91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.245 Fit side-chains REVERT: A 114 LYS cc_start: 0.7891 (ptmm) cc_final: 0.7045 (pttp) REVERT: A 121 ASN cc_start: 0.7980 (m-40) cc_final: 0.7313 (t0) REVERT: A 146 PRO cc_start: 0.7848 (Cg_endo) cc_final: 0.7331 (Cg_exo) REVERT: A 151 ILE cc_start: 0.7513 (mt) cc_final: 0.7150 (tt) REVERT: A 159 ASN cc_start: 0.7264 (t0) cc_final: 0.6954 (t0) REVERT: A 171 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: A 208 GLU cc_start: 0.7379 (tt0) cc_final: 0.7105 (tm-30) REVERT: A 210 ASN cc_start: 0.7852 (m-40) cc_final: 0.7639 (m110) REVERT: A 249 MET cc_start: 0.5569 (mtp) cc_final: 0.5180 (ttp) REVERT: A 288 LYS cc_start: 0.7611 (tppp) cc_final: 0.7213 (mmmm) REVERT: A 300 GLN cc_start: 0.6567 (mt0) cc_final: 0.6011 (tt0) REVERT: A 341 LYS cc_start: 0.6600 (tptt) cc_final: 0.6192 (tttm) REVERT: A 408 MET cc_start: 0.8077 (mmt) cc_final: 0.7682 (mpm) REVERT: A 470 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7534 (ttmm) REVERT: A 474 MET cc_start: 0.7982 (mmp) cc_final: 0.7367 (mmp) REVERT: A 475 LYS cc_start: 0.7782 (ptmt) cc_final: 0.7196 (tmmt) REVERT: C 406 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7807 (tt0) REVERT: C 467 ASP cc_start: 0.6287 (t0) cc_final: 0.6059 (t0) REVERT: C 474 GLN cc_start: 0.5675 (tt0) cc_final: 0.4923 (tp-100) REVERT: C 487 ASN cc_start: 0.5676 (OUTLIER) cc_final: 0.5212 (t0) outliers start: 8 outliers final: 4 residues processed: 89 average time/residue: 0.5767 time to fit residues: 54.0497 Evaluate side-chains 87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 491 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 487 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 15 optimal weight: 0.0070 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152285 restraints weight = 10683.859| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.05 r_work: 0.3592 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6691 Z= 0.127 Angle : 0.601 8.706 9108 Z= 0.305 Chirality : 0.042 0.131 964 Planarity : 0.004 0.033 1173 Dihedral : 4.559 33.986 968 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.15 % Allowed : 26.54 % Favored : 72.31 % 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: 0.46 (0.30), residues: 789 helix: 0.87 (0.25), residues: 408 sheet: -0.10 (0.84), residues: 45 loop : -0.23 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 482 TYR 0.028 0.002 TYR C 351 PHE 0.014 0.001 PHE C 486 TRP 0.031 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6677) covalent geometry : angle 0.58851 ( 9079) SS BOND : bond 0.00726 ( 7) SS BOND : angle 2.39943 ( 14) hydrogen bonds : bond 0.04642 ( 319) hydrogen bonds : angle 4.96918 ( 905) metal coordination : bond 0.00146 ( 2) link_NAG-ASN : bond 0.00212 ( 5) link_NAG-ASN : angle 2.05742 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.72 seconds wall clock time: 47 minutes 22.47 seconds (2842.47 seconds total)