Starting phenix.real_space_refine on Thu Jul 24 17:17:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dqa_30816/07_2025/7dqa_30816.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dqa_30816/07_2025/7dqa_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_2025/7dqa_30816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2025/7dqa_30816.map" model { file = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2025/7dqa_30816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dqa_30816/07_2025/7dqa_30816.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.70, per 1000 atoms: 1.02 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: 2.59 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.69 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: 1.79 Time building geometry restraints manager: 1.76 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- 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 : 18.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.002 TRP A 48 HIS 0.006 0.002 HIS A 34 PHE 0.016 0.003 PHE A 285 TYR 0.021 0.002 TYR C 495 ARG 0.008 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 5.09070 ( 15) hydrogen bonds : bond 0.15756 ( 319) hydrogen bonds : angle 6.98489 ( 905) metal coordination : bond 0.48187 ( 2) SS BOND : bond 0.00712 ( 7) SS BOND : angle 2.50332 ( 14) covalent geometry : bond 0.00743 ( 6677) covalent geometry : angle 0.86337 ( 9079) *********************** 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 : 0.646 Fit side-chains REVERT: A 23 GLU cc_start: 0.7176 (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: 0.6532 (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: 0.4887 (pp20) outliers start: 40 outliers final: 6 residues processed: 183 average time/residue: 1.0138 time to fit residues: 196.1915 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 : 0.695 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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 = 0.182850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152145 restraints weight = 17373.904| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.76 r_work: 0.3509 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6691 Z= 0.151 Angle : 0.669 8.817 9108 Z= 0.346 Chirality : 0.044 0.164 964 Planarity : 0.005 0.038 1173 Dihedral : 7.655 64.971 989 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.59 % Allowed : 24.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.28), residues: 789 helix: -0.29 (0.24), residues: 399 sheet: -1.34 (0.69), residues: 47 loop : -0.74 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 353 HIS 0.009 0.001 HIS A 374 PHE 0.019 0.002 PHE A 588 TYR 0.018 0.002 TYR A 385 ARG 0.008 0.001 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 5) link_NAG-ASN : angle 3.07720 ( 15) hydrogen bonds : bond 0.05370 ( 319) hydrogen bonds : angle 5.21388 ( 905) metal coordination : bond 0.01054 ( 2) SS BOND : bond 0.00662 ( 7) SS BOND : angle 2.31321 ( 14) covalent geometry : bond 0.00325 ( 6677) covalent geometry : angle 0.65202 ( 9079) *********************** 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 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.713 Fit side-chains REVERT: A 23 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 61 ASN cc_start: 0.7302 (t0) cc_final: 0.7064 (m-40) REVERT: A 151 ILE cc_start: 0.6568 (mt) cc_final: 0.6276 (mp) REVERT: A 249 MET cc_start: 0.5471 (ptt) cc_final: 0.5231 (ttp) REVERT: A 341 LYS cc_start: 0.6398 (tptt) cc_final: 0.6067 (tttm) REVERT: A 597 ASP cc_start: 0.6302 (t0) cc_final: 0.6019 (t70) REVERT: A 607 SER cc_start: 0.7701 (OUTLIER) cc_final: 0.7249 (m) REVERT: C 356 LYS cc_start: 0.7365 (mptt) cc_final: 0.7025 (mtpp) REVERT: C 467 ASP cc_start: 0.5964 (t0) cc_final: 0.5698 (t0) outliers start: 23 outliers final: 4 residues processed: 131 average time/residue: 1.0930 time to fit residues: 151.2564 Evaluate side-chains 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 54 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 194 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.181818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151864 restraints weight = 14523.884| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.79 r_work: 0.3542 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3283 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= 0.135 Angle : 0.624 10.471 9108 Z= 0.321 Chirality : 0.044 0.228 964 Planarity : 0.004 0.037 1173 Dihedral : 5.353 37.230 968 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 26.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 789 helix: 0.42 (0.25), residues: 400 sheet: -1.16 (0.66), residues: 48 loop : -0.33 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 594 HIS 0.008 0.001 HIS A 195 PHE 0.027 0.002 PHE A 285 TYR 0.018 0.002 TYR A 521 ARG 0.004 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 5) link_NAG-ASN : angle 2.72818 ( 15) hydrogen bonds : bond 0.05122 ( 319) hydrogen bonds : angle 4.87556 ( 905) metal coordination : bond 0.00100 ( 2) SS BOND : bond 0.00945 ( 7) SS BOND : angle 2.30268 ( 14) covalent geometry : bond 0.00294 ( 6677) covalent geometry : angle 0.60832 ( 9079) *********************** 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 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.663 Fit side-chains REVERT: A 61 ASN cc_start: 0.7286 (t0) cc_final: 0.7035 (m-40) REVERT: A 151 ILE cc_start: 0.6622 (mt) cc_final: 0.6348 (mp) REVERT: A 171 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: A 297 MET cc_start: 0.6717 (mtm) cc_final: 0.5949 (mtt) REVERT: A 341 LYS cc_start: 0.6379 (tptt) cc_final: 0.6048 (tttm) REVERT: C 356 LYS cc_start: 0.7308 (mptt) cc_final: 0.7098 (tttp) REVERT: C 467 ASP cc_start: 0.5788 (t0) cc_final: 0.5325 (t0) REVERT: C 468 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6774 (mm) outliers start: 14 outliers final: 4 residues processed: 99 average time/residue: 1.0677 time to fit residues: 112.0079 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 : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 511 SER 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 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.181686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151730 restraints weight = 11085.302| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.11 r_work: 0.3563 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3641 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= 0.137 Angle : 0.604 11.392 9108 Z= 0.308 Chirality : 0.043 0.160 964 Planarity : 0.004 0.032 1173 Dihedral : 4.914 35.976 968 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.87 % Allowed : 25.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 789 helix: 0.73 (0.25), residues: 399 sheet: -0.55 (0.72), residues: 46 loop : -0.24 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 540 PHE 0.011 0.001 PHE A 315 TYR 0.021 0.002 TYR A 521 ARG 0.004 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 2.61866 ( 15) hydrogen bonds : bond 0.05020 ( 319) hydrogen bonds : angle 4.80918 ( 905) metal coordination : bond 0.00182 ( 2) SS BOND : bond 0.00940 ( 7) SS BOND : angle 2.10564 ( 14) covalent geometry : bond 0.00296 ( 6677) covalent geometry : angle 0.58949 ( 9079) *********************** 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 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7344 (t0) cc_final: 0.7080 (m-40) REVERT: A 89 GLN cc_start: 0.6420 (mp10) cc_final: 0.6115 (mp10) REVERT: A 114 LYS cc_start: 0.7791 (ptmm) cc_final: 0.7022 (pttp) REVERT: A 171 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: A 297 MET cc_start: 0.6838 (mtm) cc_final: 0.6162 (mtt) REVERT: A 341 LYS cc_start: 0.6483 (tptt) cc_final: 0.6108 (tttm) REVERT: C 356 LYS cc_start: 0.7463 (mptt) cc_final: 0.7249 (tttp) REVERT: C 418 ILE cc_start: 0.7554 (mp) cc_final: 0.7326 (mp) REVERT: C 467 ASP cc_start: 0.5965 (t0) cc_final: 0.5474 (t0) REVERT: C 468 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6711 (mm) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 1.0995 time to fit residues: 117.9081 Evaluate side-chains 87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain A residue 463 VAL 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 60 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 74 optimal weight: 0.0070 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN 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 = 0.4052 r_free = 0.4052 target = 0.179158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148916 restraints weight = 17721.256| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.27 r_work: 0.3436 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3822 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 : 0.633 9.847 9108 Z= 0.321 Chirality : 0.044 0.161 964 Planarity : 0.004 0.032 1173 Dihedral : 4.982 35.667 968 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.16 % Allowed : 25.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.29), residues: 789 helix: 0.72 (0.25), residues: 402 sheet: -0.34 (0.75), residues: 47 loop : -0.30 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.016 0.002 PHE A 285 TYR 0.023 0.002 TYR A 521 ARG 0.004 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 5) link_NAG-ASN : angle 2.64160 ( 15) hydrogen bonds : bond 0.05229 ( 319) hydrogen bonds : angle 4.89496 ( 905) metal coordination : bond 0.00292 ( 2) SS BOND : bond 0.00929 ( 7) SS BOND : angle 2.81545 ( 14) covalent geometry : bond 0.00339 ( 6677) covalent geometry : angle 0.61480 ( 9079) *********************** 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 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.678 Fit side-chains REVERT: A 61 ASN cc_start: 0.7373 (t0) cc_final: 0.7055 (m-40) REVERT: A 89 GLN cc_start: 0.6391 (mp10) cc_final: 0.6089 (mp10) REVERT: A 114 LYS cc_start: 0.7745 (ptmm) cc_final: 0.7050 (pttp) REVERT: A 121 ASN cc_start: 0.7885 (m-40) cc_final: 0.7206 (t0) REVERT: A 146 PRO cc_start: 0.7271 (Cg_endo) cc_final: 0.6822 (Cg_exo) REVERT: A 163 TRP cc_start: 0.7486 (t60) cc_final: 0.7227 (t60) REVERT: A 171 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: A 249 MET cc_start: 0.5721 (mtp) cc_final: 0.5366 (ttp) REVERT: A 341 LYS cc_start: 0.6529 (tptt) cc_final: 0.6134 (tttm) REVERT: A 470 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7690 (ttpt) REVERT: C 356 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7274 (tttp) REVERT: C 467 ASP cc_start: 0.6019 (t0) cc_final: 0.5771 (t0) REVERT: C 468 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6621 (mm) outliers start: 20 outliers final: 8 residues processed: 102 average time/residue: 1.0528 time to fit residues: 113.9657 Evaluate side-chains 91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain A residue 463 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 Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.182279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.153404 restraints weight = 13662.711| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.42 r_work: 0.3511 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 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 = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6691 Z= 0.144 Angle : 0.626 8.323 9108 Z= 0.317 Chirality : 0.043 0.142 964 Planarity : 0.004 0.031 1173 Dihedral : 4.868 35.699 968 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.29), residues: 789 helix: 0.76 (0.25), residues: 403 sheet: -0.35 (0.79), residues: 46 loop : -0.29 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.017 0.002 PHE C 486 TYR 0.024 0.002 TYR C 351 ARG 0.004 0.001 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 5) link_NAG-ASN : angle 2.50718 ( 15) hydrogen bonds : bond 0.05092 ( 319) hydrogen bonds : angle 4.93444 ( 905) metal coordination : bond 0.00248 ( 2) SS BOND : bond 0.00924 ( 7) SS BOND : angle 2.75064 ( 14) covalent geometry : bond 0.00322 ( 6677) covalent geometry : angle 0.60929 ( 9079) *********************** 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 110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6420 (tp30) REVERT: A 61 ASN cc_start: 0.7264 (t0) cc_final: 0.7020 (m-40) REVERT: A 82 MET cc_start: 0.5996 (mmt) cc_final: 0.5556 (tpp) REVERT: A 89 GLN cc_start: 0.6461 (mp10) cc_final: 0.6151 (mp10) REVERT: A 114 LYS cc_start: 0.7844 (ptmm) cc_final: 0.7006 (pttp) REVERT: A 121 ASN cc_start: 0.7847 (m-40) cc_final: 0.7162 (t0) REVERT: A 146 PRO cc_start: 0.7346 (Cg_endo) cc_final: 0.6923 (Cg_exo) REVERT: A 159 ASN cc_start: 0.7068 (m-40) cc_final: 0.6652 (t0) REVERT: A 163 TRP cc_start: 0.7389 (t60) cc_final: 0.7145 (t60) REVERT: A 171 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: A 249 MET cc_start: 0.5651 (mtp) cc_final: 0.5301 (ttp) REVERT: A 341 LYS cc_start: 0.6434 (tptt) cc_final: 0.6084 (tttm) REVERT: A 470 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7504 (ttmm) REVERT: C 356 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7095 (tttp) REVERT: C 406 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 467 ASP cc_start: 0.6072 (t0) cc_final: 0.5800 (t0) REVERT: C 468 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6602 (mm) outliers start: 19 outliers final: 7 residues processed: 105 average time/residue: 1.1202 time to fit residues: 124.3685 Evaluate side-chains 96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 C residue 356 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** 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 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.179373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148801 restraints weight = 11895.522| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.29 r_work: 0.3537 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4213 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= 0.146 Angle : 0.620 7.863 9108 Z= 0.315 Chirality : 0.043 0.138 964 Planarity : 0.004 0.030 1173 Dihedral : 4.840 35.935 968 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.15 % Allowed : 27.12 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 789 helix: 0.79 (0.25), residues: 403 sheet: -0.10 (0.83), residues: 45 loop : -0.32 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.014 0.002 PHE C 486 TYR 0.026 0.002 TYR C 351 ARG 0.003 0.001 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 5) link_NAG-ASN : angle 2.45467 ( 15) hydrogen bonds : bond 0.05124 ( 319) hydrogen bonds : angle 4.93888 ( 905) metal coordination : bond 0.00269 ( 2) SS BOND : bond 0.00882 ( 7) SS BOND : angle 2.55728 ( 14) covalent geometry : bond 0.00330 ( 6677) covalent geometry : angle 0.60477 ( 9079) *********************** 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 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6580 (tp30) REVERT: A 61 ASN cc_start: 0.7356 (t0) cc_final: 0.7040 (m-40) REVERT: A 82 MET cc_start: 0.6315 (mmt) cc_final: 0.5852 (mmp) REVERT: A 114 LYS cc_start: 0.7882 (ptmm) cc_final: 0.7058 (pttp) REVERT: A 146 PRO cc_start: 0.7393 (Cg_endo) cc_final: 0.6944 (Cg_exo) REVERT: A 159 ASN cc_start: 0.7392 (m-40) cc_final: 0.6927 (t0) REVERT: A 171 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: A 249 MET cc_start: 0.5721 (mtp) cc_final: 0.5298 (ttp) REVERT: A 341 LYS cc_start: 0.6633 (tptt) cc_final: 0.6241 (tttm) REVERT: A 470 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7578 (ttmm) REVERT: A 474 MET cc_start: 0.8091 (mmp) cc_final: 0.7525 (mmp) REVERT: A 479 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6109 (tp30) REVERT: C 351 TYR cc_start: 0.7711 (p90) cc_final: 0.7466 (p90) REVERT: C 356 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7083 (tttp) REVERT: C 406 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7894 (mt-10) REVERT: C 467 ASP cc_start: 0.6198 (t0) cc_final: 0.5924 (t0) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 1.2212 time to fit residues: 122.1140 Evaluate side-chains 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0670 chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.181443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151269 restraints weight = 12995.341| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.46 r_work: 0.3556 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6691 Z= 0.130 Angle : 0.604 7.901 9108 Z= 0.306 Chirality : 0.042 0.136 964 Planarity : 0.004 0.030 1173 Dihedral : 4.702 36.150 968 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.30 % Allowed : 27.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.29), residues: 789 helix: 0.92 (0.25), residues: 406 sheet: 0.03 (0.83), residues: 44 loop : -0.25 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.016 0.001 PHE A 588 TYR 0.026 0.002 TYR C 351 ARG 0.004 0.001 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 5) link_NAG-ASN : angle 2.29391 ( 15) hydrogen bonds : bond 0.04803 ( 319) hydrogen bonds : angle 4.92275 ( 905) metal coordination : bond 0.00176 ( 2) SS BOND : bond 0.00798 ( 7) SS BOND : angle 2.43267 ( 14) covalent geometry : bond 0.00289 ( 6677) covalent geometry : angle 0.59017 ( 9079) *********************** 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 94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 3.264 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: A 61 ASN cc_start: 0.7343 (t0) cc_final: 0.7031 (m-40) REVERT: A 82 MET cc_start: 0.6132 (mmt) cc_final: 0.5739 (mmm) REVERT: A 89 GLN cc_start: 0.6446 (mp10) cc_final: 0.6161 (mp10) REVERT: A 114 LYS cc_start: 0.7879 (ptmm) cc_final: 0.7070 (pttp) REVERT: A 121 ASN cc_start: 0.7984 (m-40) cc_final: 0.7320 (t0) REVERT: A 146 PRO cc_start: 0.7413 (Cg_endo) cc_final: 0.7016 (Cg_exo) REVERT: A 159 ASN cc_start: 0.7531 (m-40) cc_final: 0.7086 (t0) REVERT: A 171 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: A 249 MET cc_start: 0.5701 (mtp) cc_final: 0.5293 (ttp) REVERT: A 341 LYS cc_start: 0.6640 (tptt) cc_final: 0.6218 (tttm) REVERT: A 383 MET cc_start: 0.8097 (mtt) cc_final: 0.7779 (mtm) REVERT: A 470 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7520 (ttmm) REVERT: A 474 MET cc_start: 0.7986 (mmp) cc_final: 0.7408 (mmp) REVERT: C 356 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6943 (tttp) REVERT: C 406 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 467 ASP cc_start: 0.6190 (t0) cc_final: 0.5902 (t0) REVERT: C 468 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6605 (mm) REVERT: C 487 ASN cc_start: 0.6091 (OUTLIER) cc_final: 0.5608 (t0) outliers start: 14 outliers final: 6 residues processed: 90 average time/residue: 2.0689 time to fit residues: 195.8893 Evaluate side-chains 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 C residue 356 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN 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 = 0.4082 r_free = 0.4082 target = 0.182416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152808 restraints weight = 14481.710| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.54 r_work: 0.3553 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6691 Z= 0.129 Angle : 0.596 8.034 9108 Z= 0.303 Chirality : 0.042 0.136 964 Planarity : 0.004 0.032 1173 Dihedral : 4.620 34.958 968 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.87 % Allowed : 27.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.30), residues: 789 helix: 0.97 (0.26), residues: 406 sheet: -0.12 (0.82), residues: 45 loop : -0.14 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.014 0.001 PHE A 588 TYR 0.028 0.002 TYR C 351 ARG 0.003 0.001 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 5) link_NAG-ASN : angle 2.16022 ( 15) hydrogen bonds : bond 0.04759 ( 319) hydrogen bonds : angle 4.95405 ( 905) metal coordination : bond 0.00174 ( 2) SS BOND : bond 0.00773 ( 7) SS BOND : angle 2.39913 ( 14) covalent geometry : bond 0.00285 ( 6677) covalent geometry : angle 0.58306 ( 9079) *********************** 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 97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.5695 (mmt) cc_final: 0.5438 (mmm) REVERT: A 89 GLN cc_start: 0.6474 (mp10) cc_final: 0.6201 (mp10) REVERT: A 114 LYS cc_start: 0.7854 (ptmm) cc_final: 0.7042 (pttp) REVERT: A 121 ASN cc_start: 0.7838 (m-40) cc_final: 0.7142 (t0) REVERT: A 146 PRO cc_start: 0.7283 (Cg_endo) cc_final: 0.6912 (Cg_exo) REVERT: A 159 ASN cc_start: 0.7417 (m-40) cc_final: 0.7011 (t0) REVERT: A 171 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: A 249 MET cc_start: 0.5427 (mtp) cc_final: 0.5165 (ttp) REVERT: A 341 LYS cc_start: 0.6519 (tptt) cc_final: 0.6148 (tttm) REVERT: A 408 MET cc_start: 0.8049 (mmt) cc_final: 0.7675 (mpm) REVERT: A 470 LYS cc_start: 0.7925 (mtpt) cc_final: 0.7484 (ttmm) REVERT: A 474 MET cc_start: 0.7943 (mmp) cc_final: 0.7333 (mmp) REVERT: A 475 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7074 (tmmt) REVERT: A 479 GLU cc_start: 0.6521 (mt-10) cc_final: 0.5944 (tp30) REVERT: C 351 TYR cc_start: 0.7477 (p90) cc_final: 0.7014 (p90) REVERT: C 356 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6915 (tttp) REVERT: C 467 ASP cc_start: 0.6041 (t0) cc_final: 0.5723 (t0) REVERT: C 468 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6542 (mm) outliers start: 11 outliers final: 5 residues processed: 94 average time/residue: 1.8422 time to fit residues: 183.1233 Evaluate side-chains 88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 475 LYS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN 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 = 0.4027 r_free = 0.4027 target = 0.176526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146251 restraints weight = 14929.229| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.67 r_work: 0.3462 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6691 Z= 0.193 Angle : 0.676 7.999 9108 Z= 0.342 Chirality : 0.045 0.138 964 Planarity : 0.004 0.031 1173 Dihedral : 5.036 34.764 968 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.01 % Allowed : 27.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.29), residues: 789 helix: 0.70 (0.25), residues: 403 sheet: 0.13 (0.84), residues: 44 loop : -0.29 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 594 HIS 0.005 0.001 HIS A 241 PHE 0.021 0.002 PHE A 588 TYR 0.028 0.002 TYR C 351 ARG 0.007 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 5) link_NAG-ASN : angle 2.30807 ( 15) hydrogen bonds : bond 0.05660 ( 319) hydrogen bonds : angle 5.15220 ( 905) metal coordination : bond 0.00475 ( 2) SS BOND : bond 0.00870 ( 7) SS BOND : angle 2.64407 ( 14) covalent geometry : bond 0.00445 ( 6677) covalent geometry : angle 0.66205 ( 9079) ********************** 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 92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.672 Fit side-chains REVERT: A 37 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6617 (tp30) REVERT: A 82 MET cc_start: 0.5800 (mmt) cc_final: 0.5554 (mmt) REVERT: A 114 LYS cc_start: 0.7880 (ptmm) cc_final: 0.7042 (pttp) REVERT: A 146 PRO cc_start: 0.7732 (Cg_endo) cc_final: 0.7252 (Cg_exo) REVERT: A 159 ASN cc_start: 0.7510 (m-40) cc_final: 0.7045 (t0) REVERT: A 249 MET cc_start: 0.5573 (mtp) cc_final: 0.5240 (ttp) REVERT: A 341 LYS cc_start: 0.6519 (tptt) cc_final: 0.6183 (tttm) REVERT: A 474 MET cc_start: 0.8077 (mmp) cc_final: 0.7469 (mmp) REVERT: A 475 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7186 (tmmt) REVERT: C 351 TYR cc_start: 0.7523 (p90) cc_final: 0.7022 (p90) REVERT: C 356 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6970 (tttp) REVERT: C 406 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7291 (tt0) REVERT: C 418 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7473 (mp) REVERT: C 467 ASP cc_start: 0.6246 (t0) cc_final: 0.5942 (t0) REVERT: C 468 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6666 (mm) outliers start: 12 outliers final: 6 residues processed: 87 average time/residue: 1.4570 time to fit residues: 133.3296 Evaluate side-chains 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.0270 chunk 71 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.179208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148889 restraints weight = 11710.930| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.20 r_work: 0.3535 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 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 = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4549 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= 0.150 Angle : 0.624 7.751 9108 Z= 0.318 Chirality : 0.043 0.135 964 Planarity : 0.004 0.030 1173 Dihedral : 4.793 34.278 968 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.01 % Allowed : 26.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 789 helix: 0.75 (0.25), residues: 409 sheet: 0.07 (0.83), residues: 44 loop : -0.28 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 594 HIS 0.006 0.001 HIS A 540 PHE 0.017 0.002 PHE A 588 TYR 0.027 0.002 TYR C 351 ARG 0.003 0.001 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 5) link_NAG-ASN : angle 2.19566 ( 15) hydrogen bonds : bond 0.05110 ( 319) hydrogen bonds : angle 5.08053 ( 905) metal coordination : bond 0.00273 ( 2) SS BOND : bond 0.00818 ( 7) SS BOND : angle 2.47549 ( 14) covalent geometry : bond 0.00338 ( 6677) covalent geometry : angle 0.61134 ( 9079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6351.95 seconds wall clock time: 114 minutes 5.50 seconds (6845.50 seconds total)